https://wiki.uio.no/projects/clsi/api.php?action=feedcontributions&user=Jonkl%40uio.no&feedformat=atomprojects/clsi - User contributions [en]2024-03-29T14:01:36ZUser contributionsMediaWiki 1.27.4https://wiki.uio.no/projects/clsi/index.php?title=MBV-INFX410_2015&diff=2084MBV-INFX410 20152020-07-26T17:59:55Z<p>Jonkl@uio.no: /* Bioinformatics for Molecular Biology - 2015 */</p>
<hr />
<div>== [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410 Bioinformatics for Molecular Biology] - 2015 ==<br />
'''''All information for 2019 and later is found on the University of Oslo Canvas pages.'''''<br />
<br />
'''''THIS IS THE WIKI FOR 2015. INFORMATION FOR 2018 IS FOUND [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410_2018 HERE]!'''''<br />
<br />
'''''Jan 15: The exam results have been submitted to the IBV administration and will be available soon. Some brief comments on the exam:'''''<br />
<br />
*This was a home exam with lots of time, permitted materials were basically "everything", and roughly 1/3 of the students had answered almost everything correctly. For this reason there was relatively little tolerance for silly mistakes such as not reading the questions properly, not answering all sub-questions, very odd/incomprehensible argumentation/spelling, and leaving parts of the exercises blank<br />
*Exercise 1b: 3 proteins are identical because they all represent identical splicing of a pre-mRNA corresponding to the human reference genome. The last sequence corresponds to a (different) individual and different splicing and uses the wrong ATG as start codon<br />
*Exercise 1h: 3 codons is 9 nucleotides, not 3. 5' end is at "the beginning" of the exon<br />
*If FTO from cow or sheep is more similar to human FTO than the other, this is completely by chance<br />
*All ''Sauropsida'' (birds and reptiles) have a common ancestor more recently than the common ancestor of ''Sauropsida'' and mammals, while amphibians are remote cousins. All the phylogenetic trees were ok<br />
*Exercise 2a: First we make one long string with all the information in the input file, then we split on the string "\n>" and get a list of fasta sequences. We loop through this list and in an inner loop split on "\n"<br />
*Exercise 2b: (i) Two main ways to do this: Best(?) is to use len() to find length of sequence string but remember to not count the end-of-line character at the end of every line. Must also use str() to convert number to string for printing. It was also possible to extract the length from the header, but in that case one should not cut out a substring of only three characters since this will only work for sequences with lengths between 100 and 999. (ii) Many ways to do this task and almost all ok<br />
*Exercise 3: You have to normalise the data because the total amount of RNA is not the same in the various samples. This might be due to different concentrations of the samples, different degree of RNA degradation etc. If you ''look'' at the data it is pretty obvious that all the top 5 miRNAs are upregulated in HCHF <br />
*Exercise 4a: This was quite difficult and time consuming, unless you had read the article "A beginners guide to SNP calling from high-throughput DNA-sequencing data" in the required reading material. Not all students had read the curriculum<br />
<br />
'''''Dec 9: The exam for the course was sent, by e-mail, to all qualified students on December 9. If you did not receive the exam, please contact Jon immediately!<br />
<br />
'''''Dec 3: The solutions for the obligatory assignment can be downloaded [[Media:Oblig_MBV-INFx410-Solutions-2015.pdf|here]]. Jon will go through the oblig with solutions on Thursday. <br />
<br />
'''''Dec 1: The handouts and material for Monday Nov 30 was [https://wiki.uio.no/projects/clsi/index.php/Statistical_Bioinformatics_2015 updated].'''''<br />
<br />
'''''Nov 25: On Friday Dec 4th, between 13:00 and 15:00, there will be a helpdesk session in lecture room Java (2. etasje). This is not a compulsory part of the course and there will not be any lectures. There will not be any new messages and no messages or hints about the exam (that is not also put on the wiki). This is an opportunity to get help with parts of the curriculum you are struggling with. Jon will be present, but will most likely not be able to answer all questions about the parts of the curriculum that has been taught by other teachers.'''''<br />
<br />
'''''Nov 25: The following rooms will be used for lectures in week 49: Monday - Postscript, Tuesday - Lille Auditorium in Kristen Nygaards hus, Wednesday - Pascal, and Thursday - C. For more information go to the [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410_2015#Time_and_place Time and place section] below.'''''<br />
<br />
'''''Nov 20: Download the obligatory and compulsory assignment [[Media:Oblig_MBV-INFx410-2015.pdf|by following this link]]. It must be returned by 09:00, Monday November 30. Good luck! Students that do not get this assignment approved, will not be allowed to take the exam.'''''<br />
<br />
'''''All students must be present at the start of the course, at 09:00, on November 9. Missing students will not be allowed to follow the course or to take the exam. If you for some reason are not able to attend, please contact Jon (See [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410_2015#Contacts contact details] below).'''''<br />
<br />
This is the wiki for the courses [http://www.uio.no/studier/emner/matnat/ibv/MBV-INF4410 MBV-INF4410] and [http://www.uio.no/studier/emner/matnat/ibv/MBV-INF9410 MBV-INF9410] offered by the Department of Biosciences and Department of Informatics at the University of Oslo (UiO). Both MBV-INF4410 (M.Sc. level) and MBV-INF9410 (Ph.D. level) are 10 study point courses. The 8 study points variant of the course (MBV-INF9410A) will not be given after 2013.<br />
<br />
The course consists of five weeks of lectures, exercises, obligatory assignments, and a take-home exam (one week). Obligatory assignments must be completed and approved before the exam and in the same semester. An additional, limited, oral examination may be arranged in cases where this is necessary for the student evaluation. The course is open also for non-UiO students. It is only necessary to be physically present in Oslo for certain parts of the course.<br />
<br />
=== Course description ===<br />
<br />
This intensive course will introduce students to bioinformatics resources and tools for molecular biology research. All the lecturers are among the&nbsp;top researchers working within the fields of bioinformatics and computational biology in the Oslo region. Students must bring their own laptop for in-course demonstrations as well as for practical lab exercises. The course is mainly intended for biology students, but also for computer science students or students from other fields of science with an interest for and some experience with molecular biology. No prior background in bioinformatics or computer science is required. All students should have a basic understanding of molecular biology, at least roughly corresponding to 5-10 university study points in molecular biology, biochemistry, or similar. ''If you are uncertain if your biology background is strong enough, please contact Jon (See contact details below) before you sign up for the course.''<br />
<br />
Course responsible is [http://folk.uio.no/jonkl Dr. Jon K. Lærdahl] (jonkl@medisin.uio.no) from the Department of Microbiology, Oslo University Hospital (OUH) - Rikshospitalet. Lærdahl is also employed by the [http://www.mn.uio.no/ifi/english/research/networks/clsi CLS initiative] at UiO and the Bioinformatics Core Facility ([http://core.rr-research.no/bioinformatics CF]) at OUH and UiO.<br />
<br />
Links to the web pages for the years 2009-2011 is found [http://bioinformatics.uio.no/wiki/Bioinformatics_course here] (Aug 2014: this server might be permanently down...), for 2012 [https://wiki.uio.no/projects/MBV-INFX410/index.php/Main_Page here], for 2013 [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410_2013 here] and for 2014 [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410_2014 here].<br />
<br />
Notes on the course format: The course has previously been given as an intensive course over two weeks with a take-home exam in the 3rd to 4th week. A take-home assignment was also a compulsory part of the 10 study points versions of the course. The compact format was ideal for students coming from outside Oslo, but it was also exhausting for students and lecturers. It gave no time to digest and dive more deeply into the various topics presented in the course. Since 2013, the course will be given over 5 weeks. However, '''''it will only be necessary to be physically present in Oslo for parts of the course''''', ''i.e.'' the lectures/exercises. '' The schedule is presented below, but there might be small adjustments to this later.''<br />
<br />
[[File:TeachingPlanMBVX410 15A2.png|thumb|center|700px]]<br />
<br />
=== Time and place ===<br />
<br />
'''The course will be offered in weeks 46 to 50, autumn 2015, ''i.e. ''starting on Monday November 9 (See schedule below).''' The take-home exam must be handed in in week 51, on Wednesday December 16. Each day of lectures/exercises will consist of three time slots for lectures and/or exercises/practical labs between 09:00 and 16:00. Lunch will usually be between 12:45 and 13:30. You will have to bring your own lunch or buy lunch in the local kantine.<br />
<br />
'''Lecture room:''' All lectures/exercises in weeks 46 and 47 will be given in lecture room '''Python''' in Ole-Johan Dahls hus (IFI2). A map showing the location of the building is found [http://www.uio.no/om/finn-fram/omrader/gaustad/ga06 here]. The building is located next to the Forskningsparken metro and tram stations. The room Python is on the 1st floor (2. etasje) in the northern end of the building, the end closest to the tram line. The easiest access to '''Python''' is through the entrance in the tunnel going through the building.<br />
<br />
In week 49 we will use the following rooms:<br />
* Monday, Nov 30th: Room '''Postscript''', 2. etasje (opposite direction of Python when you enter the building through the tunnel)<br />
* Tuesday, Dec 1st: '''Lille Auditorium''' in Kristen Nygaards hus, the building next to OJDs hus, ground floor<br />
* Wednesday, Dec 2nd: Room '''Pascal''', back in OJDs hus, 2. etasje, further along towards the south wrt. Postscript <br />
* Thursday, Dec 3rd: Room '''C''', 3. etasje, one floor up from Pascal<br />
<br />
On Friday Dec 4th, between 13:00 and 15:00, there will be a helpdesk session in lecture room Java (2. etasje). This is not a compulsory part of the course and there will not be any lectures. There will not be any new messages and no messages or hints about the exam (that is not also put on the wiki). This is an opportunity to get help with parts of the curriculum you are struggling with. Jon will be present, but will most likely not be able to answer all questions about the parts of the curriculum that has been taught by other teachers.<br />
<br />
=== Contacts ===<br />
<br />
Jon K. Lærdahl (Course coordinator) - e-mail: jonkl@medisin.uio.no, phone: +47 99 507 335<br />
<br />
Torill Rørtveit (Course administrator, registration) - e-mail: torill.rortveit@ibv.uio.no<br />
<br />
=== Computers/laptops, internet access, and UiO user account ===<br />
<br />
All students must bring a laptop with either a Windows (Windows 7 or more recent), Unix/Linux, or OS X (''i.e.'' an Apple computer) operating system.<br />
<br />
*The computer should not be more than 2-3 years old<br />
*It should be possible to connect the computer to the UiO wireless network<br />
*You must have a root/administrator password that gives you access to installing new software on the computer<br />
*Bring an external mouse, and do not rely on touchpad/trackpad only<br />
*You must have a valid UiO user account and must be able to log onto a computer on the UiO network<br />
*If you are unsure if you have a UiO user account and a valid password, you should try to log in using&nbsp;kiosk.uio.no&nbsp;or win.uio.no as described [http://www.uio.no/english/services/it/network/home-and-away/kiosk/index.html here]. If you are unable to log in, try the hints you find [http://www.uio.no/english/services/it/network/home-and-away/kiosk/programkiosk/index.html here].<br />
*Instructions (in Norwegian) about how to find your user name and get a new password can be found [http://www.uio.no/tjenester/it/brukernavn-passord/ikke-passord.html here].<br />
<br />
'''''If you are struggling with anything of the above, in particular if you have forgotten your UiO user name/password or you do not have one, you must contact Jon (See contact details above) as soon as possible, and at least one week before the start of the course.'''''<br />
<br />
'''''To get a UiO username/password at the UiO helpdesk you need valid ID.'''''<br />
<br />
On the first day of the course we will set up your laptop so that it can be used for the exercises/tutorials, the home exam and hopefully in your future work. How to get a reasonable setup is described [[Laptop Setup|here]].<br />
<br />
If you already are an expert programmer and Unix guru, go [[Biology for Informatics|here]].<br />
<br />
=== Programme ===<br />
<br />
The schedule below is tentative, and may be changed prior to, and possibly even during, the course. Requests and suggestions are welcome.<br />
<br />
{| border="1" cellpadding="2" cellspacing="1" width="100%"<br />
|-<br />
| colspan="5" align="center" bgcolor="#99ccff" | Week 46: Monday, November 09 - Friday, November 13<br />
|-<br />
| bgcolor="#dddddd" width="16%" | <br />
| bgcolor="#dddddd" width="28%" | Session 1<br />
| colspan="2" bgcolor="#dddddd" width="28%" | Session 2<br />
| bgcolor="#dddddd" | Session 3<br />
|-<br />
| <br />
| 09:00 - 10:45<br />
| colspan="2" | 11:00 - 12:45<br />
| 13:30 - 16:00<br />
|-<br />
| bgcolor="#dddddd" | Monday 9th<br />
| bgcolor="#dddddd" | <br />
[[Course introduction 2015|Course introduction]]<br />
<br />
- lectures<br />
<br />
| colspan="2" bgcolor="#dddddd" | <br />
[[Day 1 2015|Biological databases, Unix & setting up laptops]]<br />
<br />
- lectures/exercises<br />
<br />
| bgcolor="#dddddd" | <br />
[[Day 1 2015|Basic Unix]]<br />
<br />
- exercises<br />
<br />
|-<br />
| bgcolor="#dddddd" | <br />
| bgcolor="#dddddd" | Jon K Lærdahl<br />
| colspan="2" bgcolor="#dddddd" | Jon K Lærdahl<br />
| bgcolor="#dddddd" | Jon K Lærdahl<br />
|-<br />
| Tuesday 10th<br />
| <br />
[[Day 2 2015|Ensembl genome browser & Jalview]]<br />
<br />
- lectures/demo<br />
<br />
| colspan="2" | <br />
[[Day 2 2015|Working with sequences/databases]]<br />
<br />
- lectures/exercises<br />
<br />
| <br />
[[Day 2 2015|Applied sequence bioinformatics]]<br />
<br />
- exercise<br />
<br />
|-<br />
| <br />
| Jon K Lærdahl<br />
| colspan="2" | Jon K Lærdahl<br />
| Jon K Lærdahl<br />
|-<br />
| bgcolor="#dddddd" | Wednesday 11th<br />
| bgcolor="#dddddd" | <br />
[[Structural Biology Review 2015|Structural Biology Review]]<br />
<br />
- lectures/review<br />
<br />
| colspan="2" bgcolor="#dddddd" | <br />
[[Day 3 2015|More Unix & UCSC Genome browser]]<br />
<br />
- lectures/demo/exercises<br />
<br />
| bgcolor="#dddddd" | <br />
[[Day 3 2015|Galaxy/Life Portal]]<br />
<br />
- lectures/demo/exercises<br />
<br />
|-<br />
| bgcolor="#dddddd" | <br />
| bgcolor="#dddddd" | Jon K Lærdahl<br />
| colspan="2" bgcolor="#dddddd" | Jon K Lærdahl<br />
| bgcolor="#dddddd" | Jon K Lærdahl<br />
|-<br />
| Thursday 12th<br />
| <br />
[[Python workshop 2015|Python workshop]]<br />
<br />
- lectures/exercises<br />
<br />
| colspan="2" | <br />
[[Python workshop 2015|Python workshop]]<br />
<br />
- lectures/exercises<br />
<br />
| <br />
[[Python workshop 2015|Python workshop]]<br />
<br />
- lectures/exercises<br />
<br />
|-<br />
| <br />
| Karin Lagesen<br />
| colspan="2" | Karin Lagesen<br />
| Karin Lagesen<br />
|-<br />
| bgcolor="#dddddd" | Friday 13th<br />
| bgcolor="#dddddd" | <br />
[[Python workshop 2015|Python workshop]]<br />
<br />
- lectures/exercises<br />
<br />
| colspan="2" bgcolor="#dddddd" | <br />
[[Python workshop 2015|Python workshop]]<br />
<br />
- lectures/exercises<br />
<br />
| bgcolor="#dddddd" | <br />
[[Python workshop 2015|Python workshop]]<br />
<br />
- lectures/exercises<br />
<br />
|-<br />
| bgcolor="#dddddd" | <br />
| bgcolor="#dddddd" | Karin Lagesen<br />
| colspan="2" bgcolor="#dddddd" | Karin Lagesen<br />
| bgcolor="#dddddd" | Karin Lagesen<br />
|-<br />
| colspan="5" align="center" bgcolor="#99ccff" | Week 47: Monday, November 16 - Friday, November 20<br />
|-<br />
| bgcolor="#dddddd" width="16%" | <br />
| bgcolor="#dddddd" width="28%" | Session 1<br />
| colspan="2" bgcolor="#dddddd" width="28%" | Session 2<br />
| bgcolor="#dddddd" | Session 3<br />
|-<br />
| <br />
| 09:00 - 10:45<br />
| colspan="2" | 11:00 - 12:45<br />
| 13:30 - 16:00<br />
|-<br />
| bgcolor="#dddddd" | Monday 16th<br />
| colspan="2" bgcolor="#dddddd" | <br />
[[Sequence searching & MSAs 2015|Sequence searching, alignments, and multiple alignments]]<br />
<br />
- lectures (09:00 - 11:45)<br />
<br />
| colspan="2" bgcolor="#dddddd" | <br />
[[Sequence searching & MSAs 2015|Sequence searching and multiple sequence alignments]]<br />
<br />
- exercise (12:30 - 16:00)<br />
<br />
|-<br />
| bgcolor="#dddddd" | <br />
| colspan="2" bgcolor="#dddddd" | Torbjørn Rognes<br />
| colspan="2" bgcolor="#dddddd" | Jon K Lærdahl<br />
|-<br />
| Tuesday 17th<br />
| <br />
[[Structural Bioinformatics 2015|Structural Bioinformatics]]<br />
<br />
- lectures/exercises<br />
<br />
| colspan="2" | <br />
[[Structural Bioinformatics 2015|Structural Bioinformatics]]<br />
<br />
- lectures/exercises<br />
<br />
| <br />
[[Structural Bioinformatics 2015|Structural Bioinformatics]]<br />
<br />
- lectures/exercises<br />
<br />
|-<br />
| <br />
| Jon K Lærdahl<br />
| colspan="2" | Jon K Lærdahl<br />
| Jon K Lærdahl<br />
|-<br />
| bgcolor="#dddddd" | Wednesday 18th<br />
| bgcolor="#dddddd" | <br />
[[Hyperbrowser 2015|Reproducibility/Statistical epigenomics]]<br />
<br />
- lectures/exercises<br />
<br />
| colspan="2" bgcolor="#dddddd" | <br />
[[Hyperbrowser 2015|Reproducibility/Statistical epigenomics]]<br />
<br />
- lectures/exercises<br />
<br />
| bgcolor="#dddddd" | <br />
[[Hyperbrowser 2015|Reproducibility/Statistical epigenomics]]<br />
<br />
- lectures/exercises<br />
<br />
|-<br />
| bgcolor="#dddddd" | <br />
| bgcolor="#dddddd" | Sveinung Gundersen/Boris Simovski<br />
| colspan="2" bgcolor="#dddddd" | Sveinung Gundersen/Boris Simovski<br />
| bgcolor="#dddddd" | Sveinung Gundersen/Boris Simovski<br />
|-<br />
| Thursday 19th<br />
| colspan="2" | <br />
[[Docking and drug design 2015|Docking and drug discovery]]<br />
<br />
- lectures/exercises (09:00 - 11:45)<br />
<br />
| colspan="2" | <br />
[[Practical Unix/Python 2015|Practical Unix/Python exercise]]<br />
<br />
- lectures/exercises (12:30 - 16:00)<br />
<br />
|-<br />
| <br />
| colspan="2" | Bjørn Dalhus<br />
| colspan="2" | Jon K Lærdahl<br />
|-<br />
| bgcolor="#dddddd" | Friday 20th<br />
| bgcolor="#dddddd" | <br />
[[Structural Bioinformatics 2015|More Structural Bioinformatics]]<br />
<br />
- lectures/exercises<br />
<br />
| colspan="2" bgcolor="#dddddd" | <br />
[[Structural Bioinformatics 2015|More Structural Bioinformatics]]<br />
<br />
- lectures/exercises<br />
<br />
| bgcolor="#dddddd" | <br />
[[Structural Bioinformatics 2015|More Structural Bioinformatics]]<br />
<br />
- lectures/exercises<br />
<br />
|-<br />
| bgcolor="#dddddd" | <br />
| bgcolor="#dddddd" | Jon K Lærdahl<br />
| colspan="2" bgcolor="#dddddd" | Jon K Lærdahl<br />
| bgcolor="#dddddd" | Jon K Lærdahl<br />
|-<br />
| colspan="5" align="center" bgcolor="#99ccff" | Week 48: Monday, November 23 - Friday, November 27<br />
|-<br />
| colspan="5" align="center" | Work on obligatory home assignment and study days (no lectures)<br />
|-<br />
| colspan="5" align="center" bgcolor="#99ccff" | Week 49: Monday, November 30 - Thursday, December 3<br />
|-<br />
| bgcolor="#dddddd" width="16%" | <br />
| bgcolor="#dddddd" width="28%" | Session 1<br />
| colspan="2" bgcolor="#dddddd" width="28%" | Session 2<br />
| bgcolor="#dddddd" | Session 3<br />
|-<br />
| <br />
| 09:00 - 10:45<br />
| colspan="2" | 11:00 - 12:45<br />
| 13:30 - 16:00<br />
|-<br />
| bgcolor="#dddddd" | Monday 30th<br />
| bgcolor="#dddddd" | <br />
[[Statistical Bioinformatics 2015|Introduction to statistical inference and R]]<br />
<br />
- lectures<br />
<br />
| colspan="2" bgcolor="#dddddd" | <br />
[[Statistical Bioinformatics 2015|Basic R and exploring your data]]<br />
<br />
- lectures/exercises<br />
<br />
| bgcolor="#dddddd" | <br />
[[Statistical Bioinformatics 2015|Basic R and exploring your data]]<br />
<br />
- lectures/exercises<br />
<br />
|-<br />
| bgcolor="#dddddd" | <br />
| bgcolor="#dddddd" | Ole Christian Lingjærde<br />
| colspan="2" bgcolor="#dddddd" | Jon K Lærdahl/Ksenia Khelik<br />
| bgcolor="#dddddd" | Jon K Lærdahl/Ksenia Khelik<br />
|-<br />
| Tuesday 1st<br />
| <br />
[[NGS day 2015|Next generation sequencing (NGS)]]<br />
<br />
- lectures<br />
<br />
| colspan="2" | <br />
[[NGS day 2015|NGS & variant calling lab]]<br />
<br />
- lectures/exercises<br />
<br />
| <br />
[[NGS day 2015|NGS & variant calling lab]]<br />
<br />
- lectures/exercises<br />
<br />
|-<br />
| <br />
| Tim Hughes & Aravind Sundaram<br />
| colspan="2" | Tim Hughes & Aravind Sundaram<br />
| Tim Hughes & Aravind Sundaram<br />
|-<br />
| bgcolor="#dddddd" | Wednesday 2nd<br />
| bgcolor="#dddddd" | <br />
[[Analysis of transcriptome data 2015|Analysis of gene expression data using R]]<br />
<br />
- lectures/exercises<br />
<br />
| colspan="2" bgcolor="#dddddd" | <br />
[[Analysis of transcriptome data 2015|Analysis of gene expression data using R]]<br />
<br />
- lectures/exercises<br />
<br />
| bgcolor="#dddddd" | <br />
[[Analysis of transcriptome data 2015|Analysis of gene expression data using R]]<br />
<br />
- lectures/exercises<br />
|-<br />
| bgcolor="#dddddd" | <br />
| bgcolor="#dddddd" | Ståle Nygård<br />
| colspan="2" bgcolor="#dddddd" | Ståle Nygård<br />
| bgcolor="#dddddd" | Ståle Nygård<br />
|-<br />
| Thursday 3rd<br />
| <br />
[[Assembly - 2015|What does it mean to do bioinformatics?]]<br />
<br />
- lectures<br />
<br />
| colspan="2" | <br />
[[Gene lists and over-representation analysis (ORA) 2015|Gene lists & over-representation analysis (ORA)]]<br />
<br />
- lectures/exercises<br />
<br />
| <br />
End of course [[Media:EndOfCourseSummary-15.pdf|summary]]<br />
<br />
- lecture/discussion<br />
<br />
|-<br />
| <br />
| Lex Nederbragt<br />
| colspan="2" | Ståle Nygård<br />
| Jon K Lærdahl<br />
|}<br />
<br />
Ksenia Khelik from the BMI group, Ifi, will help during the Python and R courses.<br />
<br />
Ivar Grytten and Boris Simovski from the BMI group, Ifi, will help during the laptop setup session on Monday, November 09.<br />
<br />
The brief lecture on PCSK9 can be found [http://folk.uio.no/jonkl/StuffForMBV-INFx410/PCSK9_Lecture.pdf here], if you are interested. This is ''not'' a part of the curriculum.<br />
<br />
=== Required reading material/curriculum ===<br />
<br />
The curriculum comprises all lectures, lecture handouts, exercises and the reviews/articles/written material [[Additional curriculum|listed on this page]].<br />
<br />
An obligatory and compulsory assignment must be returned, by e-mail, to the course coordinator Jon K. Lærdahl (e-mail address: jonkl@medisin.uio.no) before Monday November 30, at 09:00. Note that students that do not get this assignment approved, will not be allowed to take the exam.<br />
<br />
The obligatory assignment can be downloaded [[Media:Oblig_MBV-INFx410-2015.pdf|here]].<br />
<br />
=== Exam ===<br />
<br />
'''##########################################'''<br />
<br />
'''Some messages:'''<br />
<br />
*Exercise 1, subsection i): "Zoom in on exon 2 so that..." means "Zoom in on exon 2 ''in the gene'' so that..."<br />
*Exercise 2, subsection b): The script should print out the length of the shortest and the longest sequence. It is not necessary that the script prints out the names of these sequences. You can find this manually<br />
*The exam for the course was sent, by e-mail, to all qualified students on December 9. If you did not receive the exam, please contact Jon immediately!<br />
<br />
'''##########################################'''<br />
<br />
The exam for this course will be a one week, take-home exam. Only students that have returned the obligatory assignment, and got this assignment approved, will be allowed to take the exam.<br />
<br />
The exam will be sent to all qualified participants at 3 pm, Wednesday December 9, by e-mail.<br />
<br />
Your completed exam must be returned, at the latest, at 3 pm, Wednesday December 16. It should be sent by e-mail to the course administrator Torill Rørtveit (e-mail address: torill.rortveit@ibv.uio.no). Please put the course code and your candidate number (for this course) in the subject field (''e.g.'' "Exam MBV-INF4410 Candidate:15").<br />
<br />
The exam must be handed in as a single PDF document (Microsoft Word or an Open Office Document is also acceptable). The document should be named with the course code and your candidate number only (''e.g.'' MBV-INF4410-15.pdf). '''''Do not place your name in the document.'''''<br />
<br />
An additional, limited, oral examination may be arranged in cases where this is necessary for the student evaluation.<br />
<br />
=== Bioinformatics mailing list for the Oslo region ===<br />
<br />
The mailing list for computational biology and bioinformatics in the Oslo region is cbo-all@usit.uio.no. The list has approximately 400 members. The list is used to distribute news about seminars, positions, courses, meetings and other topics that might be of interest to students and researchers with an interest in computational life science in south-eastern Norway. If you want to receive e-mails that are sent to the list, sign up here<br />
<br />
[https://sympa.uio.no/usit.uio.no/info/cbo-all https://sympa.uio.no/usit.uio.no/info/cbo-all]<br />
<br />
by following the link termed "Subscribe".<br />
<br />
=== Useful links ===<br />
<br />
Trond Hasle Amundsen's [http://www.uio.no/tjenester/it/maskin/linux/hjelp/tips/guide.html Local guide to Linux and Unix]<br />
<br />
EMBnet [http://www.embnet.org/sites/default/files/quickguides/guideUNIX.pdf Quick guide Unix]<br />
<br />
[http://www.jalview.org Jalview] and Jalview [http://www.jalview.org/refcard.pdf refcard]<br />
<br />
UCSC [http://genome.ucsc.edu Genome browser]<br />
<br />
Free [http://www.openhelix.com/ucsc UCSC Genome browser tutorial]&nbsp;&nbsp; from OpenHelix<br />
<br />
Portal to [http://galaxyproject.org Galaxy]<br />
<br />
[http://wiki.galaxyproject.org/Learn Galaxy 101 and other Galaxy screencasts/tutorials]<br />
<br />
UiO [http://lifeportal.uio.no Lifeportal] and more [http://www.uio.no/english/services/it/research/hpc/lifeportal information on the Lifeportal]<br />
<br />
The Genomic [http://hyperbrowser.uio.no/hb HyperBrowser]<br />
<br />
[http://bioinformatics.ca/links_directory Links Directory] from bioinformatics.ca<br />
<br />
The 2015 Nucleic Acids Research [http://nar.oxfordjournals.org/content/43/D1.toc Database Issue]<br />
<br />
The 2015 Nucleic Acids Research [http://nar.oxfordjournals.org/content/43/W1.toc Web Server Issue]<br />
<br />
UiO and OUS [http://core.rr-research.no/bioinformatics Bioinformatics Core Facility]</div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=MBV-INFX410&diff=2083MBV-INFX4102020-07-26T17:59:27Z<p>Jonkl@uio.no: /* Bioinformatics for Molecular Biology */</p>
<hr />
<div>== Bioinformatics for Molecular Biology ==<br />
'''''All information for 2019 and later is found on the University of Oslo Canvas pages.'''''<br />
<br />
'''''All information for 2018 is found here:''''' '''[[MBV-INFX410 2018|MBV-INFX410 2018 wiki]]. '''''Course responsible is Jon Bråte (e-mail: jon.brate@ibv.uio.no) and course administrator Torill Rørtveit (e-mail: torill.rortveit@ibv.uio.no).''<br />
<br />
'''''All information for 2017 is found here:''''' [[MBV-INFX410 2017|'''MBV-INFX410 2017 wiki''']]'''. '''''Course responsible is Jon Bråte (e-mail: jon.brate@ibv.uio.no) and course administrator Torill Rørtveit (e-mail: torill.rortveit@ibv.uio.no).''<br />
<br />
'''''All information for 2016 is found here:''''' [[MBV-INFX410 2016|'''MBV-INFX410 2016 wiki''']]'''. '''''Course responsible is Jon Bråte (e-mail: jon.brate@ibv.uio.no) and course administrator Torill Rørtveit (e-mail: torill.rortveit@ibv.uio.no).''<br />
<br />
'''''All information for 2015 is found here:''''' [[MBV-INFX410 2015|'''MBV-INFX410 2015 wiki''']] <br />
<br />
