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− | + | '''RNA-Seq workshop at Dept of Informatics, UiO''' | |
− | = | + | Wednesday 14th Dec, 2016 |
− | + | ||
− | + | Materials can be found here: | |
− | + | ||
− | + | https://etherpad.net/p/ELIXIR_Oslo_December | |
+ | <div>------------------------------------------------------------------------</div>'''RNA-Seq workshop at Dept of Informatics, UiO''' | ||
+ | |||
+ | Wednesday 5th Oct, 2016 | ||
+ | <div>------------------------------------------------------------------------</div>'''RNA-Seq workshop at Dept of Informatics, UiO''' | ||
+ | |||
+ | Wednesday 1st June, 2016 | ||
+ | <div> | ||
+ | [[:File:Elixir-pres.pptx|Elixir presentation]] | ||
+ | |||
+ | [[Media: HI-13-April-2016.pdf|NeLS presentation]] | ||
+ | |||
+ | [[Media: rna-seq-galaxy-pipeline.pdf|RNA-Seq background]] | ||
+ | |||
+ | [[:File:Rna-seq-hands-on.docx|RNA-Seq hands-on]] | ||
+ | |||
+ | NeLS file handling (please see "Handling data and storage in NeLS" document below). | ||
+ | |||
+ | <nowiki>------------------------------------------------------------------------</nowiki> | ||
+ | |||
+ | </div>'''RNA-Seq workshop at Dept of Informatics, UiO''' | ||
+ | |||
+ | Wednesday 20th April, 2016 | ||
+ | <div> | ||
+ | [[Media: Elixir-pres.pptx|Elixir presentation]] (Ståle Nygård, OUS-Radium/UiO) | ||
+ | |||
+ | [[Media: HI-13-April-2016.pdf|NeLS presentation]] (David Fredman, CBU, UiB) | ||
+ | |||
+ | [[Media: rna-seq-galaxy-pipeline.pptx|RNA-Seq background]] (Ståle Nygård, OUS-Radium/UiO) | ||
+ | |||
+ | Please also see relevant material from previous workshops below, e.g the RNA-seq hands-on by Kjell Petersen. | ||
+ | |||
+ | <nowiki>------------------------------------------------------------------------</nowiki> | ||
+ | |||
+ | </div>'''Workshop for NSC/NGC/NCGC at Dept of Informatics, UiO''' | ||
+ | |||
+ | Wednesday 18th March, 2015<div>10:00 - 10:15 : [[Media:Intro.pdf|Welcome & introduction to Elixir]]<font face="monospace, Courier">''' '''</font>(Eivind Hovig, OUS-HF - Radium/UiO) </div><div>10:15 - 10:30 : [[Media:NeLS-incl-TSD-overview.pdf|Overview of Elixir.no infrastructure and resources]] (Kjell Petersen, UiB)</div><div>10:30 - 11:00 : [[Media:Elixir_ws_mars_2015.pptx.pdf|Sensitive data]] (Gard O. Thomassen, USIT)</div><div>11:00 - 12:00 : Tjenester for Sensitive Data (TSD) - Architecture and services (Gard O. Thomassen, USIT)</div><div><br /></div><div>12:00 - 13:00 : Lunch</div><div><br /></div><div>13:00 - 14:10 : [[Media:Elixir-workshop-hands-on-2015.doc|TSD - Login [Hands-on]]] (Abdulrahman Azab, UiO)</div><div>14:10 - 14:50 : [[Media:Elixir-workshop-hands-on-2015.doc|TSD - Data transfer [Hands-on]]] (Abdulrahman Azab, UiO)</div><div><br /></div><div>14:50 - 15:00 : Coffee break</div><div><br /></div><div>15:00 - 16:00 : [[Media:Elixir-workshop-hands-on-2015.doc|TSD - Running software on the command line [Hands-on]]] (Abdulrahman