This is the wiki for the courses [http://www.uio.no/studier/emner/matnat/ibv/MBV-INF4410 MBV-INF4410] and [http://www.uio.no/studier/emner/matnat/ibv/MBV-INF9410 MBV-INF9410] offered by the Department of Biosciences and Department of Informatics at the University of Oslo (UiO). Both MBV-INF4410 (M.Sc. level) and MBV-INF9410 (Ph.D. level) are 10 study point courses. The 8 study points variant of the course (MBV-INF9410A) will no longer be given after 2013.<br />
<br />
The course consists of five weeks of lectures, exercises, obligatory assignments, and a take-home exam (one week). Obligatory assignments must be completed and approved before the exam and in the same semester. An additional, limited, oral examination may be arranged in cases where this is necessary for the student evaluation. The course is open also for non-UiO students. It is only necessary to be physically present in Oslo for certain parts of the course. <br />
<br />
=== Course description ===<br />
<br />
This intensive course will introduce students to bioinformatics resources and tools for molecular biology research. All the lecturers are among the&nbsp;top researchers working within the fields of bioinformatics and computational biology in&nbsp;the Oslo region. Students&nbsp;must bring&nbsp;their own&nbsp;lap-top for in-course demonstrations as well as for practical lab exercises. The course is mainly intended for biology students, but also for&nbsp;computer science students or students from other fields of science with&nbsp;an interest for and some experience with molecular biology. No prior background in bioinformatics or computer science is required.&nbsp;All students should have a basic understanding of molecular biology,&nbsp;at least roughly corresponding to 5-10 university study points in molecular biology, biochemistry, or similar. ''If you are uncertain if your biology background is strong enough, please contact the course administrator before you sign up for&nbsp;the course.'' <br />
<br />
'''Course responsible in 2016, 2917, and 2018 is Jon Bråte (e-mail: jon.brate@ibv.uio.no), from the Department of Biology, UiO.''' <br />
<br />
Course responsible for the years 2012 to 2015 was [http://folk.uio.no/jonkl Dr. Jon K. Lærdahl] (jonkl@medisin.uio.no) from the Department of Microbiology, Oslo University Hospital (OUH) - Rikshospitalet. Lærdahl was also employed by the [http://www.mn.uio.no/ifi/english/research/networks/clsi CLS initiative] at UiO and is employed by the Bioinformatics Core Facility ([http://core.rr-research.no/bioinformatics CF]) at OUH and UiO. <br />
<br />
The wikis for the [[MBV-INFX410 2013|2013]], [[MBV-INFX410 2014|2014]], and [[MBV-INFX410 2015|2015]] versions of the course are found behind these links. <br />
<br />
Links to the web pages for the years 2009-2011 is found [http://bioinformatics.uio.no/wiki/Bioinformatics_course here] and for 2012 [https://wiki.uio.no/projects/MBV-INFX410/index.php/Main_Page here].&nbsp;<br />
<br />
=== Contacts ===<br />
<br />
Jon Bråte (Course coordinator) - e-mail: jon.brate@ibv.uio.no<br />
<br />
Torill Rørtveit (Course administrator, registration) - e-mail: torill.rortveit@ibv.uio.no</div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=MBV-INFX410&diff=2082MBV-INFX4102020-07-26T17:59:07Z<p>Jonkl@uio.no: </p>
<hr />
<div>== Bioinformatics for Molecular Biology ==<br />
'''''All information for 2019 and later is found on University of Oslo Canvas pages.'''''<br />
<br />
'''''All information for 2018 is found here:''''' '''[[MBV-INFX410 2018|MBV-INFX410 2018 wiki]]. '''''Course responsible is Jon Bråte (e-mail: jon.brate@ibv.uio.no) and course administrator Torill Rørtveit (e-mail: torill.rortveit@ibv.uio.no).''<br />
<br />
'''''All information for 2017 is found here:''''' [[MBV-INFX410 2017|'''MBV-INFX410 2017 wiki''']]'''. '''''Course responsible is Jon Bråte (e-mail: jon.brate@ibv.uio.no) and course administrator Torill Rørtveit (e-mail: torill.rortveit@ibv.uio.no).''<br />
<br />
'''''All information for 2016 is found here:''''' [[MBV-INFX410 2016|'''MBV-INFX410 2016 wiki''']]'''. '''''Course responsible is Jon Bråte (e-mail: jon.brate@ibv.uio.no) and course administrator Torill Rørtveit (e-mail: torill.rortveit@ibv.uio.no).''<br />
<br />
'''''All information for 2015 is found here:''''' [[MBV-INFX410 2015|'''MBV-INFX410 2015 wiki''']] <br />
<br />
This is the wiki for the courses [http://www.uio.no/studier/emner/matnat/ibv/MBV-INF4410 MBV-INF4410] and [http://www.uio.no/studier/emner/matnat/ibv/MBV-INF9410 MBV-INF9410] offered by the Department of Biosciences and Department of Informatics at the University of Oslo (UiO). Both MBV-INF4410 (M.Sc. level) and MBV-INF9410 (Ph.D. level) are 10 study point courses. The 8 study points variant of the course (MBV-INF9410A) will no longer be given after 2013.<br />
<br />
The course consists of five weeks of lectures, exercises, obligatory assignments, and a take-home exam (one week). Obligatory assignments must be completed and approved before the exam and in the same semester. An additional, limited, oral examination may be arranged in cases where this is necessary for the student evaluation. The course is open also for non-UiO students. It is only necessary to be physically present in Oslo for certain parts of the course. <br />
<br />
=== Course description ===<br />
<br />
This intensive course will introduce students to bioinformatics resources and tools for molecular biology research. All the lecturers are among the&nbsp;top researchers working within the fields of bioinformatics and computational biology in&nbsp;the Oslo region. Students&nbsp;must bring&nbsp;their own&nbsp;lap-top for in-course demonstrations as well as for practical lab exercises. The course is mainly intended for biology students, but also for&nbsp;computer science students or students from other fields of science with&nbsp;an interest for and some experience with molecular biology. No prior background in bioinformatics or computer science is required.&nbsp;All students should have a basic understanding of molecular biology,&nbsp;at least roughly corresponding to 5-10 university study points in molecular biology, biochemistry, or similar. ''If you are uncertain if your biology background is strong enough, please contact the course administrator before you sign up for&nbsp;the course.'' <br />
<br />
'''Course responsible in 2016, 2917, and 2018 is Jon Bråte (e-mail: jon.brate@ibv.uio.no), from the Department of Biology, UiO.''' <br />
<br />
Course responsible for the years 2012 to 2015 was [http://folk.uio.no/jonkl Dr. Jon K. Lærdahl] (jonkl@medisin.uio.no) from the Department of Microbiology, Oslo University Hospital (OUH) - Rikshospitalet. Lærdahl was also employed by the [http://www.mn.uio.no/ifi/english/research/networks/clsi CLS initiative] at UiO and is employed by the Bioinformatics Core Facility ([http://core.rr-research.no/bioinformatics CF]) at OUH and UiO. <br />
<br />
The wikis for the [[MBV-INFX410 2013|2013]], [[MBV-INFX410 2014|2014]], and [[MBV-INFX410 2015|2015]] versions of the course are found behind these links. <br />
<br />
Links to the web pages for the years 2009-2011 is found [http://bioinformatics.uio.no/wiki/Bioinformatics_course here] and for 2012 [https://wiki.uio.no/projects/MBV-INFX410/index.php/Main_Page here].&nbsp;<br />
<br />
=== Contacts ===<br />
<br />
Jon Bråte (Course coordinator) - e-mail: jon.brate@ibv.uio.no<br />
<br />
Torill Rørtveit (Course administrator, registration) - e-mail: torill.rortveit@ibv.uio.no</div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=MBV-INFX410&diff=2081MBV-INFX4102020-07-26T17:58:03Z<p>Jonkl@uio.no: /* Bioinformatics for Molecular Biology */</p>
<hr />
<div>== Bioinformatics for Molecular Biology ==<br />
"""All information for 2019 and later is found on University of Oslo Canvas pages"""<br />
<br />
'''''All information for 2018 is found here:''''' '''[[MBV-INFX410 2018|MBV-INFX410 2018 wiki]]. '''''Course responsible is Jon Bråte (e-mail: jon.brate@ibv.uio.no) and course administrator Torill Rørtveit (e-mail: torill.rortveit@ibv.uio.no).''<br />
<br />
'''''All information for 2017 is found here:''''' [[MBV-INFX410 2017|'''MBV-INFX410 2017 wiki''']]'''. '''''Course responsible is Jon Bråte (e-mail: jon.brate@ibv.uio.no) and course administrator Torill Rørtveit (e-mail: torill.rortveit@ibv.uio.no).''<br />
<br />
'''''All information for 2016 is found here:''''' [[MBV-INFX410 2016|'''MBV-INFX410 2016 wiki''']]'''. '''''Course responsible is Jon Bråte (e-mail: jon.brate@ibv.uio.no) and course administrator Torill Rørtveit (e-mail: torill.rortveit@ibv.uio.no).''<br />
<br />
'''''All information for 2015 is found here:''''' [[MBV-INFX410 2015|'''MBV-INFX410 2015 wiki''']] <br />
<br />
This is the wiki for the courses [http://www.uio.no/studier/emner/matnat/ibv/MBV-INF4410 MBV-INF4410] and [http://www.uio.no/studier/emner/matnat/ibv/MBV-INF9410 MBV-INF9410] offered by the Department of Biosciences and Department of Informatics at the University of Oslo (UiO). Both MBV-INF4410 (M.Sc. level) and MBV-INF9410 (Ph.D. level) are 10 study point courses. The 8 study points variant of the course (MBV-INF9410A) will no longer be given after 2013.<br />
<br />
The course consists of five weeks of lectures, exercises, obligatory assignments, and a take-home exam (one week). Obligatory assignments must be completed and approved before the exam and in the same semester. An additional, limited, oral examination may be arranged in cases where this is necessary for the student evaluation. The course is open also for non-UiO students. It is only necessary to be physically present in Oslo for certain parts of the course. <br />
<br />
=== Course description ===<br />
<br />
This intensive course will introduce students to bioinformatics resources and tools for molecular biology research. All the lecturers are among the&nbsp;top researchers working within the fields of bioinformatics and computational biology in&nbsp;the Oslo region. Students&nbsp;must bring&nbsp;their own&nbsp;lap-top for in-course demonstrations as well as for practical lab exercises. The course is mainly intended for biology students, but also for&nbsp;computer science students or students from other fields of science with&nbsp;an interest for and some experience with molecular biology. No prior background in bioinformatics or computer science is required.&nbsp;All students should have a basic understanding of molecular biology,&nbsp;at least roughly corresponding to 5-10 university study points in molecular biology, biochemistry, or similar. ''If you are uncertain if your biology background is strong enough, please contact the course administrator before you sign up for&nbsp;the course.'' <br />
<br />
'''Course responsible in 2016, 2917, and 2018 is Jon Bråte (e-mail: jon.brate@ibv.uio.no), from the Department of Biology, UiO.''' <br />
<br />
Course responsible for the years 2012 to 2015 was [http://folk.uio.no/jonkl Dr. Jon K. Lærdahl] (jonkl@medisin.uio.no) from the Department of Microbiology, Oslo University Hospital (OUH) - Rikshospitalet. Lærdahl was also employed by the [http://www.mn.uio.no/ifi/english/research/networks/clsi CLS initiative] at UiO and is employed by the Bioinformatics Core Facility ([http://core.rr-research.no/bioinformatics CF]) at OUH and UiO. <br />
<br />
The wikis for the [[MBV-INFX410 2013|2013]], [[MBV-INFX410 2014|2014]], and [[MBV-INFX410 2015|2015]] versions of the course are found behind these links. <br />
<br />
Links to the web pages for the years 2009-2011 is found [http://bioinformatics.uio.no/wiki/Bioinformatics_course here] and for 2012 [https://wiki.uio.no/projects/MBV-INFX410/index.php/Main_Page here].&nbsp;<br />
<br />
=== Contacts ===<br />
<br />
Jon Bråte (Course coordinator) - e-mail: jon.brate@ibv.uio.no<br />
<br />
Torill Rørtveit (Course administrator, registration) - e-mail: torill.rortveit@ibv.uio.no</div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Structural_Bioinformatics_2018&diff=2044Structural Bioinformatics 20182018-11-19T12:37:56Z<p>Jonkl@uio.no: </p>
<hr />
<div>How to [[Media:InstallingPyMOL.pdf|install PyMOL]] (You need PyMOL installed on your laptop for all the exercises) You, most likely, do NOT NEED JAVA!<br />
<br />
Bring an external mouse! It is much easier to work in PyMOL when you do not have to rely on the trackpad<br />
<br />
Kahoots will be run at https://kahoot.it<br />
<br />
Tuesday 09:15 - 10:45: Basic Structural Biology Review [[Media:StructBiolReview A7 Part1.pdf|part 1]], [[Media:StructBiolReview A7 Part2.pdf|part 2]], and [[Media:StructBiolReview A7 Part3.pdf|part 3]] ('''Only come to this lecture if you think you need it!''')<br />
<br />
Tuesday 11:00: Structural Bioinformatics lectures [[Media:StructBioinfo_2018_Part1.pdf|part 1]], [[Media:StructBioinfo_2018_Part2.pdf|part 2]], [[Media:StructBioinfo_2018_Part3.pdf|part 3]], and [[Media:StructBioinfo_2018_Part4.pdf|part 4]]<br />
<br />
PyMOL exercise in [[Media:PyMOL Exercise-18.doc|MS Word]] and [[Media:PyMOL Exercise-Solutions-18.pdf|pdf]] (with solutions) format<br />
<br />
A second Structural Bioinformatics exercise in [[Media:StructBioinf2-18.pdf|pdf]] and [[Media:StructBioinf2-18.docx|MS Word]] format. Wait with task 7 & 8 until Wednesday, unless you know what you are doing.<br />
<br />
Wednesday 09:15: Structural Bioinformatics lectures cont.<br />
<br />
Homology Modelling exercise in [[Media:HomologyModelingExercise-18.docx|MS Word]] and [[Media:HomologyModelingExercise-Solutions-18.pdf|pdf]] (with solutions) format.<br />
<br />
Back to [[MBV-INFX410 2018|main page]]</div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:HomologyModelingExercise-18.docx&diff=2043File:HomologyModelingExercise-18.docx2018-11-19T12:37:07Z<p>Jonkl@uio.no: </p>
<hr />
<div></div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:HomologyModelingExercise-Solutions-18.pdf&diff=2042File:HomologyModelingExercise-Solutions-18.pdf2018-11-19T12:36:50Z<p>Jonkl@uio.no: </p>
<hr />
<div></div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Structural_Bioinformatics_2018&diff=2041Structural Bioinformatics 20182018-11-19T12:35:25Z<p>Jonkl@uio.no: </p>
<hr />
<div>How to [[Media:InstallingPyMOL.pdf|install PyMOL]] (You need PyMOL installed on your laptop for all the exercises) You, most likely, do NOT NEED JAVA!<br />
<br />
Bring an external mouse! It is much easier to work in PyMOL when you do not have to rely on the trackpad<br />
<br />
Kahoots will be run at https://kahoot.it<br />
<br />
Tuesday 09:15 - 10:45: Basic Structural Biology Review [[Media:StructBiolReview A7 Part1.pdf|part 1]], [[Media:StructBiolReview A7 Part2.pdf|part 2]], and [[Media:StructBiolReview A7 Part3.pdf|part 3]] ('''Only come to this lecture if you think you need it!''')<br />
<br />
Tuesday 11:00: Structural Bioinformatics lectures [[Media:StructBioinfo_2018_Part1.pdf|part 1]], [[Media:StructBioinfo_2018_Part2.pdf|part 2]], [[Media:StructBioinfo_2018_Part3.pdf|part 3]], and [[Media:StructBioinfo_2018_Part4.pdf|part 4]]<br />
<br />
PyMOL exercise in [[Media:PyMOL Exercise-18.doc|MS Word]] and [[Media:PyMOL Exercise-Solutions-18.pdf|pdf]] (with solutions) format<br />
<br />
A second Structural Bioinformatics exercise in [[Media:StructBioinf2-18.pdf|pdf]] and [[Media:StructBioinf2-18.docx|MS Word]] format. Wait with task 7 & 8 until Wednesday, unless you know what you are doing.<br />
<br />
Wednesday 09:15: Structural Bioinformatics lectures cont.<br />
<br />
Homology Modelling exercise<br />
<br />
Back to [[MBV-INFX410 2018|main page]]</div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:StructBioinf2-18.docx&diff=2040File:StructBioinf2-18.docx2018-11-19T12:33:49Z<p>Jonkl@uio.no: </p>
<hr />
<div></div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:StructBioinf2-18.pdf&diff=2039File:StructBioinf2-18.pdf2018-11-19T12:33:29Z<p>Jonkl@uio.no: </p>
<hr />
<div></div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:PyMOL_Exercise-18.doc&diff=2038File:PyMOL Exercise-18.doc2018-11-19T12:31:37Z<p>Jonkl@uio.no: </p>
<hr />
<div></div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:PyMOL_Exercise-Solutions-18.pdf&diff=2037File:PyMOL Exercise-Solutions-18.pdf2018-11-19T12:31:13Z<p>Jonkl@uio.no: </p>
<hr />
<div></div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Structural_Bioinformatics_2018&diff=2036Structural Bioinformatics 20182018-11-19T12:30:44Z<p>Jonkl@uio.no: </p>
<hr />
<div>How to [[Media:InstallingPyMOL.pdf|install PyMOL]] (You need PyMOL installed on your laptop for all the exercises) You, most likely, do NOT NEED JAVA!<br />
<br />
Bring an external mouse! It is much easier to work in PyMOL when you do not have to rely on the trackpad<br />
<br />
Kahoots will be run at https://kahoot.it<br />
<br />
Tuesday 09:15 - 10:45: Basic Structural Biology Review [[Media:StructBiolReview A7 Part1.pdf|part 1]], [[Media:StructBiolReview A7 Part2.pdf|part 2]], and [[Media:StructBiolReview A7 Part3.pdf|part 3]] ('''Only come to this lecture if you think you need it!''')<br />
<br />
Tuesday 11:00: Structural Bioinformatics lectures [[Media:StructBioinfo_2018_Part1.pdf|part 1]], [[Media:StructBioinfo_2018_Part2.pdf|part 2]], [[Media:StructBioinfo_2018_Part3.pdf|part 3]], and [[Media:StructBioinfo_2018_Part4.pdf|part 4]]<br />
<br />
PyMOL exercise in [[Media:PyMOL Exercise-18.doc|MS Word]] and [[Media:PyMOL Exercise-Solutions-18.pdf|pdf]] (with solutions) format<br />
<br />
A second Structural Bioinformatics exercise<br />
<br />
Wednesday 09:15: Structural Bioinformatics lectures cont.<br />
<br />
Homology Modelling exercise<br />
<br />
Back to [[MBV-INFX410 2018|main page]]</div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Structural_Bioinformatics_2018&diff=2035Structural Bioinformatics 20182018-11-19T12:28:17Z<p>Jonkl@uio.no: </p>
<hr />
<div>How to [[Media:InstallingPyMOL.pdf|install PyMOL]] (You need PyMOL installed on your laptop for all the exercises) You, most likely, do NOT NEED JAVA!<br />
<br />
Bring an external mouse! It is much easier to work in PyMOL when you do not have to rely on the trackpad<br />
<br />
Kahoots will be run at https://kahoot.it<br />
<br />
Tuesday 09:15 - 10:45: Basic Structural Biology Review [[Media:StructBiolReview A7 Part1.pdf|part 1]], [[Media:StructBiolReview A7 Part2.pdf|part 2]], and [[Media:StructBiolReview A7 Part3.pdf|part 3]] ('''Only come to this lecture if you think you need it!''')<br />
<br />
Tuesday 11:00: Structural Bioinformatics lectures [[Media:StructBioinfo_2018_Part1.pdf|part 1]], [[Media:StructBioinfo_2018_Part2.pdf|part 2]], [[Media:StructBioinfo_2018_Part3.pdf|part 3]], and [[Media:StructBioinfo_2018_Part4.pdf|part 4]]<br />
<br />
PyMOL exercise<br />
<br />
A second Structural Bioinformatics exercise<br />
<br />
Wednesday 09:15: Structural Bioinformatics lectures cont.<br />
<br />
Homology Modelling exercise<br />
<br />
Back to [[MBV-INFX410 2018|main page]]</div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:StructBioinfo_2018_Part4.pdf&diff=2034File:StructBioinfo 2018 Part4.pdf2018-11-19T12:27:01Z<p>Jonkl@uio.no: </p>
<hr />
<div></div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:StructBioinfo_2018_Part3.pdf&diff=2033File:StructBioinfo 2018 Part3.pdf2018-11-19T12:26:44Z<p>Jonkl@uio.no: </p>
<hr />
<div></div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:StructBioinfo_2018_Part2.pdf&diff=2032File:StructBioinfo 2018 Part2.pdf2018-11-19T12:26:27Z<p>Jonkl@uio.no: </p>
<hr />
<div></div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:StructBioinfo_2018_Part1.pdf&diff=2031File:StructBioinfo 2018 Part1.pdf2018-11-19T12:26:11Z<p>Jonkl@uio.no: </p>
<hr />
<div></div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Structural_Bioinformatics_2018&diff=2030Structural Bioinformatics 20182018-11-19T12:25:44Z<p>Jonkl@uio.no: </p>
<hr />
<div>How to [[Media:InstallingPyMOL.pdf|install PyMOL]] (You need PyMOL installed on your laptop for all the exercises) You, most likely, do NOT NEED JAVA!<br />
<br />
Bring an external mouse! It is much easier to work in PyMOL when you do not have to rely on the trackpad<br />
<br />
Kahoots will be run at https://kahoot.it<br />
<br />
Tuesday 09:15 - 10:45: Basic Structural Biology Review [[Media:StructBiolReview A7 Part1.pdf|part 1]], [[Media:StructBiolReview A7 Part2.pdf|part 2]], and [[Media:StructBiolReview A7 Part3.pdf|part 3]] ('''Only come to this lecture if you think you need it!''')<br />
<br />
Tuesday 11:00: Structural Bioinformatics lectures [[Media:StructBioinfo_2017_Part1.pdf|part 1]]<br />
<br />
PyMOL exercise<br />
<br />
A second Structural Bioinformatics exercise<br />
<br />
Wednesday 09:15: Structural Bioinformatics lectures cont.<br />
<br />
Homology Modelling exercise<br />
<br />
Back to [[MBV-INFX410 2018|main page]]</div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=MBV-INFX410&diff=2010MBV-INFX4102018-11-14T14:21:17Z<p>Jonkl@uio.no: </p>
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<div>== Bioinformatics for Molecular Biology ==<br />
'''''All information for 2018 is found here:''''' '''[[MBV-INFX410 2018|MBV-INFX410 2018 wiki]]. '''''Course responsible is Jon Bråte (e-mail: jon.brate@ibv.uio.no) and course administrator Torill Rørtveit (e-mail: torill.rortveit@ibv.uio.no).''<br />
<br />
'''''All information for 2017 is found here:''''' [[MBV-INFX410 2017|'''MBV-INFX410 2017 wiki''']]'''. '''''Course responsible is Jon Bråte (e-mail: jon.brate@ibv.uio.no) and course administrator Torill Rørtveit (e-mail: torill.rortveit@ibv.uio.no).''<br />
<br />
'''''All information for 2016 is found here:''''' [[MBV-INFX410 2016|'''MBV-INFX410 2016 wiki''']]'''. '''''Course responsible is Jon Bråte (e-mail: jon.brate@ibv.uio.no) and course administrator Torill Rørtveit (e-mail: torill.rortveit@ibv.uio.no).''<br />
<br />
'''''All information for 2015 is found here:''''' [[MBV-INFX410 2015|'''MBV-INFX410 2015 wiki''']] <br />
<br />
This is the wiki for the courses [http://www.uio.no/studier/emner/matnat/ibv/MBV-INF4410 MBV-INF4410] and [http://www.uio.no/studier/emner/matnat/ibv/MBV-INF9410 MBV-INF9410] offered by the Department of Biosciences and Department of Informatics at the University of Oslo (UiO). Both MBV-INF4410 (M.Sc. level) and MBV-INF9410 (Ph.D. level) are 10 study point courses. The 8 study points variant of the course (MBV-INF9410A) will no longer be given after 2013.<br />
<br />
The course consists of five weeks of lectures, exercises, obligatory assignments, and a take-home exam (one week). Obligatory assignments must be completed and approved before the exam and in the same semester. An additional, limited, oral examination may be arranged in cases where this is necessary for the student evaluation. The course is open also for non-UiO students. It is only necessary to be physically present in Oslo for certain parts of the course. <br />
<br />
=== Course description ===<br />
<br />
This intensive course will introduce students to bioinformatics resources and tools for molecular biology research. All the lecturers are among the&nbsp;top researchers working within the fields of bioinformatics and computational biology in&nbsp;the Oslo region. Students&nbsp;must bring&nbsp;their own&nbsp;lap-top for in-course demonstrations as well as for practical lab exercises. The course is mainly intended for biology students, but also for&nbsp;computer science students or students from other fields of science with&nbsp;an interest for and some experience with molecular biology. No prior background in bioinformatics or computer science is required.&nbsp;All students should have a basic understanding of molecular biology,&nbsp;at least roughly corresponding to 5-10 university study points in molecular biology, biochemistry, or similar. ''If you are uncertain if your biology background is strong enough, please contact the course administrator before you sign up for&nbsp;the course.'' <br />
<br />
'''Course responsible in 2016, 2917, and 2018 is Jon Bråte (e-mail: jon.brate@ibv.uio.no), from the Department of Biology, UiO.''' <br />
<br />
Course responsible for the years 2012 to 2015 was [http://folk.uio.no/jonkl Dr. Jon K. Lærdahl] (jonkl@medisin.uio.no) from the Department of Microbiology, Oslo University Hospital (OUH) - Rikshospitalet. Lærdahl was also employed by the [http://www.mn.uio.no/ifi/english/research/networks/clsi CLS initiative] at UiO and is employed by the Bioinformatics Core Facility ([http://core.rr-research.no/bioinformatics CF]) at OUH and UiO. <br />
<br />
The wikis for the [[MBV-INFX410 2013|2013]], [[MBV-INFX410 2014|2014]], and [[MBV-INFX410 2015|2015]] versions of the course are found behind these links. <br />
<br />
Links to the web pages for the years 2009-2011 is found [http://bioinformatics.uio.no/wiki/Bioinformatics_course here] and for 2012 [https://wiki.uio.no/projects/MBV-INFX410/index.php/Main_Page here].&nbsp;<br />
<br />
=== Contacts ===<br />
<br />
Jon Bråte (Course coordinator) - e-mail: jon.brate@ibv.uio.no<br />
<br />
Torill Rørtveit (Course administrator, registration) - e-mail: torill.rortveit@ibv.uio.no</div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Main_Page&diff=2009Main Page2018-11-14T14:20:37Z<p>Jonkl@uio.no: </p>
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<div>= Wiki pages for courses in Computational Life Science (CLS)/Bioinformatics at UiO =<br />
<br />
*INF-BIO5121/9121 - [http://www.uio.no/studier/emner/matnat/ifi/INF-BIO5121/ High Throughput Sequencing Technologies and Bioinformatics Analysis] ([[INF-BIOX121|INF-BIOX121 wiki]])<br />
*MBV-INF4410/9410 - [http://www.uio.no/studier/emner/matnat/ibv/MBV-INF4410/ Bioinformatics for Molecular Biology] ([[MBV-INFX410 2018|MBV-INFX410 wiki]]) (For previous years see [[MBV-INFX410|MBV-INFX410 wiki top page]])<br />
*INF-STK5010/9010 - [http://www.uio.no/studier/emner/matnat/ifi/INF-STK5010/ Statistical Bioinformatics - Learning from big data in the life sciences]<br />
<br />
For more details on the CLS initiative follow [http://www.mn.uio.no/ifi/english/research/networks/clsi this link]</div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=MBV-INFX410_2015&diff=2008MBV-INFX410 20152018-11-14T14:12:34Z<p>Jonkl@uio.no: /* Bioinformatics for Molecular Biology - 2015 */</p>
<hr />
<div>== [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410 Bioinformatics for Molecular Biology] - 2015 ==<br />
'''''THIS IS THE WIKI FOR 2015. INFORMATION FOR 2018 IS FOUND [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410_2018 HERE]!'''''<br />
<br />
'''''Jan 15: The exam results have been submitted to the IBV administration and will be available soon. Some brief comments on the exam:'''''<br />
<br />
*This was a home exam with lots of time, permitted materials were basically "everything", and roughly 1/3 of the students had answered almost everything correctly. For this reason there was relatively little tolerance for silly mistakes such as not reading the questions properly, not answering all sub-questions, very odd/incomprehensible argumentation/spelling, and leaving parts of the exercises blank<br />
*Exercise 1b: 3 proteins are identical because they all represent identical splicing of a pre-mRNA corresponding to the human reference genome. The last sequence corresponds to a (different) individual and different splicing and uses the wrong ATG as start codon<br />
*Exercise 1h: 3 codons is 9 nucleotides, not 3. 5' end is at "the beginning" of the exon<br />
*If FTO from cow or sheep is more similar to human FTO than the other, this is completely by chance<br />
*All ''Sauropsida'' (birds and reptiles) have a common ancestor more recently than the common ancestor of ''Sauropsida'' and mammals, while amphibians are remote cousins. All the phylogenetic trees were ok<br />
*Exercise 2a: First we make one long string with all the information in the input file, then we split on the string "\n>" and get a list of fasta sequences. We loop through this list and in an inner loop split on "\n"<br />
*Exercise 2b: (i) Two main ways to do this: Best(?) is to use len() to find length of sequence string but remember to not count the end-of-line character at the end of every line. Must also use str() to convert number to string for printing. It was also possible to extract the length from the header, but in that case one should not cut out a substring of only three characters since this will only work for sequences with lengths between 100 and 999. (ii) Many ways to do this task and almost all ok<br />
*Exercise 3: You have to normalise the data because the total amount of RNA is not the same in the various samples. This might be due to different concentrations of the samples, different degree of RNA degradation etc. If you ''look'' at the data it is pretty obvious that all the top 5 miRNAs are upregulated in HCHF <br />
*Exercise 4a: This was quite difficult and time consuming, unless you had read the article "A beginners guide to SNP calling from high-throughput DNA-sequencing data" in the required reading material. Not all students had read the curriculum<br />
<br />
'''''Dec 9: The exam for the course was sent, by e-mail, to all qualified students on December 9. If you did not receive the exam, please contact Jon immediately!<br />
<br />
'''''Dec 3: The solutions for the obligatory assignment can be downloaded [[Media:Oblig_MBV-INFx410-Solutions-2015.pdf|here]]. Jon will go through the oblig with solutions on Thursday. <br />
<br />
'''''Dec 1: The handouts and material for Monday Nov 30 was [https://wiki.uio.no/projects/clsi/index.php/Statistical_Bioinformatics_2015 updated].'''''<br />
<br />
'''''Nov 25: On Friday Dec 4th, between 13:00 and 15:00, there will be a helpdesk session in lecture room Java (2. etasje). This is not a compulsory part of the course and there will not be any lectures. There will not be any new messages and no messages or hints about the exam (that is not also put on the wiki). This is an opportunity to get help with parts of the curriculum you are struggling with. Jon will be present, but will most likely not be able to answer all questions about the parts of the curriculum that has been taught by other teachers.'''''<br />
<br />
'''''Nov 25: The following rooms will be used for lectures in week 49: Monday - Postscript, Tuesday - Lille Auditorium in Kristen Nygaards hus, Wednesday - Pascal, and Thursday - C. For more information go to the [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410_2015#Time_and_place Time and place section] below.'''''<br />
<br />
'''''Nov 20: Download the obligatory and compulsory assignment [[Media:Oblig_MBV-INFx410-2015.pdf|by following this link]]. It must be returned by 09:00, Monday November 30. Good luck! Students that do not get this assignment approved, will not be allowed to take the exam.'''''<br />
<br />
'''''All students must be present at the start of the course, at 09:00, on November 9. Missing students will not be allowed to follow the course or to take the exam. If you for some reason are not able to attend, please contact Jon (See [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410_2015#Contacts contact details] below).'''''<br />
<br />
This is the wiki for the courses [http://www.uio.no/studier/emner/matnat/ibv/MBV-INF4410 MBV-INF4410] and [http://www.uio.no/studier/emner/matnat/ibv/MBV-INF9410 MBV-INF9410] offered by the Department of Biosciences and Department of Informatics at the University of Oslo (UiO). Both MBV-INF4410 (M.Sc. level) and MBV-INF9410 (Ph.D. level) are 10 study point courses. The 8 study points variant of the course (MBV-INF9410A) will not be given after 2013.<br />
<br />
The course consists of five weeks of lectures, exercises, obligatory assignments, and a take-home exam (one week). Obligatory assignments must be completed and approved before the exam and in the same semester. An additional, limited, oral examination may be arranged in cases where this is necessary for the student evaluation. The course is open also for non-UiO students. It is only necessary to be physically present in Oslo for certain parts of the course.<br />
<br />
=== Course description ===<br />
<br />
This intensive course will introduce students to bioinformatics resources and tools for molecular biology research. All the lecturers are among the&nbsp;top researchers working within the fields of bioinformatics and computational biology in the Oslo region. Students must bring their own laptop for in-course demonstrations as well as for practical lab exercises. The course is mainly intended for biology students, but also for computer science students or students from other fields of science with an interest for and some experience with molecular biology. No prior background in bioinformatics or computer science is required. All students should have a basic understanding of molecular biology, at least roughly corresponding to 5-10 university study points in molecular biology, biochemistry, or similar. ''If you are uncertain if your biology background is strong enough, please contact Jon (See contact details below) before you sign up for the course.''<br />
<br />
Course responsible is [http://folk.uio.no/jonkl Dr. Jon K. Lærdahl] (jonkl@medisin.uio.no) from the Department of Microbiology, Oslo University Hospital (OUH) - Rikshospitalet. Lærdahl is also employed by the [http://www.mn.uio.no/ifi/english/research/networks/clsi CLS initiative] at UiO and the Bioinformatics Core Facility ([http://core.rr-research.no/bioinformatics CF]) at OUH and UiO.<br />
<br />
Links to the web pages for the years 2009-2011 is found [http://bioinformatics.uio.no/wiki/Bioinformatics_course here] (Aug 2014: this server might be permanently down...), for 2012 [https://wiki.uio.no/projects/MBV-INFX410/index.php/Main_Page here], for 2013 [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410_2013 here] and for 2014 [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410_2014 here].<br />
<br />
Notes on the course format: The course has previously been given as an intensive course over two weeks with a take-home exam in the 3rd to 4th week. A take-home assignment was also a compulsory part of the 10 study points versions of the course. The compact format was ideal for students coming from outside Oslo, but it was also exhausting for students and lecturers. It gave no time to digest and dive more deeply into the various topics presented in the course. Since 2013, the course will be given over 5 weeks. However, '''''it will only be necessary to be physically present in Oslo for parts of the course''''', ''i.e.'' the lectures/exercises. '' The schedule is presented below, but there might be small adjustments to this later.''<br />
<br />
[[File:TeachingPlanMBVX410 15A2.png|thumb|center|700px]]<br />
<br />
=== Time and place ===<br />
<br />
'''The course will be offered in weeks 46 to 50, autumn 2015, ''i.e. ''starting on Monday November 9 (See schedule below).''' The take-home exam must be handed in in week 51, on Wednesday December 16. Each day of lectures/exercises will consist of three time slots for lectures and/or exercises/practical labs between 09:00 and 16:00. Lunch will usually be between 12:45 and 13:30. You will have to bring your own lunch or buy lunch in the local kantine.<br />
<br />
'''Lecture room:''' All lectures/exercises in weeks 46 and 47 will be given in lecture room '''Python''' in Ole-Johan Dahls hus (IFI2). A map showing the location of the building is found [http://www.uio.no/om/finn-fram/omrader/gaustad/ga06 here]. The building is located next to the Forskningsparken metro and tram stations. The room Python is on the 1st floor (2. etasje) in the northern end of the building, the end closest to the tram line. The easiest access to '''Python''' is through the entrance in the tunnel going through the building.<br />
<br />
In week 49 we will use the following rooms:<br />
* Monday, Nov 30th: Room '''Postscript''', 2. etasje (opposite direction of Python when you enter the building through the tunnel)<br />
* Tuesday, Dec 1st: '''Lille Auditorium''' in Kristen Nygaards hus, the building next to OJDs hus, ground floor<br />
* Wednesday, Dec 2nd: Room '''Pascal''', back in OJDs hus, 2. etasje, further along towards the south wrt. Postscript <br />
* Thursday, Dec 3rd: Room '''C''', 3. etasje, one floor up from Pascal<br />
<br />
On Friday Dec 4th, between 13:00 and 15:00, there will be a helpdesk session in lecture room Java (2. etasje). This is not a compulsory part of the course and there will not be any lectures. There will not be any new messages and no messages or hints about the exam (that is not also put on the wiki). This is an opportunity to get help with parts of the curriculum you are struggling with. Jon will be present, but will most likely not be able to answer all questions about the parts of the curriculum that has been taught by other teachers.<br />
<br />
=== Contacts ===<br />
<br />
Jon K. Lærdahl (Course coordinator) - e-mail: jonkl@medisin.uio.no, phone: +47 99 507 335<br />
<br />
Torill Rørtveit (Course administrator, registration) - e-mail: torill.rortveit@ibv.uio.no<br />
<br />
=== Computers/laptops, internet access, and UiO user account ===<br />
<br />
All students must bring a laptop with either a Windows (Windows 7 or more recent), Unix/Linux, or OS X (''i.e.'' an Apple computer) operating system.<br />
<br />
*The computer should not be more than 2-3 years old<br />
*It should be possible to connect the computer to the UiO wireless network<br />
*You must have a root/administrator password that gives you access to installing new software on the computer<br />
*Bring an external mouse, and do not rely on touchpad/trackpad only<br />
*You must have a valid UiO user account and must be able to log onto a computer on the UiO network<br />
*If you are unsure if you have a UiO user account and a valid password, you should try to log in using&nbsp;kiosk.uio.no&nbsp;or win.uio.no as described [http://www.uio.no/english/services/it/network/home-and-away/kiosk/index.html here]. If you are unable to log in, try the hints you find [http://www.uio.no/english/services/it/network/home-and-away/kiosk/programkiosk/index.html here].<br />
*Instructions (in Norwegian) about how to find your user name and get a new password can be found [http://www.uio.no/tjenester/it/brukernavn-passord/ikke-passord.html here].<br />
<br />
'''''If you are struggling with anything of the above, in particular if you have forgotten your UiO user name/password or you do not have one, you must contact Jon (See contact details above) as soon as possible, and at least one week before the start of the course.'''''<br />
<br />
'''''To get a UiO username/password at the UiO helpdesk you need valid ID.'''''<br />
<br />
On the first day of the course we will set up your laptop so that it can be used for the exercises/tutorials, the home exam and hopefully in your future work. How to get a reasonable setup is described [[Laptop Setup|here]].<br />
<br />
If you already are an expert programmer and Unix guru, go [[Biology for Informatics|here]].<br />
<br />
=== Programme ===<br />
<br />
The schedule below is tentative, and may be changed prior to, and possibly even during, the course. Requests and suggestions are welcome.<br />
<br />
{| border="1" cellpadding="2" cellspacing="1" width="100%"<br />
|-<br />
| colspan="5" align="center" bgcolor="#99ccff" | Week 46: Monday, November 09 - Friday, November 13<br />
|-<br />
| bgcolor="#dddddd" width="16%" | <br />
| bgcolor="#dddddd" width="28%" | Session 1<br />
| colspan="2" bgcolor="#dddddd" width="28%" | Session 2<br />
| bgcolor="#dddddd" | Session 3<br />
|-<br />
| <br />
| 09:00 - 10:45<br />
| colspan="2" | 11:00 - 12:45<br />
| 13:30 - 16:00<br />
|-<br />
| bgcolor="#dddddd" | Monday 9th<br />
| bgcolor="#dddddd" | <br />
[[Course introduction 2015|Course introduction]]<br />
<br />
- lectures<br />
<br />
| colspan="2" bgcolor="#dddddd" | <br />
[[Day 1 2015|Biological databases, Unix & setting up laptops]]<br />
<br />
- lectures/exercises<br />
<br />
| bgcolor="#dddddd" | <br />
[[Day 1 2015|Basic Unix]]<br />
<br />
- exercises<br />
<br />
|-<br />
| bgcolor="#dddddd" | <br />
| bgcolor="#dddddd" | Jon K Lærdahl<br />
| colspan="2" bgcolor="#dddddd" | Jon K Lærdahl<br />
| bgcolor="#dddddd" | Jon K Lærdahl<br />
|-<br />
| Tuesday 10th<br />
| <br />
[[Day 2 2015|Ensembl genome browser & Jalview]]<br />
<br />
- lectures/demo<br />
<br />
| colspan="2" | <br />
[[Day 2 2015|Working with sequences/databases]]<br />
<br />
- lectures/exercises<br />
<br />
| <br />
[[Day 2 2015|Applied sequence bioinformatics]]<br />
<br />
- exercise<br />
<br />
|-<br />
| <br />
| Jon K Lærdahl<br />
| colspan="2" | Jon K Lærdahl<br />
| Jon K Lærdahl<br />
|-<br />
| bgcolor="#dddddd" | Wednesday 11th<br />
| bgcolor="#dddddd" | <br />
[[Structural Biology Review 2015|Structural Biology Review]]<br />
<br />
- lectures/review<br />
<br />
| colspan="2" bgcolor="#dddddd" | <br />
[[Day 3 2015|More Unix & UCSC Genome browser]]<br />
<br />
- lectures/demo/exercises<br />
<br />
| bgcolor="#dddddd" | <br />
[[Day 3 2015|Galaxy/Life Portal]]<br />
<br />
- lectures/demo/exercises<br />
<br />
|-<br />
| bgcolor="#dddddd" | <br />
| bgcolor="#dddddd" | Jon K Lærdahl<br />
| colspan="2" bgcolor="#dddddd" | Jon K Lærdahl<br />
| bgcolor="#dddddd" | Jon K Lærdahl<br />
|-<br />
| Thursday 12th<br />
| <br />
[[Python workshop 2015|Python workshop]]<br />
<br />
- lectures/exercises<br />
<br />
| colspan="2" | <br />
[[Python workshop 2015|Python workshop]]<br />
<br />
- lectures/exercises<br />
<br />
| <br />
[[Python workshop 2015|Python workshop]]<br />
<br />
- lectures/exercises<br />
<br />
|-<br />
| <br />
| Karin Lagesen<br />
| colspan="2" | Karin Lagesen<br />
| Karin Lagesen<br />
|-<br />
| bgcolor="#dddddd" | Friday 13th<br />
| bgcolor="#dddddd" | <br />
[[Python workshop 2015|Python workshop]]<br />
<br />
- lectures/exercises<br />
<br />
| colspan="2" bgcolor="#dddddd" | <br />
[[Python workshop 2015|Python workshop]]<br />
<br />
- lectures/exercises<br />
<br />
| bgcolor="#dddddd" | <br />
[[Python workshop 2015|Python workshop]]<br />
<br />
- lectures/exercises<br />
<br />
|-<br />
| bgcolor="#dddddd" | <br />
| bgcolor="#dddddd" | Karin Lagesen<br />
| colspan="2" bgcolor="#dddddd" | Karin Lagesen<br />
| bgcolor="#dddddd" | Karin Lagesen<br />
|-<br />
| colspan="5" align="center" bgcolor="#99ccff" | Week 47: Monday, November 16 - Friday, November 20<br />
|-<br />
| bgcolor="#dddddd" width="16%" | <br />
| bgcolor="#dddddd" width="28%" | Session 1<br />
| colspan="2" bgcolor="#dddddd" width="28%" | Session 2<br />
| bgcolor="#dddddd" | Session 3<br />
|-<br />
| <br />
| 09:00 - 10:45<br />
| colspan="2" | 11:00 - 12:45<br />
| 13:30 - 16:00<br />
|-<br />
| bgcolor="#dddddd" | Monday 16th<br />
| colspan="2" bgcolor="#dddddd" | <br />
[[Sequence searching & MSAs 2015|Sequence searching, alignments, and multiple alignments]]<br />
<br />
- lectures (09:00 - 11:45)<br />
<br />
| colspan="2" bgcolor="#dddddd" | <br />
[[Sequence searching & MSAs 2015|Sequence searching and multiple sequence alignments]]<br />
<br />
- exercise (12:30 - 16:00)<br />
<br />
|-<br />
| bgcolor="#dddddd" | <br />
| colspan="2" bgcolor="#dddddd" | Torbjørn Rognes<br />
| colspan="2" bgcolor="#dddddd" | Jon K Lærdahl<br />
|-<br />
| Tuesday 17th<br />
| <br />
[[Structural Bioinformatics 2015|Structural Bioinformatics]]<br />
<br />
- lectures/exercises<br />
<br />
| colspan="2" | <br />
[[Structural Bioinformatics 2015|Structural Bioinformatics]]<br />
<br />
- lectures/exercises<br />
<br />
| <br />
[[Structural Bioinformatics 2015|Structural Bioinformatics]]<br />
<br />
- lectures/exercises<br />
<br />
|-<br />
| <br />
| Jon K Lærdahl<br />
| colspan="2" | Jon K Lærdahl<br />
| Jon K Lærdahl<br />
|-<br />
| bgcolor="#dddddd" | Wednesday 18th<br />
| bgcolor="#dddddd" | <br />
[[Hyperbrowser 2015|Reproducibility/Statistical epigenomics]]<br />
<br />
- lectures/exercises<br />
<br />
| colspan="2" bgcolor="#dddddd" | <br />
[[Hyperbrowser 2015|Reproducibility/Statistical epigenomics]]<br />
<br />
- lectures/exercises<br />
<br />
| bgcolor="#dddddd" | <br />
[[Hyperbrowser 2015|Reproducibility/Statistical epigenomics]]<br />
<br />
- lectures/exercises<br />
<br />
|-<br />
| bgcolor="#dddddd" | <br />
| bgcolor="#dddddd" | Sveinung Gundersen/Boris Simovski<br />
| colspan="2" bgcolor="#dddddd" | Sveinung Gundersen/Boris Simovski<br />
| bgcolor="#dddddd" | Sveinung Gundersen/Boris Simovski<br />
|-<br />
| Thursday 19th<br />
| colspan="2" | <br />
[[Docking and drug design 2015|Docking and drug discovery]]<br />
<br />
- lectures/exercises (09:00 - 11:45)<br />
<br />
| colspan="2" | <br />
[[Practical Unix/Python 2015|Practical Unix/Python exercise]]<br />
<br />
- lectures/exercises (12:30 - 16:00)<br />
<br />
|-<br />
| <br />
| colspan="2" | Bjørn Dalhus<br />
| colspan="2" | Jon K Lærdahl<br />
|-<br />
| bgcolor="#dddddd" | Friday 20th<br />
| bgcolor="#dddddd" | <br />
[[Structural Bioinformatics 2015|More Structural Bioinformatics]]<br />
<br />
- lectures/exercises<br />
<br />
| colspan="2" bgcolor="#dddddd" | <br />
[[Structural Bioinformatics 2015|More Structural Bioinformatics]]<br />
<br />
- lectures/exercises<br />
<br />
| bgcolor="#dddddd" | <br />
[[Structural Bioinformatics 2015|More Structural Bioinformatics]]<br />
<br />
- lectures/exercises<br />
<br />
|-<br />
| bgcolor="#dddddd" | <br />
| bgcolor="#dddddd" | Jon K Lærdahl<br />
| colspan="2" bgcolor="#dddddd" | Jon K Lærdahl<br />
| bgcolor="#dddddd" | Jon K Lærdahl<br />
|-<br />
| colspan="5" align="center" bgcolor="#99ccff" | Week 48: Monday, November 23 - Friday, November 27<br />
|-<br />
| colspan="5" align="center" | Work on obligatory home assignment and study days (no lectures)<br />
|-<br />
| colspan="5" align="center" bgcolor="#99ccff" | Week 49: Monday, November 30 - Thursday, December 3<br />
|-<br />
| bgcolor="#dddddd" width="16%" | <br />
| bgcolor="#dddddd" width="28%" | Session 1<br />
| colspan="2" bgcolor="#dddddd" width="28%" | Session 2<br />
| bgcolor="#dddddd" | Session 3<br />
|-<br />
| <br />
| 09:00 - 10:45<br />
| colspan="2" | 11:00 - 12:45<br />
| 13:30 - 16:00<br />
|-<br />
| bgcolor="#dddddd" | Monday 30th<br />
| bgcolor="#dddddd" | <br />
[[Statistical Bioinformatics 2015|Introduction to statistical inference and R]]<br />
<br />
- lectures<br />
<br />
| colspan="2" bgcolor="#dddddd" | <br />
[[Statistical Bioinformatics 2015|Basic R and exploring your data]]<br />
<br />
- lectures/exercises<br />
<br />
| bgcolor="#dddddd" | <br />
[[Statistical Bioinformatics 2015|Basic R and exploring your data]]<br />
<br />
- lectures/exercises<br />
<br />
|-<br />
| bgcolor="#dddddd" | <br />
| bgcolor="#dddddd" | Ole Christian Lingjærde<br />
| colspan="2" bgcolor="#dddddd" | Jon K Lærdahl/Ksenia Khelik<br />
| bgcolor="#dddddd" | Jon K Lærdahl/Ksenia Khelik<br />
|-<br />
| Tuesday 1st<br />
| <br />
[[NGS day 2015|Next generation sequencing (NGS)]]<br />
<br />
- lectures<br />
<br />
| colspan="2" | <br />
[[NGS day 2015|NGS & variant calling lab]]<br />
<br />
- lectures/exercises<br />
<br />
| <br />
[[NGS day 2015|NGS & variant calling lab]]<br />
<br />
- lectures/exercises<br />
<br />
|-<br />
| <br />
| Tim Hughes & Aravind Sundaram<br />
| colspan="2" | Tim Hughes & Aravind Sundaram<br />
| Tim Hughes & Aravind Sundaram<br />
|-<br />
| bgcolor="#dddddd" | Wednesday 2nd<br />
| bgcolor="#dddddd" | <br />
[[Analysis of transcriptome data 2015|Analysis of gene expression data using R]]<br />
<br />
- lectures/exercises<br />
<br />
| colspan="2" bgcolor="#dddddd" | <br />
[[Analysis of transcriptome data 2015|Analysis of gene expression data using R]]<br />
<br />
- lectures/exercises<br />
<br />
| bgcolor="#dddddd" | <br />
[[Analysis of transcriptome data 2015|Analysis of gene expression data using R]]<br />
<br />
- lectures/exercises<br />
|-<br />
| bgcolor="#dddddd" | <br />
| bgcolor="#dddddd" | Ståle Nygård<br />
| colspan="2" bgcolor="#dddddd" | Ståle Nygård<br />
| bgcolor="#dddddd" | Ståle Nygård<br />
|-<br />
| Thursday 3rd<br />
| <br />
[[Assembly - 2015|What does it mean to do bioinformatics?]]<br />
<br />
- lectures<br />
<br />
| colspan="2" | <br />
[[Gene lists and over-representation analysis (ORA) 2015|Gene lists & over-representation analysis (ORA)]]<br />
<br />
- lectures/exercises<br />
<br />
| <br />
End of course [[Media:EndOfCourseSummary-15.pdf|summary]]<br />
<br />
- lecture/discussion<br />
<br />
|-<br />
| <br />
| Lex Nederbragt<br />
| colspan="2" | Ståle Nygård<br />
| Jon K Lærdahl<br />
|}<br />
<br />
Ksenia Khelik from the BMI group, Ifi, will help during the Python and R courses.<br />
<br />
Ivar Grytten and Boris Simovski from the BMI group, Ifi, will help during the laptop setup session on Monday, November 09.<br />
<br />
The brief lecture on PCSK9 can be found [http://folk.uio.no/jonkl/StuffForMBV-INFx410/PCSK9_Lecture.pdf here], if you are interested. This is ''not'' a part of the curriculum.<br />
<br />
=== Required reading material/curriculum ===<br />
<br />
The curriculum comprises all lectures, lecture handouts, exercises and the reviews/articles/written material [[Additional curriculum|listed on this page]].<br />
<br />
An obligatory and compulsory assignment must be returned, by e-mail, to the course coordinator Jon K. Lærdahl (e-mail address: jonkl@medisin.uio.no) before Monday November 30, at 09:00. Note that students that do not get this assignment approved, will not be allowed to take the exam.<br />
<br />
The obligatory assignment can be downloaded [[Media:Oblig_MBV-INFx410-2015.pdf|here]].<br />
<br />
=== Exam ===<br />
<br />
'''##########################################'''<br />
<br />
'''Some messages:'''<br />
<br />
*Exercise 1, subsection i): "Zoom in on exon 2 so that..." means "Zoom in on exon 2 ''in the gene'' so that..."<br />
*Exercise 2, subsection b): The script should print out the length of the shortest and the longest sequence. It is not necessary that the script prints out the names of these sequences. You can find this manually<br />
*The exam for the course was sent, by e-mail, to all qualified students on December 9. If you did not receive the exam, please contact Jon immediately!<br />
<br />
'''##########################################'''<br />
<br />
The exam for this course will be a one week, take-home exam. Only students that have returned the obligatory assignment, and got this assignment approved, will be allowed to take the exam.<br />
<br />
The exam will be sent to all qualified participants at 3 pm, Wednesday December 9, by e-mail.<br />
<br />
Your completed exam must be returned, at the latest, at 3 pm, Wednesday December 16. It should be sent by e-mail to the course administrator Torill Rørtveit (e-mail address: torill.rortveit@ibv.uio.no). Please put the course code and your candidate number (for this course) in the subject field (''e.g.'' "Exam MBV-INF4410 Candidate:15").<br />
<br />
The exam must be handed in as a single PDF document (Microsoft Word or an Open Office Document is also acceptable). The document should be named with the course code and your candidate number only (''e.g.'' MBV-INF4410-15.pdf). '''''Do not place your name in the document.'''''<br />
<br />
An additional, limited, oral examination may be arranged in cases where this is necessary for the student evaluation.<br />
<br />
=== Bioinformatics mailing list for the Oslo region ===<br />
<br />
The mailing list for computational biology and bioinformatics in the Oslo region is cbo-all@usit.uio.no. The list has approximately 400 members. The list is used to distribute news about seminars, positions, courses, meetings and other topics that might be of interest to students and researchers with an interest in computational life science in south-eastern Norway. If you want to receive e-mails that are sent to the list, sign up here<br />
<br />
[https://sympa.uio.no/usit.uio.no/info/cbo-all https://sympa.uio.no/usit.uio.no/info/cbo-all]<br />
<br />
by following the link termed "Subscribe".<br />
<br />
=== Useful links ===<br />
<br />
Trond Hasle Amundsen's [http://www.uio.no/tjenester/it/maskin/linux/hjelp/tips/guide.html Local guide to Linux and Unix]<br />
<br />
EMBnet [http://www.embnet.org/sites/default/files/quickguides/guideUNIX.pdf Quick guide Unix]<br />
<br />
[http://www.jalview.org Jalview] and Jalview [http://www.jalview.org/refcard.pdf refcard]<br />
<br />
UCSC [http://genome.ucsc.edu Genome browser]<br />
<br />
Free [http://www.openhelix.com/ucsc UCSC Genome browser tutorial]&nbsp;&nbsp; from OpenHelix<br />
<br />
Portal to [http://galaxyproject.org Galaxy]<br />
<br />
[http://wiki.galaxyproject.org/Learn Galaxy 101 and other Galaxy screencasts/tutorials]<br />
<br />
UiO [http://lifeportal.uio.no Lifeportal] and more [http://www.uio.no/english/services/it/research/hpc/lifeportal information on the Lifeportal]<br />
<br />
The Genomic [http://hyperbrowser.uio.no/hb HyperBrowser]<br />
<br />
[http://bioinformatics.ca/links_directory Links Directory] from bioinformatics.ca<br />
<br />
The 2015 Nucleic Acids Research [http://nar.oxfordjournals.org/content/43/D1.toc Database Issue]<br />
<br />
The 2015 Nucleic Acids Research [http://nar.oxfordjournals.org/content/43/W1.toc Web Server Issue]<br />
<br />
UiO and OUS [http://core.rr-research.no/bioinformatics Bioinformatics Core Facility]</div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Structural_Bioinformatics_2018&diff=2007Structural Bioinformatics 20182018-11-14T14:10:22Z<p>Jonkl@uio.no: </p>
<hr />
<div>How to [[Media:InstallingPyMOL.pdf|install PyMOL]] (You need PyMOL installed on your laptop for all the exercises) You, most likely, do NOT NEED JAVA!<br />
<br />
Bring an external mouse! It is much easier to work in PyMOL when you do not have to rely on the trackpad<br />
<br />
Kahoots will be run at https://kahoot.it<br />
<br />
Tuesday 09:15 - 10:45: Basic Structural Biology Review [[Media:StructBiolReview A7 Part1.pdf|part 1]], [[Media:StructBiolReview A7 Part2.pdf|part 2]], and [[Media:StructBiolReview A7 Part3.pdf|part 3]] ('''Only come to this lecture if you think you need it!''')<br />
<br />
Tuesday 11:00: Structural Bioinformatics lectures...<br />
<br />
PyMOL exercise<br />
<br />
A second Structural Bioinformatics exercise<br />
<br />
Wednesday 09:15: Structural Bioinformatics lectures cont.<br />
<br />
Homology Modelling exercise<br />
<br />
Back to [[MBV-INFX410 2018|main page]]</div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:StructBiolReview_A7_Part3.pdf&diff=2006File:StructBiolReview A7 Part3.pdf2018-11-14T14:09:45Z<p>Jonkl@uio.no: </p>
<hr />
<div></div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:StructBiolReview_A7_Part2.pdf&diff=2005File:StructBiolReview A7 Part2.pdf2018-11-14T14:09:31Z<p>Jonkl@uio.no: </p>
<hr />
<div></div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:StructBiolReview_A7_Part1.pdf&diff=2004File:StructBiolReview A7 Part1.pdf2018-11-14T14:09:11Z<p>Jonkl@uio.no: </p>
<hr />
<div></div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Structural_Bioinformatics_2018&diff=2003Structural Bioinformatics 20182018-11-14T14:05:54Z<p>Jonkl@uio.no: </p>
<hr />
<div>How to [[Media:InstallingPyMOL.pdf|install PyMOL]] (You need PyMOL installed on your laptop for all the exercises) You, most likely, do NOT NEED JAVA!<br />
<br />
Bring an external mouse! It is much easier to work in PyMOL when you do not have to rely on the trackpad<br />
<br />
Kahoots will be run at https://kahoot.it<br />
<br />
Tuesday 09:15 - 10:45: Basic Structural Biology Review [[Media:StructBiolReview A6 Part1.pdf|part 1]], [[Media:StructBiolReview A6 Part2.pdf|part 2]], and [[Media:StructBiolReview A6 Part3.pdf|part 3]] ('''Only come to this lecture if you think you need it!''')<br />
<br />
Tuesday 11:00: Structural Bioinformatics lectures...<br />
<br />
PyMOL exercise<br />
<br />
A second Structural Bioinformatics exercise<br />
<br />
Wednesday 09:15: Structural Bioinformatics lectures cont.<br />
<br />
Homology Modelling exercise<br />
<br />
Back to [[MBV-INFX410 2018|main page]]</div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Structural_Bioinformatics_2018&diff=2002Structural Bioinformatics 20182018-11-14T14:03:30Z<p>Jonkl@uio.no: Created page with "How to install PyMOL (You need PyMOL installed on your laptop for all the exercises) You, most likely, do NOT NEED JAVA! Bring an external mouse..."</p>
<hr />
<div>How to [[Media:InstallingPyMOL.pdf|install PyMOL]] (You need PyMOL installed on your laptop for all the exercises) You, most likely, do NOT NEED JAVA!<br />
<br />
Bring an external mouse! It is much easier to work in PyMOL when you do not have to rely on the trackpad<br />
<br />
Kahoots will be run at https://kahoot.it<br />
<br />
Tuesday 09:15 - 10:30: Basic Structural Biology Review [[Media:StructBiolReview A6 Part1.pdf|part 1]], [[Media:StructBiolReview A6 Part2.pdf|part 2]], and [[Media:StructBiolReview A6 Part3.pdf|part 3]] ('''Only come to this lecture if you think you need it!''')<br />
<br />
Tuesday 10:45: Structural Bioinformatics lectures [[Media:StructBioinfo_2017_Part1.pdf|part 1]], [[Media:StructBioinfo_2017_Part2.pdf|part 2]], [[Media:StructBioinfo_2017_Part3.pdf|part 3]], and [[Media:StructBioinfo_2017_Part4.pdf|part 4]]<br />
<br />
PyMOL exercise in [[Media:PyMOL Exercise-17.doc|MS Word]] and [[Media:PyMOL Exercise-Solutions-17.pdf|pdf]] (with solutions) format<br />
<br />
A second Structural Bioinformatics exercise in [[Media:StructBioinf2-17.pdf|pdf]] and [[Media:StructBioinf2-17.docx|MS Word]] format. Wait with task 7 & 8 until Wednesday, unless you know what you are doing<br />
<br />
Wednesday 09:15: Structural Bioinformatics lectures cont.<br />
<br />
Homology Modelling exercise in [[Media:HomologyModelingExercise-17.docx|MS Word]] and [[Media:HomologyModelingExercise-Solutions-17.pdf|pdf]] (with solutions) format<br />
<br />
Back to [[MBV-INFX410 2018|main page]]</div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=MBV-INFX410_2018&diff=2001MBV-INFX410 20182018-11-14T14:02:09Z<p>Jonkl@uio.no: /* Detailed program */</p>
<hr />
<div>== Bioinformatics for Molecular Biology - 2018 ==<br />
=== Messages ===<br />
* '''Notice that some days we will use a different room than 4424. See the [[MBV-INFX410 2018|Detailed program]]'''<br />
<br />
* '''You need to install the following software on your laptops:'''<br />
** PyMOL (https://www.pymol.org/). PyMOL is free for students but you have to register for a license. Go to "New users" and "Buy license" and click on Student/Teacher ([https://pymol.org/edu/?q=educational or click here])<br />
** R (https://www.r-project.org/)<br />
** RStudio (https://www.rstudio.com/)<br />
** Windows users only: PuTTY (http://www.putty.org/). Optional: In addition to PuTTY, windows users can also install [https://www.cygwin.com/ Cygwin] if you want to have a Unix-style environment also locally on your computer.<br />
**'''Optional:''' It could also be wise to have Fetch (for Mac) (http://fetchsoftworks.com/) and WinSCP (Windows) ([https://winscp.net/eng/index.php https://winscp.net/eng/index.php)]<br />
<br />
=== Course information ===<br />
This is the wiki for the courses [http://www.uio.no/studier/emner/matnat/ibv/MBV-INF4410 MBV-INF4410] and [http://www.uio.no/studier/emner/matnat/ibv/MBV-INF9410 MBV-INF9410] offered by the Department of Biosciences (IBV) at the University of Oslo (UiO). Both MBV-INF4410 (M.Sc. level) and MBV-INF9410 (Ph.D. level) are 10 study point courses. <br />
<br />
The course consists of five weeks of lectures, exercises, obligatory assignments, and a take-home exam (one week). Obligatory assignments must be completed and approved before the exam and in the same semester. An additional, limited, oral examination may be arranged in cases where this is necessary for the student evaluation. The course is open also for non-UiO students. It is only necessary to be physically present in Oslo for certain parts of the course.<br />
{| class="wikitable"<br />
|+General schedule for MBV-INFX410<br />
!<br />
!Mon<br />
!Tue<br />
!Wed<br />
!Thu<br />
!Fri<br />
|-<br />
!Week 46<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
|-<br />
!Week 47<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
|-<br />
!Week 48<br />
| style="background: white;" |Obligatory<br />
home assignment<br />
| style="background: white;" |Obligatory<br />
home assignment<br />
| style="background: white;" |Obligatory<br />
home assignment<br />
| style="background: white;" |Obligatory<br />
home assignment<br />
| style="background: white;" |Hand in<br />
home assignment<br />
|-<br />
!Week 49<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Exam start<br />
(home assignment)<br />
|-<br />
!Week 50<br />
| style="background: white;" |Exam<br />
(home assignment)<br />
| style="background: white;" |Exam<br />
(home assignment)<br />
| style="background: white;" |Exam<br />
(home assignment)<br />
| style="background: white;" |Exam<br />
(home assignment)<br />
| style="background: white;" |Exam end<br />
(home assignment)<br />
|}<br />
<br />
===Computers/laptops, internet access, and UiO user account ===<br />
'''All students are strongly encouraged to bring their own laptops.''' <br />
<br />
* It should be possible to connect the computer to the UiO wireless network (Eduroam)<br />
* You must have a root/administrator password that gives you access to installing new software on the computer<br />
* Please bring an '''external mouse''', and do not rely on touchpad/trackpad only<br />
* You must have a '''valid UiO user account''' and must be able to log onto a computer on the UiO network<br />
* Instructions on how to find your username and get a new password can be found [http://www.uio.no/english/services/it/username-password/no-password.html here]. '''''To get a UiO username/password at the UiO helpdesk you need valid ID.'''''<br />
'''''If you are struggling with anything of the above, in particular<nowiki> </nowiki>if you have forgotten your UiO username/password or you do not have one, you must contact Jon (see [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410_2018#Contacts contact details]) as soon as possible, and at least one week before the start of the course.'''''<br />
<br />
On the first day of the course we will set up your laptop so that<nowiki> </nowiki>it can be used for the exercises/tutorials, the home exam and hopefully<nowiki> </nowiki>in your future work. How to get a reasonable setup is described [https://wiki.uio.no/projects/clsi/index.php/Laptop_Setup here].<br />
<br />
If you already are an expert programmer and Unix guru, go [https://wiki.uio.no/projects/clsi/index.php/Biology_for_Informatics here].<br />
<br />
=== Time and place (Rooms) ===<br />
The teaching starts at 09:15 and we will end at latest 16:00. Most of the teaching will take place in '''room 4424 on the 4th floor of [https://www.uio.no/om/finn-fram/omrader/blindern/bl18/ Biology Buiding]''' [https://www.uio.no/om/finn-fram/omrader/blindern/bl18/ (Kristine Bonnevies Hus, KB).]But check the program because changes will happen.. <br />
<br />
=== Detailed program ===<br />
<br />
The times listed here are only tentative and may likely change. We will mix in small breaks here and there and try to have a lunch break between 12:00 - 13:00.<br />
{| class="wikitable"<br />
|+Tentative schedule for MBV-INFX410 2018<br />
!Week<br />
!Monday<br />
!Tuesday<br />
!Wednesday<br />
!Thursday<br />
!Friday<br />
|-<br />
|<b>46</b><br />
| style="background: white; text-align: center;" |Nov 12<br />
| style="background: white; text-align: center;" |Nov 13<br />
| style="background: white; text-align: center;" |Nov 14<br />
| style="background: white; text-align: center;" |Nov 15<br />
| style="background: white; text-align: center;" |Nov 16<br />
|-<br />
|<br />
| style="background: #cefdce; vertical-align: top;" | <br />
09:15 - 10:00 <br />
<br />
Course introduction ([http://folk.uio.no/jonbra/MBV-INF4410_2018/lectures/2018-11-12_01_Introduction.pdf lecture]) <br />
<br />
<br />
10:15 - 11:00<br />
Sequence databases ([http://folk.uio.no/jonbra/MBV-INF4410_2018/lectures/2018-11-12_02_Databases.pdf lecture]) <br />
<br />
<br />
11:15 - 12:00<br />
Basic Unix ([http://folk.uio.no/jonbra/MBV-INF4410_2018/lectures/2018-11-12_03_Basic_Unix.pdf lecture])<br />
<br />
<br />
12:00 - 13:00 <br />
<br />
Lunch <br />
<br />
<br />
13:15 - 14:00 <br />
<br />
Setting up laptops <br />
<br />
<br />
14:15 - 16:00 <br />
<br />
Basic Unix ([http://folk.uio.no/jonbra/MBV-INF4410_2018/exercises/2018-11-12_UNIXBasics-exercise.pdf excercises]) <br />
| style="background: #cefdce; vertical-align: top;" | <br />
09:15 - 11:00 <br />
<br />
Genome browsers ([http://folk.uio.no/jonbra/MBV-INF4410_2018/lectures/2018-11-13_01_GenomeBrowsers.pdf lecture] / [http://folk.uio.no/jonbra/MBV-INF4410_2018/exercises/2018-11-13-01_UCSC.pdf exercises]) and Jalview ([http://folk.uio.no/jonbra/MBV-INF4410_2018/lectures/2018-11-13_02_JalView.pdf lecture]) <br />
<br />
<br />
11:15 - 12:00<br />
<br />
Working with sequences <br />
<br />
and databases ([http://folk.uio.no/jonbra/MBV-INF4410_2018/lectures/2018-11-13_03_Working_with_sequences.pdf lecture])<br />
<br />
<br />
12:00 - 13:00<br />
<br />
Lunch <br />
<br />
<br />
13:15 - 16:00<br />
<br />
Applied sequence bioinformatics ([http://folk.uio.no/jonbra/MBV-INF4410_2018/exercises/2018-11-13-02_Applied_seq_bioinf.pdf exercises]) <br />
| style="background: #cefdce; vertical-align: top;" |<br />
10:15 - 11:00 ('''NB! Note start time''')<br />
<br />
More Unix ([http://folk.uio.no/jonbra/MBV-INF4410_2018/lectures/2018-11-14_01_MoreUnix.pdf lecture]) <br />
<br />
<br />
11:15 - 15:00<br />
<br />
Introduction to R, <br />
<br />
Basic R commands and exercises. ([http://folk.uio.no/jonbra/MBV-INF4410_2018/lectures/2018-11-14_02_R_introduction.pdf lecture], [http://folk.uio.no/jonbra/MBV-INF4410_2018/exercises/2018-11-14_Basic_R_Exercises.html exercises]) <br />
<br />
| style="background: #cefdce; vertical-align: top;" |<br />
09:15 - 16:00 <br />
<br />
Python workshop<br />
<br />
| style="background: #cefdce; vertical-align: top;" |<br />
09:15 - 16:00<br />
<br />
Python workshop<br />
<br />
|-<br />
|<b>47</b><br />
| style="background: white; text-align: center;" |Nov 19<br />
| style="background: white; text-align: center;" |Nov 20<br />
| style="background: white; text-align: center;" |Nov 21<br />
| style="background: white; text-align: center;" |Nov 22<br />
| style="background: white; text-align: center;" |Nov 23<br />
|-<br />
|<br />
| style="background: #cefdce; vertical-align: top;" |<br />
'''Room 4613'''<br />
<br />
09:15 - 16:00<br />
<br />
Sequence searching and alignments <br />
<br />
| style="background: #cefdce; vertical-align: top;" |<br />
09:15 - 16:00<br />
<br />
[[Structural Bioinformatics 2018|Structural Bioinformatics]]<br />
<br />
| style="background: #cefdce; vertical-align: top;" |<br />
09:15 - 16:00<br />
<br />
[[Structural Bioinformatics 2018|Structural Bioinformatics]]<br />
<br />
| style="background: #cefdce; vertical-align: top;" |<br />
09:15 - 12:00<br />
<br />
Unix/Python<br />
<br />
| style="background: #cefdce; vertical-align: top;" |<br />
09:15 - 16:00<br />
<br />
Statistical epigenomics<br />
<br />
<span style="color:red">Hand out oblig</span><br />
<br />
|-<br />
|<b>48</b><br />
| style="background: white; text-align: center;" |Nov 26<br />
| style="background: white; text-align: center;" |Nov 27<br />
| style="background: white; text-align: center;" |Nov 28<br />
| style="background: white; text-align: center;" |Nov 29<br />
| style="background: white; text-align: center;" |Nov 30<br />
|-<br />
|<br />
| style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment<br />
| style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment<br />
| style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment<br />
| style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment<br />
| style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment<br />
|-<br />
|<b>49</b><br />
| style="background: white; text-align: center;" |Dec 3<br />
| style="background: white; text-align: center;" |Dec 4<br />
| style="background: white; text-align: center;" |Dec 5<br />
| style="background: white; text-align: center;" |Dec 6<br />
| style="background: white; text-align: center;" |Dec 7<br />
|-<br />
|<br />
| style="background: #cefdce; vertical-align: top;" |<br />
'''Room 4613'''<br />
<br />
09:15 - 12:00<br />
<br />
Docking and drug discovery<br />
<br />
13:00 - 16:00<br />
<br />
Next Generation Sequencing, genomics, transcriptomics, Basic R<br />
<br />
| style="background: #cefdce; vertical-align: top;" |<br />
'''Room 4613'''<br />
<br />
09:15 - 16:00<br />
<br />
Next Generation Sequencing, genomics, transcriptomics, Basic R<br />
<br />
| style="background: #cefdce; vertical-align: top;" |<br />
'''Room 4613'''<br />
<br />
09:15 - 16:00<br />
<br />
Next Generation Sequencing, genomics, transcriptomics, Basic R<br />
<br />
| style="background: #cefdce; vertical-align: top;" |<br />
'''Room 4613'''<br />
<br />
09:15 - 16:00<br />
<br />
Next Generation Sequencing, genomics, transcriptomics, Basic R<br />
<br />
| style="background: #cefdce; vertical-align: top;" |<br />
'''Room 4613'''<br />
<br />
09:15 - 12:00<br />
<br />
UiO LifePortal<br />
<br />
<span style="color:red">Hand out exam</span><br />
<br />
|-<br />
|<b>50</b><br />
| style="background: white; text-align: center;" |Dec 10<br />
| style="background: white; text-align: center;" |Dec 11<br />
| style="background: white; text-align: center;" |Dec 12<br />
| style="background: white; text-align: center;" |Dec 13<br />
| style="background: white; text-align: center;" |Dec 14<br />
|-<br />
|<br />
| style="background: salmon; vertical-align: top;" |Home exam<br />
| style="background: salmon; vertical-align: top;" |Home exam<br />
| style="background: salmon; vertical-align: top;" |Home exam<br />
| style="background: salmon; vertical-align: top;" |Home exam<br />
| style="background: salmon; vertical-align: top;" |Hand in exam<br />
|}<br />
<br />
===Recommended reading material / curriculum ===<br />
The curriculum comprises all lectures, lecture handouts and exercises. The articles listed below are only recommended but not mandatory:<br />
*J. R. A. Hutchins, "Genomic Database Searching", in [https://link.springer.com/protocol/10.1007%2F978-1-4939-6622-6_10 Bioinformatics pp 225-269. Springer (2017)].<br />
*R.F. Service, "Biology's dry future", [http://dx.doi.org/10.1126/science.342.6155.186 Science <b>342</b>, 186 (2013)]<br />
*EMBnet, [http://www.embnet.org/sites/default/files/quickguides/guideUNIX.pdf A Quick Guide to UNIX]<br />
*NCBI Resource Coordinators, "Database resources of the National Center for Biotechnology Information", [http://dx.doi.org/10.1093/nar/gku1130 Nucleic Acids Res. <b>43</b>, D6 (2015)]<br />
*The UniProt Consortium, "UniProt: a hub for protein information", [http://dx.doi.org/10.1093/nar/gku989 Nucleic Acids Res. <b>43</b>, D204 (2015)]<br />
*P. Flicek ''et al.'', "Ensembl 2015", [http://dx.doi.org/10.1093/nar/gku1010 Nucleic Acids Res. <b>43</b>, D662 (2015)]<br />
*P.W. Rose ''et al.'', "The RCSB Protein Data Bank: new resources for research and education", [http://dx.doi.org/10.1093/nar/gks1200 Nucleic Acids Res. <b>41</b>, D475 (2013)]<br />
*P.J.A. Cock ''et al.'', "Biopython: freely available Python tools for computational molecular biology and bioinformatics", [http://dx.doi.org/10.1093/bioinformatics/btp163 Bioinformatics <b>25</b>, 1422 (2009)]<br />
*A.M. Waterhouse ''et al''., "Jalview Version 2--a multiple sequence alignment editor and analysis workbench", [http://dx.doi.org/10.1093/bioinformatics/btp033 Bioinformatics <b>25</b>, 1189 (2009)]<br />
*G.M. Boratyn ''et al.'', "BLAST: a more efficient report with usability improvements", [http://dx.doi.org/10.1093/nar/gkt282 Nucleic Acids Res. <b>41</b>, W29 (2013)]<br />
*J.-F. Taly ''et al.'', "Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures", [http://dx.doi.org/10.1038/nprot.2011.393 Nat. Protoc. <b>6</b>, 1669 (2011)]<br />
*L. Bordoli ''et al.'', "Protein structure homology modeling using SWISS-MODEL workspace", [http://dx.doi.org/10.1038/nprot.2008.197 Nat. Protoc. <b>4</b>, 1 (2009)]<br />
*J. Carlsson ''et al.'', "Ligand discovery from a dopamine D<sub>3</sub> receptor homology model and crystal structure", [http://dx.doi.org/10.1038/nchembio.662 Nat. Chem. Biol. <b>7</b>, 769 (2011)]<br />
*R.M. Kuhn ''et al.'', "The UCSC genome browser and associated tools", [http://dx.doi.org/10.1093/bib/bbs038 Brief. Bioinform. <b>14</b>, 144 (2013)]<br />
*J. Goecks ''et al''., "Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences", [http://dx.doi.org/10.1186/gb-2010-11-8-r86 Genome Biol. <b>11</b>, R86 (2010)]<br />
*G.K. Sandve ''et al.'', "Ten Simple Rules for reproducible computational Research", [http://dx.doi.org/10.1371/journal.pcbi.1003285 PLoS Comput. Biol. <b>9</b>, e1003285 (2013)]<br />
*G.K. Sandve ''et al.'', "The Genomic HyperBrowser: an analysis web server for genome-scale data", [http://dx.doi.org/10.1093/nar/gkt342 Nucleic Acids Res. <b>41</b>, W133 (2013)]<br />
*M.L. Mertzker, "Sequencing technologies - the next generation", [http://dx.doi.org/10.1038/nrg2626 Nat. Rev. Genet. <b>11</b>, 31 (2010)]<br />
*Nielsen, R. ''et al''., "Genotype and SNP calling from next-generation sequencing data", [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3593722/ Nat Rev Genet. (2011)].<br />
*A. Altmann ''et al.'', "A beginners guide to SNP calling from high-throughput DNA-sequencing data", [http://dx.doi.org/10.1007/s00439-012-1213-z Hum. Genet. <b>131</b>, 1541 (2012)]<br />
*N. Nagarajan & M. Pop, "Sequence assembly demystified", [http://dx.doi.org/10.1038/nrg3367 Nat. Rev. Genet. <b>14</b>, 157 (2013)]<br />
*D.W. Huang ''et al.'', "Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources", [http://dx.doi.org/10.1038/nprot.2008.211 Nat. Protoc. <b>4</b>, 44 (2009)]<br />
<br />
Other good articles (''not ''curriculum)<br />
*Z. Yang & B. Rannala, "Molecular phylogenetics: principles and practice", [http://dx.doi.org/doi:10.1038/nrg3186 Nat. Rev. Genet. <b>13</b>, 303 (2012)]<br />
<br />
=== Contacts ===<br />
Jon Bråte (Course coordinator) - e-mail: jon.brate@ibv.uio.no, phone: +47 922 44 582<br />
<br />
Torill Rørtveit (Course administrator, registration) - e-mail: torill.rortveit@ibv.uio.no<br />
<br />
=== Useful links ===<br />
<br />
[http://swcarpentry.github.io/shell-novice/reference/ Very useful reference guide on the Unix shell (created by Software Carpentry)]<br />
<br />
Trond Hasle Amundsen's [http://www.uio.no/tjenester/it/maskin/linux/hjelp/tips/guide.html Local guide to Linux and Unix]<br />
<br />
[https://github.com/EbookFoundation/free-programming-books/blob/master/free-programming-books.md#python Tons of free e-books on Python]<br />
<br />
EMBnet [http://www.embnet.org/sites/default/files/quickguides/guideUNIX.pdf Quick guide Unix]<br />
<br />
[https://github.com/stephenturner/oneliners Useful command line one-liners] by Stephen Turner<br />
<br />
[https://github.com/mcandre/cheatsheets/blob/master/nano.md Nano text editor cheat sheet]<br />
<br />
[https://github.com/EbookFoundation/free-programming-books/blob/master/free-programming-books.md Tons of free programming books, about anything really.]<br />
<br />
[http://www.jalview.org Jalview] and Jalview [http://www.jalview.org/refcard.pdf refcard]<br />
<br />
UCSC [http://genome.ucsc.edu Genome browser]<br />
<br />
Free [http://www.openhelix.com/ucsc UCSC Genome browser tutorial]&nbsp;&nbsp; from OpenHelix<br />
<br />
Portal to [http://galaxyproject.org Galaxy]<br />
<br />
[http://wiki.galaxyproject.org/Learn Galaxy 101 and other Galaxy screencasts/tutorials]<br />
<br />
UiO [http://lifeportal.uio.no Lifeportal] and more [http://www.uio.no/english/services/it/research/hpc/lifeportal information on the Lifeportal]<br />
<br />
The Genomic [http://hyperbrowser.uio.no/hb HyperBrowser]<br />
<br />
[http://bioinformatics.ca/links_directory Links Directory] from bioinformatics.ca<br />
<br />
The 2017 Nucleic Acids Research [https://academic.oup.com/nar/issue/45/D1 Database Issue]<br />
<br />
The 2015 Nucleic Acids Research [https://academic.oup.com/nar/issue/45/W1 Web Server Issue]<br />
<br />
UiO and OUS [http://core.rr-research.no/bioinformatics Bioinformatics Core Facility]<br />
<br />
[http://web.stanford.edu/class/bios221/book/introduction.html Nice introductory eBook about statistics for biology and introduction to R (including downloadable R scripts)]</div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Structural_Bioinformatics_2017&diff=1935Structural Bioinformatics 20172017-11-20T14:19:15Z<p>Jonkl@uio.no: </p>
<hr />
<div>How to [[Media:InstallingPyMOL.pdf|install PyMOL]] (You need PyMOL installed on your laptop for all the exercises) You, most likely, do NOT NEED JAVA!<br />
<br />
Bring an external mouse! It is much easier to work in PyMOL when you do not have to rely on the trackpad<br />
<br />
Kahoots will be run at https://kahoot.it<br />
<br />
Tuesday 09:15 - 10:30: Basic Structural Biology Review [[Media:StructBiolReview A6 Part1.pdf|part 1]], [[Media:StructBiolReview A6 Part2.pdf|part 2]], and [[Media:StructBiolReview A6 Part3.pdf|part 3]] ('''Only come to this lecture if you think you need it!''')<br />
<br />
Tuesday 10:45: Structural Bioinformatics lectures [[Media:StructBioinfo_2017_Part1.pdf|part 1]], [[Media:StructBioinfo_2017_Part2.pdf|part 2]], [[Media:StructBioinfo_2017_Part3.pdf|part 3]], and [[Media:StructBioinfo_2017_Part4.pdf|part 4]]<br />
<br />
PyMOL exercise in [[Media:PyMOL Exercise-17.doc|MS Word]] and [[Media:PyMOL Exercise-Solutions-17.pdf|pdf]] (with solutions) format<br />
<br />
A second Structural Bioinformatics exercise in [[Media:StructBioinf2-17.pdf|pdf]] and [[Media:StructBioinf2-17.docx|MS Word]] format. Wait with task 7 & 8 until Wednesday, unless you know what you are doing<br />
<br />
Wednesday 09:15: Structural Bioinformatics lectures cont.<br />
<br />
Homology Modelling exercise in [[Media:HomologyModelingExercise-17.docx|MS Word]] and [[Media:HomologyModelingExercise-Solutions-17.pdf|pdf]] (with solutions) format<br />
<br />
Back to [[MBV-INFX410 2017|main page]]</div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Structural_Bioinformatics_2017&diff=1934Structural Bioinformatics 20172017-11-20T14:18:45Z<p>Jonkl@uio.no: </p>
<hr />
<div>How to [[Media:InstallingPyMOL.pdf|install PyMOL]] (You need PyMOL installed on your laptop for all the exercises) You, most likely, do NOT NEED JAVA!<br />
<br />
Bring an external mouse! It is much easier to work in PyMOL when you do not have to rely on the trackpad<br />
<br />
Kahoots will be run at https://kahoot.it<br />
<br />
Tuesday 09:15 - 10:30: Basic Structural Biology Review [[Media:StructBiolReview A6 Part1.pdf|part 1]], [[Media:StructBiolReview A6 Part2.pdf|part 2]], and [[Media:StructBiolReview A6 Part3.pdf|part 3]] ('''Only come to this lecture if you think you need it!''')<br />
<br />
Tuesday 10:45: Structural Bioinformatics lectures [[Media:StructBioinfo_2017_Part1.pdf|part 1]], [[Media:StructBioinfo_2017_Part2.pdf|part 2]], [[Media:StructBioinfo_2017_Part3.pdf|part 3]], and [[Media:StructBioinfo_2017_Part4.pdf|part 4]]<br />
<br />
PyMOL exercise in [[Media:PyMOL Exercise-17.doc|MS Word]] and [[Media:PyMOL Exercise-Solutions-17.pdf|pdf]] (with solutions) format<br />
<br />
A second Structural Bioinformatics exercise in [[Media:StructBioinf2-17.pdf|pdf]] and [[Media:StructBioinf2-17.docx|MS Word]] format. Wait with task 7 & 8 until Wednesday, unless you know what you are doing<br />
<br />
Wednesday 09:15: Structural Bioinformatics lectures cont.<br />
<br />
Homology Modelling exercise in [[Media:HomologyModelingExercise-17.docx|MS Word]] and [[Media:HomologyModelingExercise-Solutions-17.pdf|pdf]] format<br />
<br />
Back to [[MBV-INFX410 2017|main page]]</div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Structural_Bioinformatics_2017&diff=1933Structural Bioinformatics 20172017-11-20T14:18:16Z<p>Jonkl@uio.no: </p>
<hr />
<div>How to [[Media:InstallingPyMOL.pdf|install PyMOL]] (You need PyMOL installed on your laptop for all the exercises) You, most likely, do NOT NEED JAVA!<br />
<br />
Bring an external mouse! It is much easier to work in PyMOL when you do not have to rely on the trackpad<br />
<br />
Kahoots will be run at https://kahoot.it<br />
<br />
Tuesday 09:15 - 10:30: Basic Structural Biology Review [[Media:StructBiolReview A6 Part1.pdf|part 1]], [[Media:StructBiolReview A6 Part2.pdf|part 2]], and [[Media:StructBiolReview A6 Part3.pdf|part 3]] ('''Only come to this lecture if you think you need it!''')<br />
<br />
Tuesday 10:45: Structural Bioinformatics lectures [[Media:StructBioinfo_2017_Part1.pdf|part 1]], [[Media:StructBioinfo_2017_Part2.pdf|part 2]], [[Media:StructBioinfo_2017_Part3.pdf|part 3]], [[Media:StructBioinfo_2017_Part4.pdf|part 4]]<br />
<br />
PyMOL exercise in [[Media:PyMOL Exercise-17.doc|MS Word]] and [[Media:PyMOL Exercise-Solutions-17.pdf|pdf]] (with solutions) format<br />
<br />
A second Structural Bioinformatics exercise in [[Media:StructBioinf2-17.pdf|pdf]] and [[Media:StructBioinf2-17.docx|MS Word]] format. Wait with task 7 & 8 until Wednesday, unless you know what you are doing<br />
<br />
Wednesday 09:15: Structural Bioinformatics lectures cont.<br />
<br />
Homology Modelling exercise in [[Media:HomologyModelingExercise-17.docx|MS Word]] and [[Media:HomologyModelingExercise-Solutions-17.pdf|pdf]] format<br />
<br />
Back to [[MBV-INFX410 2017|main page]]</div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Structural_Bioinformatics_2017&diff=1932Structural Bioinformatics 20172017-11-20T14:16:59Z<p>Jonkl@uio.no: </p>
<hr />
<div>How to [[Media:InstallingPyMOL.pdf|install PyMOL]] (You need PyMOL installed on your laptop for all the exercises) You, most likely, do NOT NEED JAVA!<br />
<br />
Bring an external mouse! It is much easier to work in PyMOL when you do not have to rely on the trackpad<br />
<br />
Kahoots will be run at https://kahoot.it<br />
<br />
Tuesday 09:15 - 10:30: Basic Structural Biology Review [[Media:StructBiolReview A6 Part1.pdf|part 1]], [[Media:StructBiolReview A6 Part2.pdf|part 2]], and [[Media:StructBiolReview A6 Part3.pdf|part 3]] ('''Only come to this lecture if you think you need it!''')<br />
<br />
Tuesday 10:45: Structural Bioinformatics lectures [[Media:StructBioinfo_2017_Part1.pdf|part 1]], [[Media:StructBioinfo_2017_Part2.pdf|part 2]], [[Media:StructBioinfo_2017_Part3.pdf|part 3]], [[Media:StructBioinfo_2017_Part4.pdf|part 4]]. <br />
<br />
PyMOL exercise in [[Media:PyMOL Exercise-17.doc|MS Word]] and [[Media:PyMOL Exercise-Solutions-17.pdf|pdf]] (with solutions) format.<br />
<br />
A second Structural Bioinformatics exercise in [[Media:StructBioinf2-17.pdf|pdf]] and [[Media:StructBioinf2-17.docx|MS Word]] format. Wait with task 7 & 8 until Wednesday, unless you know what you are doing.<br />
<br />
Wednesday 09:15: Structural Bioinformatics lectures cont.<br />
<br />
Homology Modelling exercise in [[Media:HomologyModelingExercise-17.docx|MS Word]] and [[Media:HomologyModelingExercise-Solutions-17.pdf|pdf]] format.<br />
<br />
Back to [[MBV-INFX410 2017|main page]]</div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:StructBioinfo_2017_Part4.pdf&diff=1931File:StructBioinfo 2017 Part4.pdf2017-11-20T14:14:07Z<p>Jonkl@uio.no: </p>
<hr />
<div></div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:StructBioinfo_2017_Part3.pdf&diff=1930File:StructBioinfo 2017 Part3.pdf2017-11-20T14:13:55Z<p>Jonkl@uio.no: </p>
<hr />
<div></div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:StructBioinfo_2017_Part2.pdf&diff=1929File:StructBioinfo 2017 Part2.pdf2017-11-20T14:13:41Z<p>Jonkl@uio.no: </p>
<hr />
<div></div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:StructBioinfo_2017_Part1.pdf&diff=1928File:StructBioinfo 2017 Part1.pdf2017-11-20T14:13:26Z<p>Jonkl@uio.no: </p>
<hr />
<div></div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Structural_Bioinformatics_2017&diff=1927Structural Bioinformatics 20172017-11-20T12:13:23Z<p>Jonkl@uio.no: </p>
<hr />
<div>How to [[Media:InstallingPyMOL.pdf|install PyMOL]] (You need PyMOL installed on your laptop for all the exercises) You, most likely, do NOT NEED JAVA!<br />
<br />
Bring an external mouse! It is much easier to work in PyMOL when you do not have to rely on the trackpad<br />
<br />
Kahoots will be run at https://kahoot.it<br />
<br />
Tuesday 09:15 - 10:30: Basic Structural Biology Review [[Media:StructBiolReview A6 Part1.pdf|part 1]], [[Media:StructBiolReview A6 Part2.pdf|part 2]], and [[Media:StructBiolReview A6 Part3.pdf|part 3]] ('''Only come to this lecture if you think you need it!''')<br />
<br />
Tuesday 10:45: Structural Bioinformatics lectures <br />
<br />
PyMOL exercise in [[Media:PyMOL Exercise-17.doc|MS Word]] and [[Media:PyMOL Exercise-Solutions-17.pdf|pdf]] (with solutions) format.<br />
<br />
A second Structural Bioinformatics exercise in [[Media:StructBioinf2-17.pdf|pdf]] and [[Media:StructBioinf2-17.docx|MS Word]] format. Wait with task 7 & 8 until Wednesday, unless you know what you are doing.<br />
<br />
Wednesday 09:15: Structural Bioinformatics lectures cont.<br />
<br />
Homology Modelling exercise in [[Media:HomologyModelingExercise-17.docx|MS Word]] and [[Media:HomologyModelingExercise-Solutions-17.pdf|pdf]] format.<br />
<br />
Back to [[MBV-INFX410 2017|main page]]</div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Structural_Bioinformatics_2017&diff=1926Structural Bioinformatics 20172017-11-20T12:12:30Z<p>Jonkl@uio.no: </p>
<hr />
<div>How to [[Media:InstallingPyMOL.pdf|install PyMOL]] (You need PyMOL installed on your laptop for all the exercises) You, most likely, do NOT NEED JAVA!<br />
<br />
Bring an external mouse! It is much easier to work in PyMOL when you do not have to rely on the trackpad<br />
<br />
Kahoots will be run at https://kahoot.it<br />
<br />
Tuesday 09:15 - 10:30: Basic Structural Biology Review [[Media:StructBiolReview A6 Part1.pdf|part 1]], [[Media:StructBiolReview A6 Part2.pdf|part 2]], and [[Media:StructBiolReview A6 Part3.pdf|part 3]] ('''Only come to this lecture if you think you need it!''')<br />
<br />
Tuesday 10:45: Structural Bioinformatics lectures <br />
<br />
PyMOL exercise in [[Media:PyMOL Exercise-17.doc|MS Word]] and [[Media:PyMOL Exercise-Solutions-17.pdf|pdf]] (with solutions) format.<br />
<br />
THE REST OF THIS PAGE IS NOT YET FINISHED! COME BACK LATER!!<br />
<br />
A second Structural Bioinformatics exercise in [[Media:StructBioinf2-17.pdf|pdf]] and [[Media:StructBioinf2-17.docx|MS Word]] format. Wait with task 7 & 8 until Wednesday, unless you know what you are doing.<br />
<br />
Wednesday 09:15: Structural Bioinformatics lectures cont.<br />
<br />
Homology Modelling exercise in [[Media:HomologyModelingExercise-17.docx|MS Word]] and [[Media:HomologyModelingExercise-Solutions-17.pdf|pdf]] format.<br />
<br />
Back to [[MBV-INFX410 2017|main page]]</div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=Structural_Bioinformatics_2017&diff=1925Structural Bioinformatics 20172017-11-20T12:11:49Z<p>Jonkl@uio.no: </p>
<hr />
<div>How to [[Media:InstallingPyMOL.pdf|install PyMOL]] (You need PyMOL installed on your laptop for all the exercises) You, most likely, do NOT NEED JAVA!<br />
<br />
Bring an external mouse! It is much easier to work in PyMOL when you do not have to rely on the trackpad<br />
<br />
Kahoots will be run at https://kahoot.it<br />
<br />
Tuesday 09:15 - 10:30: Basic Structural Biology Review [[Media:StructBiolReview A6 Part1.pdf|part 1]], [[Media:StructBiolReview A6 Part2.pdf|part 2]], and [[Media:StructBiolReview A6 Part3.pdf|part 3]] ('''Only come to this lecture if you think you need it!''')<br />
<br />
Tuesday 10:45: Structural Bioinformatics lectures <br />
<br />
PyMOL exercise in [[Media:PyMOL Exercise-17.doc|MS Word]] and [[Media:PyMOL Exercise-Solutions-17.pdf|pdf]] (with solutions) format.<br />
<br />
THE REST OF THIS PAGE IS NOT YET FINISHED! COME BACK LATER!!<br />
<br />
A second Structural Bioinformatics exercise in [[Media:StructBioinf2-17.pdf/pdf]] and [[Media:StructBioinf2-17.docx/MS Word]] format. Wait with task 7 & 8 until Wednesday, unless you know what you are doing.<br />
<br />
Wednesday 09:15: Structural Bioinformatics lectures cont.<br />
<br />
Homology Modelling exercise in [[Media:HomologyModelingExercise-17.docx|MS Word]] and [[Media:HomologyModelingExercise-Solutions-17.pdf|pdf]] format.<br />
<br />
Back to [[MBV-INFX410 2017|main page]]</div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:HomologyModelingExercise-Solutions-17.pdf&diff=1924File:HomologyModelingExercise-Solutions-17.pdf2017-11-20T12:08:55Z<p>Jonkl@uio.no: </p>
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<div></div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:HomologyModelingExercise-17.docx&diff=1923File:HomologyModelingExercise-17.docx2017-11-20T12:08:43Z<p>Jonkl@uio.no: </p>
<hr />
<div></div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:StructBioinf2-17.docx&diff=1922File:StructBioinf2-17.docx2017-11-20T12:08:29Z<p>Jonkl@uio.no: </p>
<hr />
<div></div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=File:StructBioinf2-17.pdf&diff=1921File:StructBioinf2-17.pdf2017-11-20T12:08:07Z<p>Jonkl@uio.no: </p>
<hr />
<div></div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=MBV-INFX410_2017&diff=1920MBV-INFX410 20172017-11-20T10:18:59Z<p>Jonkl@uio.no: /* Bioinformatics for Molecular Biology - 2017 */</p>
<hr />
<div>== [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410 Bioinformatics for Molecular Biology] - 2017 ==<br />
=== Messages ===<br />
* '''20 nov: NB! In order to get everybody at an acceptable level in structural biology, before we start the Structural Bioinformatics lectures/exercises on Tuesday Nov 21, there will be a Structural Biology Review lecture in the morning, at 09:15. See handouts/slides [[Structural Bioinformatics 2017|here]]. Take a look at these and decide if you need to follow the Structural Biology Review lecture. If you decide that you do not need this and that you already know ''everything'' we will go through in this lecture, come at 10:45 on Tuesday Nov 21.'''<br />
* '''16 nov: NB! Notice room change for Python workshop 17 nov: Seminarrom U30 in [https://www.uio.no/om/finn-fram/omrader/blindern/bl20/ Helga Enghs Hus.] Go in the main door and down one floor.'''<br />
* '''''All students must be present at the start of the course, on November 13 at 09:15 in room 4613 in [https://www.uio.no/om/finn-fram/omrader/blindern/bl18/ Kristine Bonnevies (KB) Hus (biology building)]. Missing students will not be allowed to follow the course or to take the exam. If you for some reason are not able to attend, please contact Jon Bråte (See [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410_2016#Contacts contact details] below).'''''<br />
* '''All students must bring their own laptops, including an external mouse.'''<br />
* '''You need to install the following software on your laptops (we will help you with this):'''<br />
** Anaconda (https://www.anaconda.com/download/)<br />
** PyMOL (https://www.pymol.org/)<br />
** JalView Desktop (http://www.jalview.org/) - could maybe also run by pressing the "Launch Jalview Desktop" button<br />
** PuTTY (http://www.putty.org/)<br />
** R (https://www.r-project.org/) '''Install''' '''inside Anaconda instead''' <br />
** RStudio (https://www.rstudio.com/) '''Install''' '''inside Anaconda instead'''<br />
**'''Optional:''' It could also be wise to have Fetch (for Mac) (http://fetchsoftworks.com/) and WinSCP (Windows) ([https://winscp.net/eng/index.php https://winscp.net/eng/index.php)]<br />
<br />
=== Course information ===<br />
This is the wiki for the courses [http://www.uio.no/studier/emner/matnat/ibv/MBV-INF4410 MBV-INF4410] and [http://www.uio.no/studier/emner/matnat/ibv/MBV-INF9410 MBV-INF9410] offered by the Department of Biosciences (IBV) at the University of Oslo (UiO). Both MBV-INF4410 (M.Sc. level) and MBV-INF9410 (Ph.D. level) are 10 study point courses. <br />
<br />
The course consists of five weeks of lectures, exercises, obligatory assignments, and a take-home exam (one week). Obligatory assignments must be completed and approved before the exam and in the same semester. An additional, limited, oral examination may be arranged in cases where this is necessary for the student evaluation. The course is open also for non-UiO students. It is only necessary to be physically present in Oslo for certain parts of the course.<br />
{| class="wikitable"<br />
|+General schedule for MBV-INFX410<br />
!<br />
!Mon<br />
!Tue<br />
!Wed<br />
!Thu<br />
!Fri<br />
|-<br />
!Week 46<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
|-<br />
!Week 47<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
|-<br />
!Week 48<br />
| style="background: white;" |Obligatory<br />
home assignment<br />
| style="background: white;" |Obligatory<br />
home assignment<br />
| style="background: white;" |Obligatory<br />
home assignment<br />
| style="background: white;" |Obligatory<br />
home assignment<br />
| style="background: white;" |Hand in<br />
home assignment<br />
|-<br />
!Week 49<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Exam start<br />
(home assignment)<br />
|-<br />
!Week 50<br />
| style="background: white;" |Exam<br />
(home assignment)<br />
| style="background: white;" |Exam<br />
(home assignment)<br />
| style="background: white;" |Exam<br />
(home assignment)<br />
| style="background: white;" |Exam<br />
(home assignment)<br />
| style="background: white;" |Exam end<br />
(home assignment)<br />
|}<br />
<br />
=== Computers/laptops, internet access, and UiO user account ===<br />
'''All students are strongly encouraged to bring their own laptops.''' <br />
<br />
* It should be possible to connect the computer to the UiO wireless network (probably Eduroam)<br />
* You must have a root/administrator password that gives you access to installing new software on the computer<br />
* Please bring an '''external mouse''', and do not rely on touchpad/trackpad only<br />
* You must have a '''valid UiO user account''' and must be able to log onto a computer on the UiO network<br />
* Instructions on how to find your username and get a new password can be found [http://www.uio.no/english/services/it/username-password/no-password.html here]. '''''To get a UiO username/password at the UiO helpdesk you need valid ID.'''''<br />
'''''If you are struggling with anything of the above, in particular<nowiki> </nowiki>if you have forgotten your UiO user name/password or you do not have one, you must contact Jon (see [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410_2016#Contacts contact details]) as soon as possible, and at least one week before the start of the course.'''''<br />
<br />
On the first day of the course we will set up your laptop so that<nowiki> </nowiki>it can be used for the exercises/tutorials, the home exam and hopefully<nowiki> </nowiki>in your future work. How to get a reasonable setup is described [https://wiki.uio.no/projects/clsi/index.php/Laptop_Setup here].<br />
<br />
If you already are an expert programmer and Unix guru, go [https://wiki.uio.no/projects/clsi/index.php/Biology_for_Informatics here].<br />
<br />
=== Time and place (Rooms) ===<br />
The teaching starts at 09:15 and we will end at latest 16:00. Most of the teaching will take place in room 4613 on the 4th floor of Biology Buiding (Kristine Bonnevies Hus, KB). Some days we have to change rooms so check the detailed program regularly. <br />
<br />
=== Detailed program ===<br />
<br />
The times listed here are only tentative and may likely change. We will mix in small breaks here and there and try to have a lunch break between 12:00 - 13:00.<br />
{| class="wikitable"<br />
|+Tentative schedule for MBV-INFX410 2017<br />
!Week<br />
!Monday<br />
!Tuesday<br />
!Wednesday<br />
!Thursday<br />
!Friday<br />
|-<br />
|<b>46</b><br />
| style="background: white; text-align: center;" |Nov 13<br />
| style="background: white; text-align: center;" |Nov 14<br />
| style="background: white; text-align: center;" |Nov 15<br />
| style="background: white; text-align: center;" |Nov 16<br />
| style="background: white; text-align: center;" |Nov 17<br />
|-<br />
|<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613''' <br />
09:15 - 10:00 <br />
<br />
Course introduction ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-13_01_Introduction.pdf lecture]) <br />
<br />
10:15 - 11:00 <br />
<br />
<br />
Sequence databases ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-13_02_Databases.pdf lecture])<br />
<br />
11:15 - 12:00<br />
<br />
<br />
Basic Unix ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-13_03_Basic_Unix.pdf lecture]) <br />
<br />
<br />
12:00 - 13:00 <br />
<br />
Lunch <br />
<br />
<br />
13:15 - 14:00 <br />
<br />
Setting up laptops <br />
<br />
<br />
14:15 - 16:00 <br />
<br />
Basic Unix ([http://folk.uio.no/jonbra/MBV-INF4410_2017/exercises/2017-11-13_UNIXBasics-exercise.pdf exercises]) <br />
| style="background: #cefdce; vertical-align: top;" |'''Room 3213''' <br />
09:15 - 11:00 <br />
<br />
Genome browsers ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-14_01_GenomeBrowsers.pdf lecture] / [http://folk.uio.no/jonbra/MBV-INF4410_2017/exercises/2017-11-14-01_UCSC.pdf exercises]) and Jalview ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-14_02_JalView.pdf lecture]) <br />
<br />
<br />
11:15 - 12:00<br />
<br />
Working with sequences <br />
<br />
and databases ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-14_03_Working_with_sequences.pdf lecture])<br />
<br />
<br />
12:00 - 13:00<br />
<br />
Lunch <br />
<br />
<br />
13:15 - 16:00<br />
<br />
Applied sequence bioinformatics ([http://folk.uio.no/jonbra/MBV-INF4410_2017/exercises/2017-11-14-02_Applied_seq_bioinf.pdf exercises]) <br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 12:00<br />
<br />
UiO LifePortal ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-15_01_Lifeportal_course.pdf lecture])<br />
<br />
<br />
12:00 - 13:00<br />
<br />
Lunch <br />
<br />
<br />
13:15 - 14:00 <br />
<br />
More Unix ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-15_02_MoreUnix.pdf lecture]) <br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4424'''<br />
09:15 - 16:00 <br />
<br />
[[Lectures / exercises|Python workshop]]<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''NB! Notice room change: Seminarrom U30 Helga Enghs Hus (see [https://wiki.uio.no/projects/clsi/index.php?title=MBV-INFX410_2017#Messages Messages])'''<br />
<br />
09:15 - 16:00<br />
<br />
[[Lectures / exercises|Python workshop]]<br />
<br />
|-<br />
|<b>47</b><br />
| style="background: white; text-align: center;" |Nov 20<br />
| style="background: white; text-align: center;" |Nov 21<br />
| style="background: white; text-align: center;" |Nov 22<br />
| style="background: white; text-align: center;" |Nov 23<br />
| style="background: white; text-align: center;" |Nov 24<br />
|-<br />
|<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Sequence searching and alignments ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-20_mbvinf4410-bioinf.pdf lecture] / [http://folk.uio.no/jonbra/MBV-INF4410_2017/exercises/2017-11-20_AlignmentsAndMSAs.pdf exercises]) <br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
[[Structural Bioinformatics 2017|Structural Bioinformatics]]<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
[[Structural Bioinformatics 2017|Structural Bioinformatics]]<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4424'''<br />
<br />
09:15 - 12:00<br />
<br />
Docking and drug discovery<br />
<br />
<br />
13:15 - 14:00<br />
<br />
Practical Unix/Python<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 2203a'''<br />
<br />
09:15 - 12:00<br />
<br />
"Catch-up" / "Snublegruppe" (You can ask questions from the first two weeks)<br />
<br />
<span style="color:red">Hand out oblig</span><br />
<br />
|-<br />
|<b>48</b><br />
| style="background: white; text-align: center;" |Nov 27<br />
| style="background: white; text-align: center;" |Nov 28<br />
| style="background: white; text-align: center;" |Nov 29<br />
| style="background: white; text-align: center;" |Nov 30<br />
| style="background: white; text-align: center;" |Dec 1<br />
|-<br />
|<br />
| style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment<br />
| style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment<br />
| style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment<br />
| style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment<br />
| style="background: #87CEFA; vertical-align: top;" |Hand in home assignment<br />
|-<br />
|<b>49</b><br />
| style="background: white; text-align: center;" |Dec 4<br />
| style="background: white; text-align: center;" |Dec 5<br />
| style="background: white; text-align: center;" |Dec 6<br />
| style="background: white; text-align: center;" |Dec 7<br />
| style="background: white; text-align: center;" |Dec 8<br />
|-<br />
|<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Next Generation Sequencing & variant calling<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Introduction to R<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Analysing transcriptome data using R<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Analysing transcriptome data using R<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Statistical epigenomics<br />
<br />
<span style="color:red">Hand out exam</span><br />
<br />
|-<br />
|<b>50</b><br />
| style="background: white; text-align: center;" |Dec 11<br />
| style="background: white; text-align: center;" |Dec 12<br />
| style="background: white; text-align: center;" |Dec 13<br />
| style="background: white; text-align: center;" |Dec 14<br />
| style="background: white; text-align: center;" |Dec 15<br />
|-<br />
|<br />
| style="background: salmon; vertical-align: top;" |Home exam<br />
| style="background: salmon; vertical-align: top;" |Home exam<br />
| style="background: salmon; vertical-align: top;" |Home exam<br />
| style="background: salmon; vertical-align: top;" |Home exam<br />
| style="background: salmon; vertical-align: top;" |Hand in exam<br />
|}<br />
<br />
=== Recommended reading material / curriculum ===<br />
The curriculum comprises all lectures, lecture handouts and exercises, in addition to the articles listed below:<br />
*J. R. A. Hutchins, "Genomic Database Searching", in [https://link.springer.com/protocol/10.1007%2F978-1-4939-6622-6_10 Bioinformatics pp 225-269. Springer (2017)].<br />
*R.F. Service, "Biology's dry future", [http://dx.doi.org/10.1126/science.342.6155.186 Science <b>342</b>, 186 (2013)]<br />
*EMBnet, [http://www.embnet.org/sites/default/files/quickguides/guideUNIX.pdf A Quick Guide to UNIX]<br />
*NCBI Resource Coordinators, "Database resources of the National Center for Biotechnology Information", [http://dx.doi.org/10.1093/nar/gku1130 Nucleic Acids Res. <b>43</b>, D6 (2015)]<br />
*The UniProt Consortium, "UniProt: a hub for protein information", [http://dx.doi.org/10.1093/nar/gku989 Nucleic Acids Res. <b>43</b>, D204 (2015)]<br />
*P. Flicek ''et al.'', "Ensembl 2015", [http://dx.doi.org/10.1093/nar/gku1010 Nucleic Acids Res. <b>43</b>, D662 (2015)]<br />
*P.W. Rose ''et al.'', "The RCSB Protein Data Bank: new resources for research and education", [http://dx.doi.org/10.1093/nar/gks1200 Nucleic Acids Res. <b>41</b>, D475 (2013)]<br />
*P.J.A. Cock ''et al.'', "Biopython: freely available Python tools for computational molecular biology and bioinformatics", [http://dx.doi.org/10.1093/bioinformatics/btp163 Bioinformatics <b>25</b>, 1422 (2009)]<br />
*A.M. Waterhouse ''et al''., "Jalview Version 2--a multiple sequence alignment editor and analysis workbench", [http://dx.doi.org/10.1093/bioinformatics/btp033 Bioinformatics <b>25</b>, 1189 (2009)]<br />
*G.M. Boratyn ''et al.'', "BLAST: a more efficient report with usability improvements", [http://dx.doi.org/10.1093/nar/gkt282 Nucleic Acids Res. <b>41</b>, W29 (2013)]<br />
*J.-F. Taly ''et al.'', "Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures", [http://dx.doi.org/10.1038/nprot.2011.393 Nat. Protoc. <b>6</b>, 1669 (2011)]<br />
*L. Bordoli ''et al.'', "Protein structure homology modeling using SWISS-MODEL workspace", [http://dx.doi.org/10.1038/nprot.2008.197 Nat. Protoc. <b>4</b>, 1 (2009)]<br />
*J. Carlsson ''et al.'', "Ligand discovery from a dopamine D<sub>3</sub> receptor homology model and crystal structure", [http://dx.doi.org/10.1038/nchembio.662 Nat. Chem. Biol. <b>7</b>, 769 (2011)]<br />
*R.M. Kuhn ''et al.'', "The UCSC genome browser and associated tools", [http://dx.doi.org/10.1093/bib/bbs038 Brief. Bioinform. <b>14</b>, 144 (2013)]<br />
*J. Goecks ''et al''., "Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences", [http://dx.doi.org/10.1186/gb-2010-11-8-r86 Genome Biol. <b>11</b>, R86 (2010)]<br />
*G.K. Sandve ''et al.'', "Ten Simple Rules for reproducible computational Research", [http://dx.doi.org/10.1371/journal.pcbi.1003285 PLoS Comput. Biol. <b>9</b>, e1003285 (2013)]<br />
*G.K. Sandve ''et al.'', "The Genomic HyperBrowser: an analysis web server for genome-scale data", [http://dx.doi.org/10.1093/nar/gkt342 Nucleic Acids Res. <b>41</b>, W133 (2013)]<br />
*M.L. Mertzker, "Sequencing technologies - the next generation", [http://dx.doi.org/10.1038/nrg2626 Nat. Rev. Genet. <b>11</b>, 31 (2010)]<br />
*A. Altmann ''et al.'', "A beginners guide to SNP calling from high-throughput DNA-sequencing data", [http://dx.doi.org/10.1007/s00439-012-1213-z Hum. Genet. <b>131</b>, 1541 (2012)]<br />
*N. Nagarajan & M. Pop, "Sequence assembly demystified", [http://dx.doi.org/10.1038/nrg3367 Nat. Rev. Genet. <b>14</b>, 157 (2013)]<br />
*D.W. Huang ''et al.'', "Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources", [http://dx.doi.org/10.1038/nprot.2008.211 Nat. Protoc. <b>4</b>, 44 (2009)]<br />
<br />
Other good articles (''not ''curriculum)<br />
*Z. Yang & B. Rannala, "Molecular phylogenetics: principles and practice", [http://dx.doi.org/doi:10.1038/nrg3186 Nat. Rev. Genet. <b>13</b>, 303 (2012)]<br />
<br />
=== Contacts ===<br />
Jon Bråte (Course coordinator) - e-mail: jon.brate@ibv.uio.no, phone: +47 922 44 582<br />
<br />
Torill Rørtveit (Course administrator, registration) - e-mail: torill.rortveit@ibv.uio.no<br />
<br />
=== Useful links ===<br />
<br />
[http://swcarpentry.github.io/shell-novice/reference/ Very useful reference guide on the Unix shell (created by Software Carpentry)]<br />
<br />
Trond Hasle Amundsen's [http://www.uio.no/tjenester/it/maskin/linux/hjelp/tips/guide.html Local guide to Linux and Unix]<br />
<br />
[https://github.com/EbookFoundation/free-programming-books/blob/master/free-programming-books.md#python Tons of free e-books on Python]<br />
<br />
EMBnet [http://www.embnet.org/sites/default/files/quickguides/guideUNIX.pdf Quick guide Unix]<br />
<br />
[https://github.com/stephenturner/oneliners Useful command line one-liners] by Stephen Turner<br />
<br />
[https://github.com/mcandre/cheatsheets/blob/master/nano.md Nano text editor cheat sheet]<br />
<br />
[https://github.com/EbookFoundation/free-programming-books/blob/master/free-programming-books.md Tons of free programming books, about anything really.]<br />
<br />
[http://www.jalview.org Jalview] and Jalview [http://www.jalview.org/refcard.pdf refcard]<br />
<br />
UCSC [http://genome.ucsc.edu Genome browser]<br />
<br />
Free [http://www.openhelix.com/ucsc UCSC Genome browser tutorial]&nbsp;&nbsp; from OpenHelix<br />
<br />
Portal to [http://galaxyproject.org Galaxy]<br />
<br />
[http://wiki.galaxyproject.org/Learn Galaxy 101 and other Galaxy screencasts/tutorials]<br />
<br />
UiO [http://lifeportal.uio.no Lifeportal] and more [http://www.uio.no/english/services/it/research/hpc/lifeportal information on the Lifeportal]<br />
<br />
The Genomic [http://hyperbrowser.uio.no/hb HyperBrowser]<br />
<br />
[http://bioinformatics.ca/links_directory Links Directory] from bioinformatics.ca<br />
<br />
The 2017 Nucleic Acids Research [https://academic.oup.com/nar/issue/45/D1 Database Issue]<br />
<br />
The 2015 Nucleic Acids Research [https://academic.oup.com/nar/issue/45/W1 Web Server Issue]<br />
<br />
UiO and OUS [http://core.rr-research.no/bioinformatics Bioinformatics Core Facility]</div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=MBV-INFX410_2017&diff=1919MBV-INFX410 20172017-11-20T10:18:30Z<p>Jonkl@uio.no: /* Messages */</p>
<hr />
<div>== [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410 Bioinformatics for Molecular Biology] - 2017 ==<br />
=== Messages ===<br />
* '''20 nov: NB! In order to get everybody at an acceptable level in structural biology, before we start the Structural Bioinformatics lectures/exercises on Tuesday Nov 21, there will be a Structural Biology Review lecture in the morning, at 09:15. See handouts/slides [[Structural Bioinformatics 2017|here]]. Take a look at these and decide if you need to follow the Structural Biology Review lecture. If you decide that you do not need this and that you already know everything we will go through in this lecture, come at 10:45 on Tuesday Nov 21.'''<br />
* '''16 nov: NB! Notice room change for Python workshop 17 nov: Seminarrom U30 in [https://www.uio.no/om/finn-fram/omrader/blindern/bl20/ Helga Enghs Hus.] Go in the main door and down one floor.'''<br />
* '''''All students must be present at the start of the course, on November 13 at 09:15 in room 4613 in [https://www.uio.no/om/finn-fram/omrader/blindern/bl18/ Kristine Bonnevies (KB) Hus (biology building)]. Missing students will not be allowed to follow the course or to take the exam. If you for some reason are not able to attend, please contact Jon Bråte (See [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410_2016#Contacts contact details] below).'''''<br />
* '''All students must bring their own laptops, including an external mouse.'''<br />
* '''You need to install the following software on your laptops (we will help you with this):'''<br />
** Anaconda (https://www.anaconda.com/download/)<br />
** PyMOL (https://www.pymol.org/)<br />
** JalView Desktop (http://www.jalview.org/) - could maybe also run by pressing the "Launch Jalview Desktop" button<br />
** PuTTY (http://www.putty.org/)<br />
** R (https://www.r-project.org/) '''Install''' '''inside Anaconda instead''' <br />
** RStudio (https://www.rstudio.com/) '''Install''' '''inside Anaconda instead'''<br />
**'''Optional:''' It could also be wise to have Fetch (for Mac) (http://fetchsoftworks.com/) and WinSCP (Windows) ([https://winscp.net/eng/index.php https://winscp.net/eng/index.php)]<br />
<br />
=== Course information ===<br />
This is the wiki for the courses [http://www.uio.no/studier/emner/matnat/ibv/MBV-INF4410 MBV-INF4410] and [http://www.uio.no/studier/emner/matnat/ibv/MBV-INF9410 MBV-INF9410] offered by the Department of Biosciences (IBV) at the University of Oslo (UiO). Both MBV-INF4410 (M.Sc. level) and MBV-INF9410 (Ph.D. level) are 10 study point courses. <br />
<br />
The course consists of five weeks of lectures, exercises, obligatory assignments, and a take-home exam (one week). Obligatory assignments must be completed and approved before the exam and in the same semester. An additional, limited, oral examination may be arranged in cases where this is necessary for the student evaluation. The course is open also for non-UiO students. It is only necessary to be physically present in Oslo for certain parts of the course.<br />
{| class="wikitable"<br />
|+General schedule for MBV-INFX410<br />
!<br />
!Mon<br />
!Tue<br />
!Wed<br />
!Thu<br />
!Fri<br />
|-<br />
!Week 46<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
|-<br />
!Week 47<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
|-<br />
!Week 48<br />
| style="background: white;" |Obligatory<br />
home assignment<br />
| style="background: white;" |Obligatory<br />
home assignment<br />
| style="background: white;" |Obligatory<br />
home assignment<br />
| style="background: white;" |Obligatory<br />
home assignment<br />
| style="background: white;" |Hand in<br />
home assignment<br />
|-<br />
!Week 49<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Exam start<br />
(home assignment)<br />
|-<br />
!Week 50<br />
| style="background: white;" |Exam<br />
(home assignment)<br />
| style="background: white;" |Exam<br />
(home assignment)<br />
| style="background: white;" |Exam<br />
(home assignment)<br />
| style="background: white;" |Exam<br />
(home assignment)<br />
| style="background: white;" |Exam end<br />
(home assignment)<br />
|}<br />
<br />
=== Computers/laptops, internet access, and UiO user account ===<br />
'''All students are strongly encouraged to bring their own laptops.''' <br />
<br />
* It should be possible to connect the computer to the UiO wireless network (probably Eduroam)<br />
* You must have a root/administrator password that gives you access to installing new software on the computer<br />
* Please bring an '''external mouse''', and do not rely on touchpad/trackpad only<br />
* You must have a '''valid UiO user account''' and must be able to log onto a computer on the UiO network<br />
* Instructions on how to find your username and get a new password can be found [http://www.uio.no/english/services/it/username-password/no-password.html here]. '''''To get a UiO username/password at the UiO helpdesk you need valid ID.'''''<br />
'''''If you are struggling with anything of the above, in particular<nowiki> </nowiki>if you have forgotten your UiO user name/password or you do not have one, you must contact Jon (see [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410_2016#Contacts contact details]) as soon as possible, and at least one week before the start of the course.'''''<br />
<br />
On the first day of the course we will set up your laptop so that<nowiki> </nowiki>it can be used for the exercises/tutorials, the home exam and hopefully<nowiki> </nowiki>in your future work. How to get a reasonable setup is described [https://wiki.uio.no/projects/clsi/index.php/Laptop_Setup here].<br />
<br />
If you already are an expert programmer and Unix guru, go [https://wiki.uio.no/projects/clsi/index.php/Biology_for_Informatics here].<br />
<br />
=== Time and place (Rooms) ===<br />
The teaching starts at 09:15 and we will end at latest 16:00. Most of the teaching will take place in room 4613 on the 4th floor of Biology Buiding (Kristine Bonnevies Hus, KB). Some days we have to change rooms so check the detailed program regularly. <br />
<br />
=== Detailed program ===<br />
<br />
The times listed here are only tentative and may likely change. We will mix in small breaks here and there and try to have a lunch break between 12:00 - 13:00.<br />
{| class="wikitable"<br />
|+Tentative schedule for MBV-INFX410 2017<br />
!Week<br />
!Monday<br />
!Tuesday<br />
!Wednesday<br />
!Thursday<br />
!Friday<br />
|-<br />
|<b>46</b><br />
| style="background: white; text-align: center;" |Nov 13<br />
| style="background: white; text-align: center;" |Nov 14<br />
| style="background: white; text-align: center;" |Nov 15<br />
| style="background: white; text-align: center;" |Nov 16<br />
| style="background: white; text-align: center;" |Nov 17<br />
|-<br />
|<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613''' <br />
09:15 - 10:00 <br />
<br />
Course introduction ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-13_01_Introduction.pdf lecture]) <br />
<br />
10:15 - 11:00 <br />
<br />
<br />
Sequence databases ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-13_02_Databases.pdf lecture])<br />
<br />
11:15 - 12:00<br />
<br />
<br />
Basic Unix ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-13_03_Basic_Unix.pdf lecture]) <br />
<br />
<br />
12:00 - 13:00 <br />
<br />
Lunch <br />
<br />
<br />
13:15 - 14:00 <br />
<br />
Setting up laptops <br />
<br />
<br />
14:15 - 16:00 <br />
<br />
Basic Unix ([http://folk.uio.no/jonbra/MBV-INF4410_2017/exercises/2017-11-13_UNIXBasics-exercise.pdf exercises]) <br />
| style="background: #cefdce; vertical-align: top;" |'''Room 3213''' <br />
09:15 - 11:00 <br />
<br />
Genome browsers ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-14_01_GenomeBrowsers.pdf lecture] / [http://folk.uio.no/jonbra/MBV-INF4410_2017/exercises/2017-11-14-01_UCSC.pdf exercises]) and Jalview ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-14_02_JalView.pdf lecture]) <br />
<br />
<br />
11:15 - 12:00<br />
<br />
Working with sequences <br />
<br />
and databases ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-14_03_Working_with_sequences.pdf lecture])<br />
<br />
<br />
12:00 - 13:00<br />
<br />
Lunch <br />
<br />
<br />
13:15 - 16:00<br />
<br />
Applied sequence bioinformatics ([http://folk.uio.no/jonbra/MBV-INF4410_2017/exercises/2017-11-14-02_Applied_seq_bioinf.pdf exercises]) <br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 12:00<br />
<br />
UiO LifePortal ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-15_01_Lifeportal_course.pdf lecture])<br />
<br />
<br />
12:00 - 13:00<br />
<br />
Lunch <br />
<br />
<br />
13:15 - 14:00 <br />
<br />
More Unix ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-15_02_MoreUnix.pdf lecture]) <br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4424'''<br />
09:15 - 16:00 <br />
<br />
[[Lectures / exercises|Python workshop]]<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''NB! Notice room change: Seminarrom U30 Helga Enghs Hus (see [https://wiki.uio.no/projects/clsi/index.php?title=MBV-INFX410_2017#Messages Messages])'''<br />
<br />
09:15 - 16:00<br />
<br />
[[Lectures / exercises|Python workshop]]<br />
<br />
|-<br />
|<b>47</b><br />
| style="background: white; text-align: center;" |Nov 20<br />
| style="background: white; text-align: center;" |Nov 21<br />
| style="background: white; text-align: center;" |Nov 22<br />
| style="background: white; text-align: center;" |Nov 23<br />
| style="background: white; text-align: center;" |Nov 24<br />
|-<br />
|<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Sequence searching and alignments ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-20_mbvinf4410-bioinf.pdf lecture] / [http://folk.uio.no/jonbra/MBV-INF4410_2017/exercises/2017-11-20_AlignmentsAndMSAs.pdf exercises]) <br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
[[Structural Bioinformatics 2017|Structural Bioinformatics]]<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
[[Structural Bioinformatics 2017|Structural Bioinformatics]]<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4424'''<br />
<br />
09:15 - 12:00<br />
<br />
Docking and drug discovery<br />
<br />
<br />
13:15 - 14:00<br />
<br />
Practical Unix/Python<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 2203a'''<br />
<br />
09:15 - 12:00<br />
<br />
"Catch-up" / "Snublegruppe" (You can ask questions from the first two weeks)<br />
<br />
<span style="color:red">Hand out oblig</span><br />
<br />
|-<br />
|<b>48</b><br />
| style="background: white; text-align: center;" |Nov 27<br />
| style="background: white; text-align: center;" |Nov 28<br />
| style="background: white; text-align: center;" |Nov 29<br />
| style="background: white; text-align: center;" |Nov 30<br />
| style="background: white; text-align: center;" |Dec 1<br />
|-<br />
|<br />
| style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment<br />
| style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment<br />
| style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment<br />
| style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment<br />
| style="background: #87CEFA; vertical-align: top;" |Hand in home assignment<br />
|-<br />
|<b>49</b><br />
| style="background: white; text-align: center;" |Dec 4<br />
| style="background: white; text-align: center;" |Dec 5<br />
| style="background: white; text-align: center;" |Dec 6<br />
| style="background: white; text-align: center;" |Dec 7<br />
| style="background: white; text-align: center;" |Dec 8<br />
|-<br />
|<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Next Generation Sequencing & variant calling<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Introduction to R<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Analysing transcriptome data using R<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Analysing transcriptome data using R<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Statistical epigenomics<br />
<br />
<span style="color:red">Hand out exam</span><br />
<br />
|-<br />
|<b>50</b><br />
| style="background: white; text-align: center;" |Dec 11<br />
| style="background: white; text-align: center;" |Dec 12<br />
| style="background: white; text-align: center;" |Dec 13<br />
| style="background: white; text-align: center;" |Dec 14<br />
| style="background: white; text-align: center;" |Dec 15<br />
|-<br />
|<br />
| style="background: salmon; vertical-align: top;" |Home exam<br />
| style="background: salmon; vertical-align: top;" |Home exam<br />
| style="background: salmon; vertical-align: top;" |Home exam<br />
| style="background: salmon; vertical-align: top;" |Home exam<br />
| style="background: salmon; vertical-align: top;" |Hand in exam<br />
|}<br />
<br />
=== Recommended reading material / curriculum ===<br />
The curriculum comprises all lectures, lecture handouts and exercises, in addition to the articles listed below:<br />
*J. R. A. Hutchins, "Genomic Database Searching", in [https://link.springer.com/protocol/10.1007%2F978-1-4939-6622-6_10 Bioinformatics pp 225-269. Springer (2017)].<br />
*R.F. Service, "Biology's dry future", [http://dx.doi.org/10.1126/science.342.6155.186 Science <b>342</b>, 186 (2013)]<br />
*EMBnet, [http://www.embnet.org/sites/default/files/quickguides/guideUNIX.pdf A Quick Guide to UNIX]<br />
*NCBI Resource Coordinators, "Database resources of the National Center for Biotechnology Information", [http://dx.doi.org/10.1093/nar/gku1130 Nucleic Acids Res. <b>43</b>, D6 (2015)]<br />
*The UniProt Consortium, "UniProt: a hub for protein information", [http://dx.doi.org/10.1093/nar/gku989 Nucleic Acids Res. <b>43</b>, D204 (2015)]<br />
*P. Flicek ''et al.'', "Ensembl 2015", [http://dx.doi.org/10.1093/nar/gku1010 Nucleic Acids Res. <b>43</b>, D662 (2015)]<br />
*P.W. Rose ''et al.'', "The RCSB Protein Data Bank: new resources for research and education", [http://dx.doi.org/10.1093/nar/gks1200 Nucleic Acids Res. <b>41</b>, D475 (2013)]<br />
*P.J.A. Cock ''et al.'', "Biopython: freely available Python tools for computational molecular biology and bioinformatics", [http://dx.doi.org/10.1093/bioinformatics/btp163 Bioinformatics <b>25</b>, 1422 (2009)]<br />
*A.M. Waterhouse ''et al''., "Jalview Version 2--a multiple sequence alignment editor and analysis workbench", [http://dx.doi.org/10.1093/bioinformatics/btp033 Bioinformatics <b>25</b>, 1189 (2009)]<br />
*G.M. Boratyn ''et al.'', "BLAST: a more efficient report with usability improvements", [http://dx.doi.org/10.1093/nar/gkt282 Nucleic Acids Res. <b>41</b>, W29 (2013)]<br />
*J.-F. Taly ''et al.'', "Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures", [http://dx.doi.org/10.1038/nprot.2011.393 Nat. Protoc. <b>6</b>, 1669 (2011)]<br />
*L. Bordoli ''et al.'', "Protein structure homology modeling using SWISS-MODEL workspace", [http://dx.doi.org/10.1038/nprot.2008.197 Nat. Protoc. <b>4</b>, 1 (2009)]<br />
*J. Carlsson ''et al.'', "Ligand discovery from a dopamine D<sub>3</sub> receptor homology model and crystal structure", [http://dx.doi.org/10.1038/nchembio.662 Nat. Chem. Biol. <b>7</b>, 769 (2011)]<br />
*R.M. Kuhn ''et al.'', "The UCSC genome browser and associated tools", [http://dx.doi.org/10.1093/bib/bbs038 Brief. Bioinform. <b>14</b>, 144 (2013)]<br />
*J. Goecks ''et al''., "Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences", [http://dx.doi.org/10.1186/gb-2010-11-8-r86 Genome Biol. <b>11</b>, R86 (2010)]<br />
*G.K. Sandve ''et al.'', "Ten Simple Rules for reproducible computational Research", [http://dx.doi.org/10.1371/journal.pcbi.1003285 PLoS Comput. Biol. <b>9</b>, e1003285 (2013)]<br />
*G.K. Sandve ''et al.'', "The Genomic HyperBrowser: an analysis web server for genome-scale data", [http://dx.doi.org/10.1093/nar/gkt342 Nucleic Acids Res. <b>41</b>, W133 (2013)]<br />
*M.L. Mertzker, "Sequencing technologies - the next generation", [http://dx.doi.org/10.1038/nrg2626 Nat. Rev. Genet. <b>11</b>, 31 (2010)]<br />
*A. Altmann ''et al.'', "A beginners guide to SNP calling from high-throughput DNA-sequencing data", [http://dx.doi.org/10.1007/s00439-012-1213-z Hum. Genet. <b>131</b>, 1541 (2012)]<br />
*N. Nagarajan & M. Pop, "Sequence assembly demystified", [http://dx.doi.org/10.1038/nrg3367 Nat. Rev. Genet. <b>14</b>, 157 (2013)]<br />
*D.W. Huang ''et al.'', "Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources", [http://dx.doi.org/10.1038/nprot.2008.211 Nat. Protoc. <b>4</b>, 44 (2009)]<br />
<br />
Other good articles (''not ''curriculum)<br />
*Z. Yang & B. Rannala, "Molecular phylogenetics: principles and practice", [http://dx.doi.org/doi:10.1038/nrg3186 Nat. Rev. Genet. <b>13</b>, 303 (2012)]<br />
<br />
=== Contacts ===<br />
Jon Bråte (Course coordinator) - e-mail: jon.brate@ibv.uio.no, phone: +47 922 44 582<br />
<br />
Torill Rørtveit (Course administrator, registration) - e-mail: torill.rortveit@ibv.uio.no<br />
<br />
=== Useful links ===<br />
<br />
[http://swcarpentry.github.io/shell-novice/reference/ Very useful reference guide on the Unix shell (created by Software Carpentry)]<br />
<br />
Trond Hasle Amundsen's [http://www.uio.no/tjenester/it/maskin/linux/hjelp/tips/guide.html Local guide to Linux and Unix]<br />
<br />
[https://github.com/EbookFoundation/free-programming-books/blob/master/free-programming-books.md#python Tons of free e-books on Python]<br />
<br />
EMBnet [http://www.embnet.org/sites/default/files/quickguides/guideUNIX.pdf Quick guide Unix]<br />
<br />
[https://github.com/stephenturner/oneliners Useful command line one-liners] by Stephen Turner<br />
<br />
[https://github.com/mcandre/cheatsheets/blob/master/nano.md Nano text editor cheat sheet]<br />
<br />
[https://github.com/EbookFoundation/free-programming-books/blob/master/free-programming-books.md Tons of free programming books, about anything really.]<br />
<br />
[http://www.jalview.org Jalview] and Jalview [http://www.jalview.org/refcard.pdf refcard]<br />
<br />
UCSC [http://genome.ucsc.edu Genome browser]<br />
<br />
Free [http://www.openhelix.com/ucsc UCSC Genome browser tutorial]&nbsp;&nbsp; from OpenHelix<br />
<br />
Portal to [http://galaxyproject.org Galaxy]<br />
<br />
[http://wiki.galaxyproject.org/Learn Galaxy 101 and other Galaxy screencasts/tutorials]<br />
<br />
UiO [http://lifeportal.uio.no Lifeportal] and more [http://www.uio.no/english/services/it/research/hpc/lifeportal information on the Lifeportal]<br />
<br />
The Genomic [http://hyperbrowser.uio.no/hb HyperBrowser]<br />
<br />
[http://bioinformatics.ca/links_directory Links Directory] from bioinformatics.ca<br />
<br />
The 2017 Nucleic Acids Research [https://academic.oup.com/nar/issue/45/D1 Database Issue]<br />
<br />
The 2015 Nucleic Acids Research [https://academic.oup.com/nar/issue/45/W1 Web Server Issue]<br />
<br />
UiO and OUS [http://core.rr-research.no/bioinformatics Bioinformatics Core Facility]</div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=MBV-INFX410_2017&diff=1918MBV-INFX410 20172017-11-20T10:16:53Z<p>Jonkl@uio.no: /* Messages */</p>
<hr />
<div>== [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410 Bioinformatics for Molecular Biology] - 2017 ==<br />
=== Messages ===<br />
* '''20 nov: NB! In order to get everybody at an acceptable level in structural biology, before we start the Structural Bioinformatics lectures/exercises on Tuesday Nov 21, there will be a Structural Biology Review lecture in the morning, at 09:15. See handouts/slides [[Structural Bioinformatics 2017|here]]. Take a look at these and decide if you need to follow the Structural Biology Review lecture. If you decide that you do not need this, come at 10:45 on Tuesday Nov 21.'''<br />
* '''16 nov: NB! Notice room change for Python workshop 17 nov: Seminarrom U30 in [https://www.uio.no/om/finn-fram/omrader/blindern/bl20/ Helga Enghs Hus.] Go in the main door and down one floor.'''<br />
* '''''All students must be present at the start of the course, on November 13 at 09:15 in room 4613 in [https://www.uio.no/om/finn-fram/omrader/blindern/bl18/ Kristine Bonnevies (KB) Hus (biology building)]. Missing students will not be allowed to follow the course or to take the exam. If you for some reason are not able to attend, please contact Jon Bråte (See [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410_2016#Contacts contact details] below).'''''<br />
* '''All students must bring their own laptops, including an external mouse.'''<br />
* '''You need to install the following software on your laptops (we will help you with this):'''<br />
** Anaconda (https://www.anaconda.com/download/)<br />
** PyMOL (https://www.pymol.org/)<br />
** JalView Desktop (http://www.jalview.org/) - could maybe also run by pressing the "Launch Jalview Desktop" button<br />
** PuTTY (http://www.putty.org/)<br />
** R (https://www.r-project.org/) '''Install''' '''inside Anaconda instead''' <br />
** RStudio (https://www.rstudio.com/) '''Install''' '''inside Anaconda instead'''<br />
**'''Optional:''' It could also be wise to have Fetch (for Mac) (http://fetchsoftworks.com/) and WinSCP (Windows) ([https://winscp.net/eng/index.php https://winscp.net/eng/index.php)]<br />
<br />
=== Course information ===<br />
This is the wiki for the courses [http://www.uio.no/studier/emner/matnat/ibv/MBV-INF4410 MBV-INF4410] and [http://www.uio.no/studier/emner/matnat/ibv/MBV-INF9410 MBV-INF9410] offered by the Department of Biosciences (IBV) at the University of Oslo (UiO). Both MBV-INF4410 (M.Sc. level) and MBV-INF9410 (Ph.D. level) are 10 study point courses. <br />
<br />
The course consists of five weeks of lectures, exercises, obligatory assignments, and a take-home exam (one week). Obligatory assignments must be completed and approved before the exam and in the same semester. An additional, limited, oral examination may be arranged in cases where this is necessary for the student evaluation. The course is open also for non-UiO students. It is only necessary to be physically present in Oslo for certain parts of the course.<br />
{| class="wikitable"<br />
|+General schedule for MBV-INFX410<br />
!<br />
!Mon<br />
!Tue<br />
!Wed<br />
!Thu<br />
!Fri<br />
|-<br />
!Week 46<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
|-<br />
!Week 47<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
|-<br />
!Week 48<br />
| style="background: white;" |Obligatory<br />
home assignment<br />
| style="background: white;" |Obligatory<br />
home assignment<br />
| style="background: white;" |Obligatory<br />
home assignment<br />
| style="background: white;" |Obligatory<br />
home assignment<br />
| style="background: white;" |Hand in<br />
home assignment<br />
|-<br />
!Week 49<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Exam start<br />
(home assignment)<br />
|-<br />
!Week 50<br />
| style="background: white;" |Exam<br />
(home assignment)<br />
| style="background: white;" |Exam<br />
(home assignment)<br />
| style="background: white;" |Exam<br />
(home assignment)<br />
| style="background: white;" |Exam<br />
(home assignment)<br />
| style="background: white;" |Exam end<br />
(home assignment)<br />
|}<br />
<br />
=== Computers/laptops, internet access, and UiO user account ===<br />
'''All students are strongly encouraged to bring their own laptops.''' <br />
<br />
* It should be possible to connect the computer to the UiO wireless network (probably Eduroam)<br />
* You must have a root/administrator password that gives you access to installing new software on the computer<br />
* Please bring an '''external mouse''', and do not rely on touchpad/trackpad only<br />
* You must have a '''valid UiO user account''' and must be able to log onto a computer on the UiO network<br />
* Instructions on how to find your username and get a new password can be found [http://www.uio.no/english/services/it/username-password/no-password.html here]. '''''To get a UiO username/password at the UiO helpdesk you need valid ID.'''''<br />
'''''If you are struggling with anything of the above, in particular<nowiki> </nowiki>if you have forgotten your UiO user name/password or you do not have one, you must contact Jon (see [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410_2016#Contacts contact details]) as soon as possible, and at least one week before the start of the course.'''''<br />
<br />
On the first day of the course we will set up your laptop so that<nowiki> </nowiki>it can be used for the exercises/tutorials, the home exam and hopefully<nowiki> </nowiki>in your future work. How to get a reasonable setup is described [https://wiki.uio.no/projects/clsi/index.php/Laptop_Setup here].<br />
<br />
If you already are an expert programmer and Unix guru, go [https://wiki.uio.no/projects/clsi/index.php/Biology_for_Informatics here].<br />
<br />
=== Time and place (Rooms) ===<br />
The teaching starts at 09:15 and we will end at latest 16:00. Most of the teaching will take place in room 4613 on the 4th floor of Biology Buiding (Kristine Bonnevies Hus, KB). Some days we have to change rooms so check the detailed program regularly. <br />
<br />
=== Detailed program ===<br />
<br />
The times listed here are only tentative and may likely change. We will mix in small breaks here and there and try to have a lunch break between 12:00 - 13:00.<br />
{| class="wikitable"<br />
|+Tentative schedule for MBV-INFX410 2017<br />
!Week<br />
!Monday<br />
!Tuesday<br />
!Wednesday<br />
!Thursday<br />
!Friday<br />
|-<br />
|<b>46</b><br />
| style="background: white; text-align: center;" |Nov 13<br />
| style="background: white; text-align: center;" |Nov 14<br />
| style="background: white; text-align: center;" |Nov 15<br />
| style="background: white; text-align: center;" |Nov 16<br />
| style="background: white; text-align: center;" |Nov 17<br />
|-<br />
|<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613''' <br />
09:15 - 10:00 <br />
<br />
Course introduction ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-13_01_Introduction.pdf lecture]) <br />
<br />
10:15 - 11:00 <br />
<br />
<br />
Sequence databases ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-13_02_Databases.pdf lecture])<br />
<br />
11:15 - 12:00<br />
<br />
<br />
Basic Unix ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-13_03_Basic_Unix.pdf lecture]) <br />
<br />
<br />
12:00 - 13:00 <br />
<br />
Lunch <br />
<br />
<br />
13:15 - 14:00 <br />
<br />
Setting up laptops <br />
<br />
<br />
14:15 - 16:00 <br />
<br />
Basic Unix ([http://folk.uio.no/jonbra/MBV-INF4410_2017/exercises/2017-11-13_UNIXBasics-exercise.pdf exercises]) <br />
| style="background: #cefdce; vertical-align: top;" |'''Room 3213''' <br />
09:15 - 11:00 <br />
<br />
Genome browsers ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-14_01_GenomeBrowsers.pdf lecture] / [http://folk.uio.no/jonbra/MBV-INF4410_2017/exercises/2017-11-14-01_UCSC.pdf exercises]) and Jalview ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-14_02_JalView.pdf lecture]) <br />
<br />
<br />
11:15 - 12:00<br />
<br />
Working with sequences <br />
<br />
and databases ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-14_03_Working_with_sequences.pdf lecture])<br />
<br />
<br />
12:00 - 13:00<br />
<br />
Lunch <br />
<br />
<br />
13:15 - 16:00<br />
<br />
Applied sequence bioinformatics ([http://folk.uio.no/jonbra/MBV-INF4410_2017/exercises/2017-11-14-02_Applied_seq_bioinf.pdf exercises]) <br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 12:00<br />
<br />
UiO LifePortal ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-15_01_Lifeportal_course.pdf lecture])<br />
<br />
<br />
12:00 - 13:00<br />
<br />
Lunch <br />
<br />
<br />
13:15 - 14:00 <br />
<br />
More Unix ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-15_02_MoreUnix.pdf lecture]) <br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4424'''<br />
09:15 - 16:00 <br />
<br />
[[Lectures / exercises|Python workshop]]<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''NB! Notice room change: Seminarrom U30 Helga Enghs Hus (see [https://wiki.uio.no/projects/clsi/index.php?title=MBV-INFX410_2017#Messages Messages])'''<br />
<br />
09:15 - 16:00<br />
<br />
[[Lectures / exercises|Python workshop]]<br />
<br />
|-<br />
|<b>47</b><br />
| style="background: white; text-align: center;" |Nov 20<br />
| style="background: white; text-align: center;" |Nov 21<br />
| style="background: white; text-align: center;" |Nov 22<br />
| style="background: white; text-align: center;" |Nov 23<br />
| style="background: white; text-align: center;" |Nov 24<br />
|-<br />
|<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Sequence searching and alignments ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-20_mbvinf4410-bioinf.pdf lecture] / [http://folk.uio.no/jonbra/MBV-INF4410_2017/exercises/2017-11-20_AlignmentsAndMSAs.pdf exercises]) <br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
[[Structural Bioinformatics 2017|Structural Bioinformatics]]<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
[[Structural Bioinformatics 2017|Structural Bioinformatics]]<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4424'''<br />
<br />
09:15 - 12:00<br />
<br />
Docking and drug discovery<br />
<br />
<br />
13:15 - 14:00<br />
<br />
Practical Unix/Python<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 2203a'''<br />
<br />
09:15 - 12:00<br />
<br />
"Catch-up" / "Snublegruppe" (You can ask questions from the first two weeks)<br />
<br />
<span style="color:red">Hand out oblig</span><br />
<br />
|-<br />
|<b>48</b><br />
| style="background: white; text-align: center;" |Nov 27<br />
| style="background: white; text-align: center;" |Nov 28<br />
| style="background: white; text-align: center;" |Nov 29<br />
| style="background: white; text-align: center;" |Nov 30<br />
| style="background: white; text-align: center;" |Dec 1<br />
|-<br />
|<br />
| style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment<br />
| style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment<br />
| style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment<br />
| style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment<br />
| style="background: #87CEFA; vertical-align: top;" |Hand in home assignment<br />
|-<br />
|<b>49</b><br />
| style="background: white; text-align: center;" |Dec 4<br />
| style="background: white; text-align: center;" |Dec 5<br />
| style="background: white; text-align: center;" |Dec 6<br />
| style="background: white; text-align: center;" |Dec 7<br />
| style="background: white; text-align: center;" |Dec 8<br />
|-<br />
|<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Next Generation Sequencing & variant calling<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Introduction to R<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Analysing transcriptome data using R<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Analysing transcriptome data using R<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Statistical epigenomics<br />
<br />
<span style="color:red">Hand out exam</span><br />
<br />
|-<br />
|<b>50</b><br />
| style="background: white; text-align: center;" |Dec 11<br />
| style="background: white; text-align: center;" |Dec 12<br />
| style="background: white; text-align: center;" |Dec 13<br />
| style="background: white; text-align: center;" |Dec 14<br />
| style="background: white; text-align: center;" |Dec 15<br />
|-<br />
|<br />
| style="background: salmon; vertical-align: top;" |Home exam<br />
| style="background: salmon; vertical-align: top;" |Home exam<br />
| style="background: salmon; vertical-align: top;" |Home exam<br />
| style="background: salmon; vertical-align: top;" |Home exam<br />
| style="background: salmon; vertical-align: top;" |Hand in exam<br />
|}<br />
<br />
=== Recommended reading material / curriculum ===<br />
The curriculum comprises all lectures, lecture handouts and exercises, in addition to the articles listed below:<br />
*J. R. A. Hutchins, "Genomic Database Searching", in [https://link.springer.com/protocol/10.1007%2F978-1-4939-6622-6_10 Bioinformatics pp 225-269. Springer (2017)].<br />
*R.F. Service, "Biology's dry future", [http://dx.doi.org/10.1126/science.342.6155.186 Science <b>342</b>, 186 (2013)]<br />
*EMBnet, [http://www.embnet.org/sites/default/files/quickguides/guideUNIX.pdf A Quick Guide to UNIX]<br />
*NCBI Resource Coordinators, "Database resources of the National Center for Biotechnology Information", [http://dx.doi.org/10.1093/nar/gku1130 Nucleic Acids Res. <b>43</b>, D6 (2015)]<br />
*The UniProt Consortium, "UniProt: a hub for protein information", [http://dx.doi.org/10.1093/nar/gku989 Nucleic Acids Res. <b>43</b>, D204 (2015)]<br />
*P. Flicek ''et al.'', "Ensembl 2015", [http://dx.doi.org/10.1093/nar/gku1010 Nucleic Acids Res. <b>43</b>, D662 (2015)]<br />
*P.W. Rose ''et al.'', "The RCSB Protein Data Bank: new resources for research and education", [http://dx.doi.org/10.1093/nar/gks1200 Nucleic Acids Res. <b>41</b>, D475 (2013)]<br />
*P.J.A. Cock ''et al.'', "Biopython: freely available Python tools for computational molecular biology and bioinformatics", [http://dx.doi.org/10.1093/bioinformatics/btp163 Bioinformatics <b>25</b>, 1422 (2009)]<br />
*A.M. Waterhouse ''et al''., "Jalview Version 2--a multiple sequence alignment editor and analysis workbench", [http://dx.doi.org/10.1093/bioinformatics/btp033 Bioinformatics <b>25</b>, 1189 (2009)]<br />
*G.M. Boratyn ''et al.'', "BLAST: a more efficient report with usability improvements", [http://dx.doi.org/10.1093/nar/gkt282 Nucleic Acids Res. <b>41</b>, W29 (2013)]<br />
*J.-F. Taly ''et al.'', "Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures", [http://dx.doi.org/10.1038/nprot.2011.393 Nat. Protoc. <b>6</b>, 1669 (2011)]<br />
*L. Bordoli ''et al.'', "Protein structure homology modeling using SWISS-MODEL workspace", [http://dx.doi.org/10.1038/nprot.2008.197 Nat. Protoc. <b>4</b>, 1 (2009)]<br />
*J. Carlsson ''et al.'', "Ligand discovery from a dopamine D<sub>3</sub> receptor homology model and crystal structure", [http://dx.doi.org/10.1038/nchembio.662 Nat. Chem. Biol. <b>7</b>, 769 (2011)]<br />
*R.M. Kuhn ''et al.'', "The UCSC genome browser and associated tools", [http://dx.doi.org/10.1093/bib/bbs038 Brief. Bioinform. <b>14</b>, 144 (2013)]<br />
*J. Goecks ''et al''., "Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences", [http://dx.doi.org/10.1186/gb-2010-11-8-r86 Genome Biol. <b>11</b>, R86 (2010)]<br />
*G.K. Sandve ''et al.'', "Ten Simple Rules for reproducible computational Research", [http://dx.doi.org/10.1371/journal.pcbi.1003285 PLoS Comput. Biol. <b>9</b>, e1003285 (2013)]<br />
*G.K. Sandve ''et al.'', "The Genomic HyperBrowser: an analysis web server for genome-scale data", [http://dx.doi.org/10.1093/nar/gkt342 Nucleic Acids Res. <b>41</b>, W133 (2013)]<br />
*M.L. Mertzker, "Sequencing technologies - the next generation", [http://dx.doi.org/10.1038/nrg2626 Nat. Rev. Genet. <b>11</b>, 31 (2010)]<br />
*A. Altmann ''et al.'', "A beginners guide to SNP calling from high-throughput DNA-sequencing data", [http://dx.doi.org/10.1007/s00439-012-1213-z Hum. Genet. <b>131</b>, 1541 (2012)]<br />
*N. Nagarajan & M. Pop, "Sequence assembly demystified", [http://dx.doi.org/10.1038/nrg3367 Nat. Rev. Genet. <b>14</b>, 157 (2013)]<br />
*D.W. Huang ''et al.'', "Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources", [http://dx.doi.org/10.1038/nprot.2008.211 Nat. Protoc. <b>4</b>, 44 (2009)]<br />
<br />
Other good articles (''not ''curriculum)<br />
*Z. Yang & B. Rannala, "Molecular phylogenetics: principles and practice", [http://dx.doi.org/doi:10.1038/nrg3186 Nat. Rev. Genet. <b>13</b>, 303 (2012)]<br />
<br />
=== Contacts ===<br />
Jon Bråte (Course coordinator) - e-mail: jon.brate@ibv.uio.no, phone: +47 922 44 582<br />
<br />
Torill Rørtveit (Course administrator, registration) - e-mail: torill.rortveit@ibv.uio.no<br />
<br />
=== Useful links ===<br />
<br />
[http://swcarpentry.github.io/shell-novice/reference/ Very useful reference guide on the Unix shell (created by Software Carpentry)]<br />
<br />
Trond Hasle Amundsen's [http://www.uio.no/tjenester/it/maskin/linux/hjelp/tips/guide.html Local guide to Linux and Unix]<br />
<br />
[https://github.com/EbookFoundation/free-programming-books/blob/master/free-programming-books.md#python Tons of free e-books on Python]<br />
<br />
EMBnet [http://www.embnet.org/sites/default/files/quickguides/guideUNIX.pdf Quick guide Unix]<br />
<br />
[https://github.com/stephenturner/oneliners Useful command line one-liners] by Stephen Turner<br />
<br />
[https://github.com/mcandre/cheatsheets/blob/master/nano.md Nano text editor cheat sheet]<br />
<br />
[https://github.com/EbookFoundation/free-programming-books/blob/master/free-programming-books.md Tons of free programming books, about anything really.]<br />
<br />
[http://www.jalview.org Jalview] and Jalview [http://www.jalview.org/refcard.pdf refcard]<br />
<br />
UCSC [http://genome.ucsc.edu Genome browser]<br />
<br />
Free [http://www.openhelix.com/ucsc UCSC Genome browser tutorial]&nbsp;&nbsp; from OpenHelix<br />
<br />
Portal to [http://galaxyproject.org Galaxy]<br />
<br />
[http://wiki.galaxyproject.org/Learn Galaxy 101 and other Galaxy screencasts/tutorials]<br />
<br />
UiO [http://lifeportal.uio.no Lifeportal] and more [http://www.uio.no/english/services/it/research/hpc/lifeportal information on the Lifeportal]<br />
<br />
The Genomic [http://hyperbrowser.uio.no/hb HyperBrowser]<br />
<br />
[http://bioinformatics.ca/links_directory Links Directory] from bioinformatics.ca<br />
<br />
The 2017 Nucleic Acids Research [https://academic.oup.com/nar/issue/45/D1 Database Issue]<br />
<br />
The 2015 Nucleic Acids Research [https://academic.oup.com/nar/issue/45/W1 Web Server Issue]<br />
<br />
UiO and OUS [http://core.rr-research.no/bioinformatics Bioinformatics Core Facility]</div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=MBV-INFX410_2017&diff=1917MBV-INFX410 20172017-11-20T10:15:07Z<p>Jonkl@uio.no: /* Bioinformatics for Molecular Biology - 2017 */</p>
<hr />
<div>== [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410 Bioinformatics for Molecular Biology] - 2017 ==<br />
=== Messages ===<br />
* '''20 nov: NB! In order to get everybody at an acceptable level in structural biology, before we start the Structural Bioinformatics lectures/exercises on Tuesday Nov 21, there will be a Structural Biology Review lecture in the morning. See handouts/slides [[Structural Bioinformatics 2017|here]]. Take a look at these and decide if you need to follow the Structural Biology Review lecture. If you decide you do not need this, come at 10:45 on Tuesday Nov 21.'''<br />
* '''16 nov: NB! Notice room change for Python workshop 17 nov: Seminarrom U30 in [https://www.uio.no/om/finn-fram/omrader/blindern/bl20/ Helga Enghs Hus.] Go in the main door and down one floor.'''<br />
* '''''All students must be present at the start of the course, on November 13 at 09:15 in room 4613 in [https://www.uio.no/om/finn-fram/omrader/blindern/bl18/ Kristine Bonnevies (KB) Hus (biology building)]. Missing students will not be allowed to follow the course or to take the exam. If you for some reason are not able to attend, please contact Jon Bråte (See [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410_2016#Contacts contact details] below).'''''<br />
* '''All students must bring their own laptops, including an external mouse.'''<br />
* '''You need to install the following software on your laptops (we will help you with this):'''<br />
** Anaconda (https://www.anaconda.com/download/)<br />
** PyMOL (https://www.pymol.org/)<br />
** JalView Desktop (http://www.jalview.org/) - could maybe also run by pressing the "Launch Jalview Desktop" button<br />
** PuTTY (http://www.putty.org/)<br />
** R (https://www.r-project.org/) '''Install''' '''inside Anaconda instead''' <br />
** RStudio (https://www.rstudio.com/) '''Install''' '''inside Anaconda instead'''<br />
**'''Optional:''' It could also be wise to have Fetch (for Mac) (http://fetchsoftworks.com/) and WinSCP (Windows) ([https://winscp.net/eng/index.php https://winscp.net/eng/index.php)]<br />
<br />
=== Course information ===<br />
This is the wiki for the courses [http://www.uio.no/studier/emner/matnat/ibv/MBV-INF4410 MBV-INF4410] and [http://www.uio.no/studier/emner/matnat/ibv/MBV-INF9410 MBV-INF9410] offered by the Department of Biosciences (IBV) at the University of Oslo (UiO). Both MBV-INF4410 (M.Sc. level) and MBV-INF9410 (Ph.D. level) are 10 study point courses. <br />
<br />
The course consists of five weeks of lectures, exercises, obligatory assignments, and a take-home exam (one week). Obligatory assignments must be completed and approved before the exam and in the same semester. An additional, limited, oral examination may be arranged in cases where this is necessary for the student evaluation. The course is open also for non-UiO students. It is only necessary to be physically present in Oslo for certain parts of the course.<br />
{| class="wikitable"<br />
|+General schedule for MBV-INFX410<br />
!<br />
!Mon<br />
!Tue<br />
!Wed<br />
!Thu<br />
!Fri<br />
|-<br />
!Week 46<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
|-<br />
!Week 47<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
|-<br />
!Week 48<br />
| style="background: white;" |Obligatory<br />
home assignment<br />
| style="background: white;" |Obligatory<br />
home assignment<br />
| style="background: white;" |Obligatory<br />
home assignment<br />
| style="background: white;" |Obligatory<br />
home assignment<br />
| style="background: white;" |Hand in<br />
home assignment<br />
|-<br />
!Week 49<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Exam start<br />
(home assignment)<br />
|-<br />
!Week 50<br />
| style="background: white;" |Exam<br />
(home assignment)<br />
| style="background: white;" |Exam<br />
(home assignment)<br />
| style="background: white;" |Exam<br />
(home assignment)<br />
| style="background: white;" |Exam<br />
(home assignment)<br />
| style="background: white;" |Exam end<br />
(home assignment)<br />
|}<br />
<br />
=== Computers/laptops, internet access, and UiO user account ===<br />
'''All students are strongly encouraged to bring their own laptops.''' <br />
<br />
* It should be possible to connect the computer to the UiO wireless network (probably Eduroam)<br />
* You must have a root/administrator password that gives you access to installing new software on the computer<br />
* Please bring an '''external mouse''', and do not rely on touchpad/trackpad only<br />
* You must have a '''valid UiO user account''' and must be able to log onto a computer on the UiO network<br />
* Instructions on how to find your username and get a new password can be found [http://www.uio.no/english/services/it/username-password/no-password.html here]. '''''To get a UiO username/password at the UiO helpdesk you need valid ID.'''''<br />
'''''If you are struggling with anything of the above, in particular<nowiki> </nowiki>if you have forgotten your UiO user name/password or you do not have one, you must contact Jon (see [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410_2016#Contacts contact details]) as soon as possible, and at least one week before the start of the course.'''''<br />
<br />
On the first day of the course we will set up your laptop so that<nowiki> </nowiki>it can be used for the exercises/tutorials, the home exam and hopefully<nowiki> </nowiki>in your future work. How to get a reasonable setup is described [https://wiki.uio.no/projects/clsi/index.php/Laptop_Setup here].<br />
<br />
If you already are an expert programmer and Unix guru, go [https://wiki.uio.no/projects/clsi/index.php/Biology_for_Informatics here].<br />
<br />
=== Time and place (Rooms) ===<br />
The teaching starts at 09:15 and we will end at latest 16:00. Most of the teaching will take place in room 4613 on the 4th floor of Biology Buiding (Kristine Bonnevies Hus, KB). Some days we have to change rooms so check the detailed program regularly. <br />
<br />
=== Detailed program ===<br />
<br />
The times listed here are only tentative and may likely change. We will mix in small breaks here and there and try to have a lunch break between 12:00 - 13:00.<br />
{| class="wikitable"<br />
|+Tentative schedule for MBV-INFX410 2017<br />
!Week<br />
!Monday<br />
!Tuesday<br />
!Wednesday<br />
!Thursday<br />
!Friday<br />
|-<br />
|<b>46</b><br />
| style="background: white; text-align: center;" |Nov 13<br />
| style="background: white; text-align: center;" |Nov 14<br />
| style="background: white; text-align: center;" |Nov 15<br />
| style="background: white; text-align: center;" |Nov 16<br />
| style="background: white; text-align: center;" |Nov 17<br />
|-<br />
|<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613''' <br />
09:15 - 10:00 <br />
<br />
Course introduction ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-13_01_Introduction.pdf lecture]) <br />
<br />
10:15 - 11:00 <br />
<br />
<br />
Sequence databases ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-13_02_Databases.pdf lecture])<br />
<br />
11:15 - 12:00<br />
<br />
<br />
Basic Unix ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-13_03_Basic_Unix.pdf lecture]) <br />
<br />
<br />
12:00 - 13:00 <br />
<br />
Lunch <br />
<br />
<br />
13:15 - 14:00 <br />
<br />
Setting up laptops <br />
<br />
<br />
14:15 - 16:00 <br />
<br />
Basic Unix ([http://folk.uio.no/jonbra/MBV-INF4410_2017/exercises/2017-11-13_UNIXBasics-exercise.pdf exercises]) <br />
| style="background: #cefdce; vertical-align: top;" |'''Room 3213''' <br />
09:15 - 11:00 <br />
<br />
Genome browsers ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-14_01_GenomeBrowsers.pdf lecture] / [http://folk.uio.no/jonbra/MBV-INF4410_2017/exercises/2017-11-14-01_UCSC.pdf exercises]) and Jalview ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-14_02_JalView.pdf lecture]) <br />
<br />
<br />
11:15 - 12:00<br />
<br />
Working with sequences <br />
<br />
and databases ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-14_03_Working_with_sequences.pdf lecture])<br />
<br />
<br />
12:00 - 13:00<br />
<br />
Lunch <br />
<br />
<br />
13:15 - 16:00<br />
<br />
Applied sequence bioinformatics ([http://folk.uio.no/jonbra/MBV-INF4410_2017/exercises/2017-11-14-02_Applied_seq_bioinf.pdf exercises]) <br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 12:00<br />
<br />
UiO LifePortal ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-15_01_Lifeportal_course.pdf lecture])<br />
<br />
<br />
12:00 - 13:00<br />
<br />
Lunch <br />
<br />
<br />
13:15 - 14:00 <br />
<br />
More Unix ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-15_02_MoreUnix.pdf lecture]) <br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4424'''<br />
09:15 - 16:00 <br />
<br />
[[Lectures / exercises|Python workshop]]<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''NB! Notice room change: Seminarrom U30 Helga Enghs Hus (see [https://wiki.uio.no/projects/clsi/index.php?title=MBV-INFX410_2017#Messages Messages])'''<br />
<br />
09:15 - 16:00<br />
<br />
[[Lectures / exercises|Python workshop]]<br />
<br />
|-<br />
|<b>47</b><br />
| style="background: white; text-align: center;" |Nov 20<br />
| style="background: white; text-align: center;" |Nov 21<br />
| style="background: white; text-align: center;" |Nov 22<br />
| style="background: white; text-align: center;" |Nov 23<br />
| style="background: white; text-align: center;" |Nov 24<br />
|-<br />
|<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Sequence searching and alignments ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-20_mbvinf4410-bioinf.pdf lecture] / [http://folk.uio.no/jonbra/MBV-INF4410_2017/exercises/2017-11-20_AlignmentsAndMSAs.pdf exercises]) <br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
[[Structural Bioinformatics 2017|Structural Bioinformatics]]<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
[[Structural Bioinformatics 2017|Structural Bioinformatics]]<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4424'''<br />
<br />
09:15 - 12:00<br />
<br />
Docking and drug discovery<br />
<br />
<br />
13:15 - 14:00<br />
<br />
Practical Unix/Python<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 2203a'''<br />
<br />
09:15 - 12:00<br />
<br />
"Catch-up" / "Snublegruppe" (You can ask questions from the first two weeks)<br />
<br />
<span style="color:red">Hand out oblig</span><br />
<br />
|-<br />
|<b>48</b><br />
| style="background: white; text-align: center;" |Nov 27<br />
| style="background: white; text-align: center;" |Nov 28<br />
| style="background: white; text-align: center;" |Nov 29<br />
| style="background: white; text-align: center;" |Nov 30<br />
| style="background: white; text-align: center;" |Dec 1<br />
|-<br />
|<br />
| style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment<br />
| style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment<br />
| style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment<br />
| style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment<br />
| style="background: #87CEFA; vertical-align: top;" |Hand in home assignment<br />
|-<br />
|<b>49</b><br />
| style="background: white; text-align: center;" |Dec 4<br />
| style="background: white; text-align: center;" |Dec 5<br />
| style="background: white; text-align: center;" |Dec 6<br />
| style="background: white; text-align: center;" |Dec 7<br />
| style="background: white; text-align: center;" |Dec 8<br />
|-<br />
|<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Next Generation Sequencing & variant calling<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Introduction to R<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Analysing transcriptome data using R<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Analysing transcriptome data using R<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Statistical epigenomics<br />
<br />
<span style="color:red">Hand out exam</span><br />
<br />
|-<br />
|<b>50</b><br />
| style="background: white; text-align: center;" |Dec 11<br />
| style="background: white; text-align: center;" |Dec 12<br />
| style="background: white; text-align: center;" |Dec 13<br />
| style="background: white; text-align: center;" |Dec 14<br />
| style="background: white; text-align: center;" |Dec 15<br />
|-<br />
|<br />
| style="background: salmon; vertical-align: top;" |Home exam<br />
| style="background: salmon; vertical-align: top;" |Home exam<br />
| style="background: salmon; vertical-align: top;" |Home exam<br />
| style="background: salmon; vertical-align: top;" |Home exam<br />
| style="background: salmon; vertical-align: top;" |Hand in exam<br />
|}<br />
<br />
=== Recommended reading material / curriculum ===<br />
The curriculum comprises all lectures, lecture handouts and exercises, in addition to the articles listed below:<br />
*J. R. A. Hutchins, "Genomic Database Searching", in [https://link.springer.com/protocol/10.1007%2F978-1-4939-6622-6_10 Bioinformatics pp 225-269. Springer (2017)].<br />
*R.F. Service, "Biology's dry future", [http://dx.doi.org/10.1126/science.342.6155.186 Science <b>342</b>, 186 (2013)]<br />
*EMBnet, [http://www.embnet.org/sites/default/files/quickguides/guideUNIX.pdf A Quick Guide to UNIX]<br />
*NCBI Resource Coordinators, "Database resources of the National Center for Biotechnology Information", [http://dx.doi.org/10.1093/nar/gku1130 Nucleic Acids Res. <b>43</b>, D6 (2015)]<br />
*The UniProt Consortium, "UniProt: a hub for protein information", [http://dx.doi.org/10.1093/nar/gku989 Nucleic Acids Res. <b>43</b>, D204 (2015)]<br />
*P. Flicek ''et al.'', "Ensembl 2015", [http://dx.doi.org/10.1093/nar/gku1010 Nucleic Acids Res. <b>43</b>, D662 (2015)]<br />
*P.W. Rose ''et al.'', "The RCSB Protein Data Bank: new resources for research and education", [http://dx.doi.org/10.1093/nar/gks1200 Nucleic Acids Res. <b>41</b>, D475 (2013)]<br />
*P.J.A. Cock ''et al.'', "Biopython: freely available Python tools for computational molecular biology and bioinformatics", [http://dx.doi.org/10.1093/bioinformatics/btp163 Bioinformatics <b>25</b>, 1422 (2009)]<br />
*A.M. Waterhouse ''et al''., "Jalview Version 2--a multiple sequence alignment editor and analysis workbench", [http://dx.doi.org/10.1093/bioinformatics/btp033 Bioinformatics <b>25</b>, 1189 (2009)]<br />
*G.M. Boratyn ''et al.'', "BLAST: a more efficient report with usability improvements", [http://dx.doi.org/10.1093/nar/gkt282 Nucleic Acids Res. <b>41</b>, W29 (2013)]<br />
*J.-F. Taly ''et al.'', "Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures", [http://dx.doi.org/10.1038/nprot.2011.393 Nat. Protoc. <b>6</b>, 1669 (2011)]<br />
*L. Bordoli ''et al.'', "Protein structure homology modeling using SWISS-MODEL workspace", [http://dx.doi.org/10.1038/nprot.2008.197 Nat. Protoc. <b>4</b>, 1 (2009)]<br />
*J. Carlsson ''et al.'', "Ligand discovery from a dopamine D<sub>3</sub> receptor homology model and crystal structure", [http://dx.doi.org/10.1038/nchembio.662 Nat. Chem. Biol. <b>7</b>, 769 (2011)]<br />
*R.M. Kuhn ''et al.'', "The UCSC genome browser and associated tools", [http://dx.doi.org/10.1093/bib/bbs038 Brief. Bioinform. <b>14</b>, 144 (2013)]<br />
*J. Goecks ''et al''., "Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences", [http://dx.doi.org/10.1186/gb-2010-11-8-r86 Genome Biol. <b>11</b>, R86 (2010)]<br />
*G.K. Sandve ''et al.'', "Ten Simple Rules for reproducible computational Research", [http://dx.doi.org/10.1371/journal.pcbi.1003285 PLoS Comput. Biol. <b>9</b>, e1003285 (2013)]<br />
*G.K. Sandve ''et al.'', "The Genomic HyperBrowser: an analysis web server for genome-scale data", [http://dx.doi.org/10.1093/nar/gkt342 Nucleic Acids Res. <b>41</b>, W133 (2013)]<br />
*M.L. Mertzker, "Sequencing technologies - the next generation", [http://dx.doi.org/10.1038/nrg2626 Nat. Rev. Genet. <b>11</b>, 31 (2010)]<br />
*A. Altmann ''et al.'', "A beginners guide to SNP calling from high-throughput DNA-sequencing data", [http://dx.doi.org/10.1007/s00439-012-1213-z Hum. Genet. <b>131</b>, 1541 (2012)]<br />
*N. Nagarajan & M. Pop, "Sequence assembly demystified", [http://dx.doi.org/10.1038/nrg3367 Nat. Rev. Genet. <b>14</b>, 157 (2013)]<br />
*D.W. Huang ''et al.'', "Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources", [http://dx.doi.org/10.1038/nprot.2008.211 Nat. Protoc. <b>4</b>, 44 (2009)]<br />
<br />
Other good articles (''not ''curriculum)<br />
*Z. Yang & B. Rannala, "Molecular phylogenetics: principles and practice", [http://dx.doi.org/doi:10.1038/nrg3186 Nat. Rev. Genet. <b>13</b>, 303 (2012)]<br />
<br />
=== Contacts ===<br />
Jon Bråte (Course coordinator) - e-mail: jon.brate@ibv.uio.no, phone: +47 922 44 582<br />
<br />
Torill Rørtveit (Course administrator, registration) - e-mail: torill.rortveit@ibv.uio.no<br />
<br />
=== Useful links ===<br />
<br />
[http://swcarpentry.github.io/shell-novice/reference/ Very useful reference guide on the Unix shell (created by Software Carpentry)]<br />
<br />
Trond Hasle Amundsen's [http://www.uio.no/tjenester/it/maskin/linux/hjelp/tips/guide.html Local guide to Linux and Unix]<br />
<br />
[https://github.com/EbookFoundation/free-programming-books/blob/master/free-programming-books.md#python Tons of free e-books on Python]<br />
<br />
EMBnet [http://www.embnet.org/sites/default/files/quickguides/guideUNIX.pdf Quick guide Unix]<br />
<br />
[https://github.com/stephenturner/oneliners Useful command line one-liners] by Stephen Turner<br />
<br />
[https://github.com/mcandre/cheatsheets/blob/master/nano.md Nano text editor cheat sheet]<br />
<br />
[https://github.com/EbookFoundation/free-programming-books/blob/master/free-programming-books.md Tons of free programming books, about anything really.]<br />
<br />
[http://www.jalview.org Jalview] and Jalview [http://www.jalview.org/refcard.pdf refcard]<br />
<br />
UCSC [http://genome.ucsc.edu Genome browser]<br />
<br />
Free [http://www.openhelix.com/ucsc UCSC Genome browser tutorial]&nbsp;&nbsp; from OpenHelix<br />
<br />
Portal to [http://galaxyproject.org Galaxy]<br />
<br />
[http://wiki.galaxyproject.org/Learn Galaxy 101 and other Galaxy screencasts/tutorials]<br />
<br />
UiO [http://lifeportal.uio.no Lifeportal] and more [http://www.uio.no/english/services/it/research/hpc/lifeportal information on the Lifeportal]<br />
<br />
The Genomic [http://hyperbrowser.uio.no/hb HyperBrowser]<br />
<br />
[http://bioinformatics.ca/links_directory Links Directory] from bioinformatics.ca<br />
<br />
The 2017 Nucleic Acids Research [https://academic.oup.com/nar/issue/45/D1 Database Issue]<br />
<br />
The 2015 Nucleic Acids Research [https://academic.oup.com/nar/issue/45/W1 Web Server Issue]<br />
<br />
UiO and OUS [http://core.rr-research.no/bioinformatics Bioinformatics Core Facility]</div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=MBV-INFX410_2017&diff=1916MBV-INFX410 20172017-11-20T10:14:50Z<p>Jonkl@uio.no: /* Messages */</p>
<hr />
<div>== [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410 Bioinformatics for Molecular Biology] - 2017 ==<br />
=== Messages ===<br />
* '''20 nov: NB! In order to get everybody at an acceptable level in Structural Biology, before we start the Structural Bioinformatics lectures/exercises on Tuesday Nov 21, there will be a Structural Biology Review lecture in the morning. See handouts/slides [[Structural Bioinformatics 2017|here]]. Take a look at these and decide if you need to follow the Structural Biology Review lecture. If you decide you do not need this, come at 10:45 on Tuesday Nov 21.'''<br />
* '''16 nov: NB! Notice room change for Python workshop 17 nov: Seminarrom U30 in [https://www.uio.no/om/finn-fram/omrader/blindern/bl20/ Helga Enghs Hus.] Go in the main door and down one floor.'''<br />
* '''''All students must be present at the start of the course, on November 13 at 09:15 in room 4613 in [https://www.uio.no/om/finn-fram/omrader/blindern/bl18/ Kristine Bonnevies (KB) Hus (biology building)]. Missing students will not be allowed to follow the course or to take the exam. If you for some reason are not able to attend, please contact Jon Bråte (See [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410_2016#Contacts contact details] below).'''''<br />
* '''All students must bring their own laptops, including an external mouse.'''<br />
* '''You need to install the following software on your laptops (we will help you with this):'''<br />
** Anaconda (https://www.anaconda.com/download/)<br />
** PyMOL (https://www.pymol.org/)<br />
** JalView Desktop (http://www.jalview.org/) - could maybe also run by pressing the "Launch Jalview Desktop" button<br />
** PuTTY (http://www.putty.org/)<br />
** R (https://www.r-project.org/) '''Install''' '''inside Anaconda instead''' <br />
** RStudio (https://www.rstudio.com/) '''Install''' '''inside Anaconda instead'''<br />
**'''Optional:''' It could also be wise to have Fetch (for Mac) (http://fetchsoftworks.com/) and WinSCP (Windows) ([https://winscp.net/eng/index.php https://winscp.net/eng/index.php)]<br />
<br />
=== Course information ===<br />
This is the wiki for the courses [http://www.uio.no/studier/emner/matnat/ibv/MBV-INF4410 MBV-INF4410] and [http://www.uio.no/studier/emner/matnat/ibv/MBV-INF9410 MBV-INF9410] offered by the Department of Biosciences (IBV) at the University of Oslo (UiO). Both MBV-INF4410 (M.Sc. level) and MBV-INF9410 (Ph.D. level) are 10 study point courses. <br />
<br />
The course consists of five weeks of lectures, exercises, obligatory assignments, and a take-home exam (one week). Obligatory assignments must be completed and approved before the exam and in the same semester. An additional, limited, oral examination may be arranged in cases where this is necessary for the student evaluation. The course is open also for non-UiO students. It is only necessary to be physically present in Oslo for certain parts of the course.<br />
{| class="wikitable"<br />
|+General schedule for MBV-INFX410<br />
!<br />
!Mon<br />
!Tue<br />
!Wed<br />
!Thu<br />
!Fri<br />
|-<br />
!Week 46<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
|-<br />
!Week 47<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
|-<br />
!Week 48<br />
| style="background: white;" |Obligatory<br />
home assignment<br />
| style="background: white;" |Obligatory<br />
home assignment<br />
| style="background: white;" |Obligatory<br />
home assignment<br />
| style="background: white;" |Obligatory<br />
home assignment<br />
| style="background: white;" |Hand in<br />
home assignment<br />
|-<br />
!Week 49<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Exam start<br />
(home assignment)<br />
|-<br />
!Week 50<br />
| style="background: white;" |Exam<br />
(home assignment)<br />
| style="background: white;" |Exam<br />
(home assignment)<br />
| style="background: white;" |Exam<br />
(home assignment)<br />
| style="background: white;" |Exam<br />
(home assignment)<br />
| style="background: white;" |Exam end<br />
(home assignment)<br />
|}<br />
<br />
=== Computers/laptops, internet access, and UiO user account ===<br />
'''All students are strongly encouraged to bring their own laptops.''' <br />
<br />
* It should be possible to connect the computer to the UiO wireless network (probably Eduroam)<br />
* You must have a root/administrator password that gives you access to installing new software on the computer<br />
* Please bring an '''external mouse''', and do not rely on touchpad/trackpad only<br />
* You must have a '''valid UiO user account''' and must be able to log onto a computer on the UiO network<br />
* Instructions on how to find your username and get a new password can be found [http://www.uio.no/english/services/it/username-password/no-password.html here]. '''''To get a UiO username/password at the UiO helpdesk you need valid ID.'''''<br />
'''''If you are struggling with anything of the above, in particular<nowiki> </nowiki>if you have forgotten your UiO user name/password or you do not have one, you must contact Jon (see [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410_2016#Contacts contact details]) as soon as possible, and at least one week before the start of the course.'''''<br />
<br />
On the first day of the course we will set up your laptop so that<nowiki> </nowiki>it can be used for the exercises/tutorials, the home exam and hopefully<nowiki> </nowiki>in your future work. How to get a reasonable setup is described [https://wiki.uio.no/projects/clsi/index.php/Laptop_Setup here].<br />
<br />
If you already are an expert programmer and Unix guru, go [https://wiki.uio.no/projects/clsi/index.php/Biology_for_Informatics here].<br />
<br />
=== Time and place (Rooms) ===<br />
The teaching starts at 09:15 and we will end at latest 16:00. Most of the teaching will take place in room 4613 on the 4th floor of Biology Buiding (Kristine Bonnevies Hus, KB). Some days we have to change rooms so check the detailed program regularly. <br />
<br />
=== Detailed program ===<br />
<br />
The times listed here are only tentative and may likely change. We will mix in small breaks here and there and try to have a lunch break between 12:00 - 13:00.<br />
{| class="wikitable"<br />
|+Tentative schedule for MBV-INFX410 2017<br />
!Week<br />
!Monday<br />
!Tuesday<br />
!Wednesday<br />
!Thursday<br />
!Friday<br />
|-<br />
|<b>46</b><br />
| style="background: white; text-align: center;" |Nov 13<br />
| style="background: white; text-align: center;" |Nov 14<br />
| style="background: white; text-align: center;" |Nov 15<br />
| style="background: white; text-align: center;" |Nov 16<br />
| style="background: white; text-align: center;" |Nov 17<br />
|-<br />
|<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613''' <br />
09:15 - 10:00 <br />
<br />
Course introduction ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-13_01_Introduction.pdf lecture]) <br />
<br />
10:15 - 11:00 <br />
<br />
<br />
Sequence databases ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-13_02_Databases.pdf lecture])<br />
<br />
11:15 - 12:00<br />
<br />
<br />
Basic Unix ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-13_03_Basic_Unix.pdf lecture]) <br />
<br />
<br />
12:00 - 13:00 <br />
<br />
Lunch <br />
<br />
<br />
13:15 - 14:00 <br />
<br />
Setting up laptops <br />
<br />
<br />
14:15 - 16:00 <br />
<br />
Basic Unix ([http://folk.uio.no/jonbra/MBV-INF4410_2017/exercises/2017-11-13_UNIXBasics-exercise.pdf exercises]) <br />
| style="background: #cefdce; vertical-align: top;" |'''Room 3213''' <br />
09:15 - 11:00 <br />
<br />
Genome browsers ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-14_01_GenomeBrowsers.pdf lecture] / [http://folk.uio.no/jonbra/MBV-INF4410_2017/exercises/2017-11-14-01_UCSC.pdf exercises]) and Jalview ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-14_02_JalView.pdf lecture]) <br />
<br />
<br />
11:15 - 12:00<br />
<br />
Working with sequences <br />
<br />
and databases ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-14_03_Working_with_sequences.pdf lecture])<br />
<br />
<br />
12:00 - 13:00<br />
<br />
Lunch <br />
<br />
<br />
13:15 - 16:00<br />
<br />
Applied sequence bioinformatics ([http://folk.uio.no/jonbra/MBV-INF4410_2017/exercises/2017-11-14-02_Applied_seq_bioinf.pdf exercises]) <br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 12:00<br />
<br />
UiO LifePortal ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-15_01_Lifeportal_course.pdf lecture])<br />
<br />
<br />
12:00 - 13:00<br />
<br />
Lunch <br />
<br />
<br />
13:15 - 14:00 <br />
<br />
More Unix ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-15_02_MoreUnix.pdf lecture]) <br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4424'''<br />
09:15 - 16:00 <br />
<br />
[[Lectures / exercises|Python workshop]]<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''NB! Notice room change: Seminarrom U30 Helga Enghs Hus (see [https://wiki.uio.no/projects/clsi/index.php?title=MBV-INFX410_2017#Messages Messages])'''<br />
<br />
09:15 - 16:00<br />
<br />
[[Lectures / exercises|Python workshop]]<br />
<br />
|-<br />
|<b>47</b><br />
| style="background: white; text-align: center;" |Nov 20<br />
| style="background: white; text-align: center;" |Nov 21<br />
| style="background: white; text-align: center;" |Nov 22<br />
| style="background: white; text-align: center;" |Nov 23<br />
| style="background: white; text-align: center;" |Nov 24<br />
|-<br />
|<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Sequence searching and alignments ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-20_mbvinf4410-bioinf.pdf lecture] / [http://folk.uio.no/jonbra/MBV-INF4410_2017/exercises/2017-11-20_AlignmentsAndMSAs.pdf exercises]) <br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
[[Structural Bioinformatics 2017|Structural Bioinformatics]]<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
[[Structural Bioinformatics 2017|Structural Bioinformatics]]<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4424'''<br />
<br />
09:15 - 12:00<br />
<br />
Docking and drug discovery<br />
<br />
<br />
13:15 - 14:00<br />
<br />
Practical Unix/Python<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 2203a'''<br />
<br />
09:15 - 12:00<br />
<br />
"Catch-up" / "Snublegruppe" (You can ask questions from the first two weeks)<br />
<br />
<span style="color:red">Hand out oblig</span><br />
<br />
|-<br />
|<b>48</b><br />
| style="background: white; text-align: center;" |Nov 27<br />
| style="background: white; text-align: center;" |Nov 28<br />
| style="background: white; text-align: center;" |Nov 29<br />
| style="background: white; text-align: center;" |Nov 30<br />
| style="background: white; text-align: center;" |Dec 1<br />
|-<br />
|<br />
| style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment<br />
| style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment<br />
| style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment<br />
| style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment<br />
| style="background: #87CEFA; vertical-align: top;" |Hand in home assignment<br />
|-<br />
|<b>49</b><br />
| style="background: white; text-align: center;" |Dec 4<br />
| style="background: white; text-align: center;" |Dec 5<br />
| style="background: white; text-align: center;" |Dec 6<br />
| style="background: white; text-align: center;" |Dec 7<br />
| style="background: white; text-align: center;" |Dec 8<br />
|-<br />
|<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Next Generation Sequencing & variant calling<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Introduction to R<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Analysing transcriptome data using R<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Analysing transcriptome data using R<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Statistical epigenomics<br />
<br />
<span style="color:red">Hand out exam</span><br />
<br />
|-<br />
|<b>50</b><br />
| style="background: white; text-align: center;" |Dec 11<br />
| style="background: white; text-align: center;" |Dec 12<br />
| style="background: white; text-align: center;" |Dec 13<br />
| style="background: white; text-align: center;" |Dec 14<br />
| style="background: white; text-align: center;" |Dec 15<br />
|-<br />
|<br />
| style="background: salmon; vertical-align: top;" |Home exam<br />
| style="background: salmon; vertical-align: top;" |Home exam<br />
| style="background: salmon; vertical-align: top;" |Home exam<br />
| style="background: salmon; vertical-align: top;" |Home exam<br />
| style="background: salmon; vertical-align: top;" |Hand in exam<br />
|}<br />
<br />
=== Recommended reading material / curriculum ===<br />
The curriculum comprises all lectures, lecture handouts and exercises, in addition to the articles listed below:<br />
*J. R. A. Hutchins, "Genomic Database Searching", in [https://link.springer.com/protocol/10.1007%2F978-1-4939-6622-6_10 Bioinformatics pp 225-269. Springer (2017)].<br />
*R.F. Service, "Biology's dry future", [http://dx.doi.org/10.1126/science.342.6155.186 Science <b>342</b>, 186 (2013)]<br />
*EMBnet, [http://www.embnet.org/sites/default/files/quickguides/guideUNIX.pdf A Quick Guide to UNIX]<br />
*NCBI Resource Coordinators, "Database resources of the National Center for Biotechnology Information", [http://dx.doi.org/10.1093/nar/gku1130 Nucleic Acids Res. <b>43</b>, D6 (2015)]<br />
*The UniProt Consortium, "UniProt: a hub for protein information", [http://dx.doi.org/10.1093/nar/gku989 Nucleic Acids Res. <b>43</b>, D204 (2015)]<br />
*P. Flicek ''et al.'', "Ensembl 2015", [http://dx.doi.org/10.1093/nar/gku1010 Nucleic Acids Res. <b>43</b>, D662 (2015)]<br />
*P.W. Rose ''et al.'', "The RCSB Protein Data Bank: new resources for research and education", [http://dx.doi.org/10.1093/nar/gks1200 Nucleic Acids Res. <b>41</b>, D475 (2013)]<br />
*P.J.A. Cock ''et al.'', "Biopython: freely available Python tools for computational molecular biology and bioinformatics", [http://dx.doi.org/10.1093/bioinformatics/btp163 Bioinformatics <b>25</b>, 1422 (2009)]<br />
*A.M. Waterhouse ''et al''., "Jalview Version 2--a multiple sequence alignment editor and analysis workbench", [http://dx.doi.org/10.1093/bioinformatics/btp033 Bioinformatics <b>25</b>, 1189 (2009)]<br />
*G.M. Boratyn ''et al.'', "BLAST: a more efficient report with usability improvements", [http://dx.doi.org/10.1093/nar/gkt282 Nucleic Acids Res. <b>41</b>, W29 (2013)]<br />
*J.-F. Taly ''et al.'', "Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures", [http://dx.doi.org/10.1038/nprot.2011.393 Nat. Protoc. <b>6</b>, 1669 (2011)]<br />
*L. Bordoli ''et al.'', "Protein structure homology modeling using SWISS-MODEL workspace", [http://dx.doi.org/10.1038/nprot.2008.197 Nat. Protoc. <b>4</b>, 1 (2009)]<br />
*J. Carlsson ''et al.'', "Ligand discovery from a dopamine D<sub>3</sub> receptor homology model and crystal structure", [http://dx.doi.org/10.1038/nchembio.662 Nat. Chem. Biol. <b>7</b>, 769 (2011)]<br />
*R.M. Kuhn ''et al.'', "The UCSC genome browser and associated tools", [http://dx.doi.org/10.1093/bib/bbs038 Brief. Bioinform. <b>14</b>, 144 (2013)]<br />
*J. Goecks ''et al''., "Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences", [http://dx.doi.org/10.1186/gb-2010-11-8-r86 Genome Biol. <b>11</b>, R86 (2010)]<br />
*G.K. Sandve ''et al.'', "Ten Simple Rules for reproducible computational Research", [http://dx.doi.org/10.1371/journal.pcbi.1003285 PLoS Comput. Biol. <b>9</b>, e1003285 (2013)]<br />
*G.K. Sandve ''et al.'', "The Genomic HyperBrowser: an analysis web server for genome-scale data", [http://dx.doi.org/10.1093/nar/gkt342 Nucleic Acids Res. <b>41</b>, W133 (2013)]<br />
*M.L. Mertzker, "Sequencing technologies - the next generation", [http://dx.doi.org/10.1038/nrg2626 Nat. Rev. Genet. <b>11</b>, 31 (2010)]<br />
*A. Altmann ''et al.'', "A beginners guide to SNP calling from high-throughput DNA-sequencing data", [http://dx.doi.org/10.1007/s00439-012-1213-z Hum. Genet. <b>131</b>, 1541 (2012)]<br />
*N. Nagarajan & M. Pop, "Sequence assembly demystified", [http://dx.doi.org/10.1038/nrg3367 Nat. Rev. Genet. <b>14</b>, 157 (2013)]<br />
*D.W. Huang ''et al.'', "Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources", [http://dx.doi.org/10.1038/nprot.2008.211 Nat. Protoc. <b>4</b>, 44 (2009)]<br />
<br />
Other good articles (''not ''curriculum)<br />
*Z. Yang & B. Rannala, "Molecular phylogenetics: principles and practice", [http://dx.doi.org/doi:10.1038/nrg3186 Nat. Rev. Genet. <b>13</b>, 303 (2012)]<br />
<br />
=== Contacts ===<br />
Jon Bråte (Course coordinator) - e-mail: jon.brate@ibv.uio.no, phone: +47 922 44 582<br />
<br />
Torill Rørtveit (Course administrator, registration) - e-mail: torill.rortveit@ibv.uio.no<br />
<br />
=== Useful links ===<br />
<br />
[http://swcarpentry.github.io/shell-novice/reference/ Very useful reference guide on the Unix shell (created by Software Carpentry)]<br />
<br />
Trond Hasle Amundsen's [http://www.uio.no/tjenester/it/maskin/linux/hjelp/tips/guide.html Local guide to Linux and Unix]<br />
<br />
[https://github.com/EbookFoundation/free-programming-books/blob/master/free-programming-books.md#python Tons of free e-books on Python]<br />
<br />
EMBnet [http://www.embnet.org/sites/default/files/quickguides/guideUNIX.pdf Quick guide Unix]<br />
<br />
[https://github.com/stephenturner/oneliners Useful command line one-liners] by Stephen Turner<br />
<br />
[https://github.com/mcandre/cheatsheets/blob/master/nano.md Nano text editor cheat sheet]<br />
<br />
[https://github.com/EbookFoundation/free-programming-books/blob/master/free-programming-books.md Tons of free programming books, about anything really.]<br />
<br />
[http://www.jalview.org Jalview] and Jalview [http://www.jalview.org/refcard.pdf refcard]<br />
<br />
UCSC [http://genome.ucsc.edu Genome browser]<br />
<br />
Free [http://www.openhelix.com/ucsc UCSC Genome browser tutorial]&nbsp;&nbsp; from OpenHelix<br />
<br />
Portal to [http://galaxyproject.org Galaxy]<br />
<br />
[http://wiki.galaxyproject.org/Learn Galaxy 101 and other Galaxy screencasts/tutorials]<br />
<br />
UiO [http://lifeportal.uio.no Lifeportal] and more [http://www.uio.no/english/services/it/research/hpc/lifeportal information on the Lifeportal]<br />
<br />
The Genomic [http://hyperbrowser.uio.no/hb HyperBrowser]<br />
<br />
[http://bioinformatics.ca/links_directory Links Directory] from bioinformatics.ca<br />
<br />
The 2017 Nucleic Acids Research [https://academic.oup.com/nar/issue/45/D1 Database Issue]<br />
<br />
The 2015 Nucleic Acids Research [https://academic.oup.com/nar/issue/45/W1 Web Server Issue]<br />
<br />
UiO and OUS [http://core.rr-research.no/bioinformatics Bioinformatics Core Facility]</div>Jonkl@uio.nohttps://wiki.uio.no/projects/clsi/index.php?title=MBV-INFX410_2017&diff=1915MBV-INFX410 20172017-11-20T10:13:05Z<p>Jonkl@uio.no: /* Bioinformatics for Molecular Biology - 2017 */</p>
<hr />
<div>== [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410 Bioinformatics for Molecular Biology] - 2017 ==<br />
=== Messages ===<br />
* '''20 nov: NB! In order to get everybody at an acceptable level in Structural Biology, before we start the Structural Bioinformatics lectures/exercises on Tuesday Nov 21, there will be a Structural Biology Review lecture in the morning. See handouts/slides [[Structural Bioinformatics 2017|here]] '''<br />
* '''16 nov: NB! Notice room change for Python workshop 17 nov: Seminarrom U30 in [https://www.uio.no/om/finn-fram/omrader/blindern/bl20/ Helga Enghs Hus.] Go in the main door and down one floor.'''<br />
* '''''All students must be present at the start of the course, on November 13 at 09:15 in room 4613 in [https://www.uio.no/om/finn-fram/omrader/blindern/bl18/ Kristine Bonnevies (KB) Hus (biology building)]. Missing students will not be allowed to follow the course or to take the exam. If you for some reason are not able to attend, please contact Jon Bråte (See [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410_2016#Contacts contact details] below).'''''<br />
* '''All students must bring their own laptops, including an external mouse.'''<br />
* '''You need to install the following software on your laptops (we will help you with this):'''<br />
** Anaconda (https://www.anaconda.com/download/)<br />
** PyMOL (https://www.pymol.org/)<br />
** JalView Desktop (http://www.jalview.org/) - could maybe also run by pressing the "Launch Jalview Desktop" button<br />
** PuTTY (http://www.putty.org/)<br />
** R (https://www.r-project.org/) '''Install''' '''inside Anaconda instead''' <br />
** RStudio (https://www.rstudio.com/) '''Install''' '''inside Anaconda instead'''<br />
**'''Optional:''' It could also be wise to have Fetch (for Mac) (http://fetchsoftworks.com/) and WinSCP (Windows) ([https://winscp.net/eng/index.php https://winscp.net/eng/index.php)]<br />
<br />
=== Course information ===<br />
This is the wiki for the courses [http://www.uio.no/studier/emner/matnat/ibv/MBV-INF4410 MBV-INF4410] and [http://www.uio.no/studier/emner/matnat/ibv/MBV-INF9410 MBV-INF9410] offered by the Department of Biosciences (IBV) at the University of Oslo (UiO). Both MBV-INF4410 (M.Sc. level) and MBV-INF9410 (Ph.D. level) are 10 study point courses. <br />
<br />
The course consists of five weeks of lectures, exercises, obligatory assignments, and a take-home exam (one week). Obligatory assignments must be completed and approved before the exam and in the same semester. An additional, limited, oral examination may be arranged in cases where this is necessary for the student evaluation. The course is open also for non-UiO students. It is only necessary to be physically present in Oslo for certain parts of the course.<br />
{| class="wikitable"<br />
|+General schedule for MBV-INFX410<br />
!<br />
!Mon<br />
!Tue<br />
!Wed<br />
!Thu<br />
!Fri<br />
|-<br />
!Week 46<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
|-<br />
!Week 47<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
|-<br />
!Week 48<br />
| style="background: white;" |Obligatory<br />
home assignment<br />
| style="background: white;" |Obligatory<br />
home assignment<br />
| style="background: white;" |Obligatory<br />
home assignment<br />
| style="background: white;" |Obligatory<br />
home assignment<br />
| style="background: white;" |Hand in<br />
home assignment<br />
|-<br />
!Week 49<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Lectures/<br />
exercises<br />
| style="background: white;" |Exam start<br />
(home assignment)<br />
|-<br />
!Week 50<br />
| style="background: white;" |Exam<br />
(home assignment)<br />
| style="background: white;" |Exam<br />
(home assignment)<br />
| style="background: white;" |Exam<br />
(home assignment)<br />
| style="background: white;" |Exam<br />
(home assignment)<br />
| style="background: white;" |Exam end<br />
(home assignment)<br />
|}<br />
<br />
=== Computers/laptops, internet access, and UiO user account ===<br />
'''All students are strongly encouraged to bring their own laptops.''' <br />
<br />
* It should be possible to connect the computer to the UiO wireless network (probably Eduroam)<br />
* You must have a root/administrator password that gives you access to installing new software on the computer<br />
* Please bring an '''external mouse''', and do not rely on touchpad/trackpad only<br />
* You must have a '''valid UiO user account''' and must be able to log onto a computer on the UiO network<br />
* Instructions on how to find your username and get a new password can be found [http://www.uio.no/english/services/it/username-password/no-password.html here]. '''''To get a UiO username/password at the UiO helpdesk you need valid ID.'''''<br />
'''''If you are struggling with anything of the above, in particular<nowiki> </nowiki>if you have forgotten your UiO user name/password or you do not have one, you must contact Jon (see [https://wiki.uio.no/projects/clsi/index.php/MBV-INFX410_2016#Contacts contact details]) as soon as possible, and at least one week before the start of the course.'''''<br />
<br />
On the first day of the course we will set up your laptop so that<nowiki> </nowiki>it can be used for the exercises/tutorials, the home exam and hopefully<nowiki> </nowiki>in your future work. How to get a reasonable setup is described [https://wiki.uio.no/projects/clsi/index.php/Laptop_Setup here].<br />
<br />
If you already are an expert programmer and Unix guru, go [https://wiki.uio.no/projects/clsi/index.php/Biology_for_Informatics here].<br />
<br />
=== Time and place (Rooms) ===<br />
The teaching starts at 09:15 and we will end at latest 16:00. Most of the teaching will take place in room 4613 on the 4th floor of Biology Buiding (Kristine Bonnevies Hus, KB). Some days we have to change rooms so check the detailed program regularly. <br />
<br />
=== Detailed program ===<br />
<br />
The times listed here are only tentative and may likely change. We will mix in small breaks here and there and try to have a lunch break between 12:00 - 13:00.<br />
{| class="wikitable"<br />
|+Tentative schedule for MBV-INFX410 2017<br />
!Week<br />
!Monday<br />
!Tuesday<br />
!Wednesday<br />
!Thursday<br />
!Friday<br />
|-<br />
|<b>46</b><br />
| style="background: white; text-align: center;" |Nov 13<br />
| style="background: white; text-align: center;" |Nov 14<br />
| style="background: white; text-align: center;" |Nov 15<br />
| style="background: white; text-align: center;" |Nov 16<br />
| style="background: white; text-align: center;" |Nov 17<br />
|-<br />
|<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613''' <br />
09:15 - 10:00 <br />
<br />
Course introduction ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-13_01_Introduction.pdf lecture]) <br />
<br />
10:15 - 11:00 <br />
<br />
<br />
Sequence databases ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-13_02_Databases.pdf lecture])<br />
<br />
11:15 - 12:00<br />
<br />
<br />
Basic Unix ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-13_03_Basic_Unix.pdf lecture]) <br />
<br />
<br />
12:00 - 13:00 <br />
<br />
Lunch <br />
<br />
<br />
13:15 - 14:00 <br />
<br />
Setting up laptops <br />
<br />
<br />
14:15 - 16:00 <br />
<br />
Basic Unix ([http://folk.uio.no/jonbra/MBV-INF4410_2017/exercises/2017-11-13_UNIXBasics-exercise.pdf exercises]) <br />
| style="background: #cefdce; vertical-align: top;" |'''Room 3213''' <br />
09:15 - 11:00 <br />
<br />
Genome browsers ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-14_01_GenomeBrowsers.pdf lecture] / [http://folk.uio.no/jonbra/MBV-INF4410_2017/exercises/2017-11-14-01_UCSC.pdf exercises]) and Jalview ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-14_02_JalView.pdf lecture]) <br />
<br />
<br />
11:15 - 12:00<br />
<br />
Working with sequences <br />
<br />
and databases ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-14_03_Working_with_sequences.pdf lecture])<br />
<br />
<br />
12:00 - 13:00<br />
<br />
Lunch <br />
<br />
<br />
13:15 - 16:00<br />
<br />
Applied sequence bioinformatics ([http://folk.uio.no/jonbra/MBV-INF4410_2017/exercises/2017-11-14-02_Applied_seq_bioinf.pdf exercises]) <br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 12:00<br />
<br />
UiO LifePortal ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-15_01_Lifeportal_course.pdf lecture])<br />
<br />
<br />
12:00 - 13:00<br />
<br />
Lunch <br />
<br />
<br />
13:15 - 14:00 <br />
<br />
More Unix ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-15_02_MoreUnix.pdf lecture]) <br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4424'''<br />
09:15 - 16:00 <br />
<br />
[[Lectures / exercises|Python workshop]]<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''NB! Notice room change: Seminarrom U30 Helga Enghs Hus (see [https://wiki.uio.no/projects/clsi/index.php?title=MBV-INFX410_2017#Messages Messages])'''<br />
<br />
09:15 - 16:00<br />
<br />
[[Lectures / exercises|Python workshop]]<br />
<br />
|-<br />
|<b>47</b><br />
| style="background: white; text-align: center;" |Nov 20<br />
| style="background: white; text-align: center;" |Nov 21<br />
| style="background: white; text-align: center;" |Nov 22<br />
| style="background: white; text-align: center;" |Nov 23<br />
| style="background: white; text-align: center;" |Nov 24<br />
|-<br />
|<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Sequence searching and alignments ([http://folk.uio.no/jonbra/MBV-INF4410_2017/lectures/2017-11-20_mbvinf4410-bioinf.pdf lecture] / [http://folk.uio.no/jonbra/MBV-INF4410_2017/exercises/2017-11-20_AlignmentsAndMSAs.pdf exercises]) <br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
[[Structural Bioinformatics 2017|Structural Bioinformatics]]<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
[[Structural Bioinformatics 2017|Structural Bioinformatics]]<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4424'''<br />
<br />
09:15 - 12:00<br />
<br />
Docking and drug discovery<br />
<br />
<br />
13:15 - 14:00<br />
<br />
Practical Unix/Python<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 2203a'''<br />
<br />
09:15 - 12:00<br />
<br />
"Catch-up" / "Snublegruppe" (You can ask questions from the first two weeks)<br />
<br />
<span style="color:red">Hand out oblig</span><br />
<br />
|-<br />
|<b>48</b><br />
| style="background: white; text-align: center;" |Nov 27<br />
| style="background: white; text-align: center;" |Nov 28<br />
| style="background: white; text-align: center;" |Nov 29<br />
| style="background: white; text-align: center;" |Nov 30<br />
| style="background: white; text-align: center;" |Dec 1<br />
|-<br />
|<br />
| style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment<br />
| style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment<br />
| style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment<br />
| style="background: #87CEFA; vertical-align: top;" |Obligatory home assignment<br />
| style="background: #87CEFA; vertical-align: top;" |Hand in home assignment<br />
|-<br />
|<b>49</b><br />
| style="background: white; text-align: center;" |Dec 4<br />
| style="background: white; text-align: center;" |Dec 5<br />
| style="background: white; text-align: center;" |Dec 6<br />
| style="background: white; text-align: center;" |Dec 7<br />
| style="background: white; text-align: center;" |Dec 8<br />
|-<br />
|<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Next Generation Sequencing & variant calling<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Introduction to R<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Analysing transcriptome data using R<br />
<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Analysing transcriptome data using R<br />
| style="background: #cefdce; vertical-align: top;" |'''Room 4613'''<br />
09:15 - 16:00<br />
<br />
Statistical epigenomics<br />
<br />
<span style="color:red">Hand out exam</span><br />
<br />
|-<br />
|<b>50</b><br />
| style="background: white; text-align: center;" |Dec 11<br />
| style="background: white; text-align: center;" |Dec 12<br />
| style="background: white; text-align: center;" |Dec 13<br />
| style="background: white; text-align: center;" |Dec 14<br />
| style="background: white; text-align: center;" |Dec 15<br />
|-<br />
|<br />
| style="background: salmon; vertical-align: top;" |Home exam<br />
| style="background: salmon; vertical-align: top;" |Home exam<br />
| style="background: salmon; vertical-align: top;" |Home exam<br />
| style="background: salmon; vertical-align: top;" |Home exam<br />
| style="background: salmon; vertical-align: top;" |Hand in exam<br />
|}<br />
<br />
=== Recommended reading material / curriculum ===<br />
The curriculum comprises all lectures, lecture handouts and exercises, in addition to the articles listed below:<br />
*J. R. A. Hutchins, "Genomic Database Searching", in [https://link.springer.com/protocol/10.1007%2F978-1-4939-6622-6_10 Bioinformatics pp 225-269. Springer (2017)].<br />
*R.F. Service, "Biology's dry future", [http://dx.doi.org/10.1126/science.342.6155.186 Science <b>342</b>, 186 (2013)]<br />
*EMBnet, [http://www.embnet.org/sites/default/files/quickguides/guideUNIX.pdf A Quick Guide to UNIX]<br />
*NCBI Resource Coordinators, "Database resources of the National Center for Biotechnology Information", [http://dx.doi.org/10.1093/nar/gku1130 Nucleic Acids Res. <b>43</b>, D6 (2015)]<br />
*The UniProt Consortium, "UniProt: a hub for protein information", [http://dx.doi.org/10.1093/nar/gku989 Nucleic Acids Res. <b>43</b>, D204 (2015)]<br />
*P. Flicek ''et al.'', "Ensembl 2015", [http://dx.doi.org/10.1093/nar/gku1010 Nucleic Acids Res. <b>43</b>, D662 (2015)]<br />
*P.W. Rose ''et al.'', "The RCSB Protein Data Bank: new resources for research and education", [http://dx.doi.org/10.1093/nar/gks1200 Nucleic Acids Res. <b>41</b>, D475 (2013)]<br />
*P.J.A. Cock ''et al.'', "Biopython: freely available Python tools for computational molecular biology and bioinformatics", [http://dx.doi.org/10.1093/bioinformatics/btp163 Bioinformatics <b>25</b>, 1422 (2009)]<br />
*A.M. Waterhouse ''et al''., "Jalview Version 2--a multiple sequence alignment editor and analysis workbench", [http://dx.doi.org/10.1093/bioinformatics/btp033 Bioinformatics <b>25</b>, 1189 (2009)]<br />
*G.M. Boratyn ''et al.'', "BLAST: a more efficient report with usability improvements", [http://dx.doi.org/10.1093/nar/gkt282 Nucleic Acids Res. <b>41</b>, W29 (2013)]<br />
*J.-F. Taly ''et al.'', "Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures", [http://dx.doi.org/10.1038/nprot.2011.393 Nat. Protoc. <b>6</b>, 1669 (2011)]<br />
*L. Bordoli ''et al.'', "Protein structure homology modeling using SWISS-MODEL workspace", [http://dx.doi.org/10.1038/nprot.2008.197 Nat. Protoc. <b>4</b>, 1 (2009)]<br />
*J. Carlsson ''et al.'', "Ligand discovery from a dopamine D<sub>3</sub> receptor homology model and crystal structure", [http://dx.doi.org/10.1038/nchembio.662 Nat. Chem. Biol. <b>7</b>, 769 (2011)]<br />
*R.M. Kuhn ''et al.'', "The UCSC genome browser and associated tools", [http://dx.doi.org/10.1093/bib/bbs038 Brief. Bioinform. <b>14</b>, 144 (2013)]<br />
*J. Goecks ''et al''., "Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences", [http://dx.doi.org/10.1186/gb-2010-11-8-r86 Genome Biol. <b>11</b>, R86 (2010)]<br />
*G.K. Sandve ''et al.'', "Ten Simple Rules for reproducible computational Research", [http://dx.doi.org/10.1371/journal.pcbi.1003285 PLoS Comput. Biol. <b>9</b>, e1003285 (2013)]<br />
*G.K. Sandve ''et al.'', "The Genomic HyperBrowser: an analysis web server for genome-scale data", [http://dx.doi.org/10.1093/nar/gkt342 Nucleic Acids Res. <b>41</b>, W133 (2013)]<br />
*M.L. Mertzker, "Sequencing technologies - the next generation", [http://dx.doi.org/10.1038/nrg2626 Nat. Rev. Genet. <b>11</b>, 31 (2010)]<br />
*A. Altmann ''et al.'', "A beginners guide to SNP calling from high-throughput DNA-sequencing data", [http://dx.doi.org/10.1007/s00439-012-1213-z Hum. Genet. <b>131</b>, 1541 (2012)]<br />
*N. Nagarajan & M. Pop, "Sequence assembly demystified", [http://dx.doi.org/10.1038/nrg3367 Nat. Rev. Genet. <b>14</b>, 157 (2013)]<br />
*D.W. Huang ''et al.'', "Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources", [http://dx.doi.org/10.1038/nprot.2008.211 Nat. Protoc. <b>4</b>, 44 (2009)]<br />
<br />
Other good articles (''not ''curriculum)<br />
*Z. Yang & B. Rannala, "Molecular phylogenetics: principles and practice", [http://dx.doi.org/doi:10.1038/nrg3186 Nat. Rev. Genet. <b>13</b>, 303 (2012)]<br />
<br />
=== Contacts ===<br />
Jon Bråte (Course coordinator) - e-mail: jon.brate@ibv.uio.no, phone: +47 922 44 582<br />
<br />
Torill Rørtveit (Course administrator, registration) - e-mail: torill.rortveit@ibv.uio.no<br />
<br />
=== Useful links ===<br />
<br />
[http://swcarpentry.github.io/shell-novice/reference/ Very useful reference guide on the Unix shell (created by Software Carpentry)]<br />
<br />
Trond Hasle Amundsen's [http://www.uio.no/tjenester/it/maskin/linux/hjelp/tips/guide.html Local guide to Linux and Unix]<br />
<br />
[https://github.com/EbookFoundation/free-programming-books/blob/master/free-programming-books.md#python Tons of free e-books on Python]<br />
<br />
EMBnet [http://www.embnet.org/sites/default/files/quickguides/guideUNIX.pdf Quick guide Unix]<br />
<br />
[https://github.com/stephenturner/oneliners Useful command line one-liners] by Stephen Turner<br />
<br />
[https://github.com/mcandre/cheatsheets/blob/master/nano.md Nano text editor cheat sheet]<br />
<br />
[https://github.com/EbookFoundation/free-programming-books/blob/master/free-programming-books.md Tons of free programming books, about anything really.]<br />
<br />
[http://www.jalview.org Jalview] and Jalview [http://www.jalview.org/refcard.pdf refcard]<br />
<br />
UCSC [http://genome.ucsc.edu Genome browser]<br />
<br />
Free [http://www.openhelix.com/ucsc UCSC Genome browser tutorial]&nbsp;&nbsp; from OpenHelix<br />
<br />
Portal to [http://galaxyproject.org Galaxy]<br />
<br />
[http://wiki.galaxyproject.org/Learn Galaxy 101 and other Galaxy screencasts/tutorials]<br />
<br />
UiO [http://lifeportal.uio.no Lifeportal] and more [http://www.uio.no/english/services/it/research/hpc/lifeportal information on the Lifeportal]<br />
<br />
The Genomic [http://hyperbrowser.uio.no/hb HyperBrowser]<br />
<br />
[http://bioinformatics.ca/links_directory Links Directory] from bioinformatics.ca<br />
<br />
The 2017 Nucleic Acids Research [https://academic.oup.com/nar/issue/45/D1 Database Issue]<br />
<br />
The 2015 Nucleic Acids Research [https://academic.oup.com/nar/issue/45/W1 Web Server Issue]<br />
<br />
UiO and OUS [http://core.rr-research.no/bioinformatics Bioinformatics Core Facility]</div>Jonkl@uio.no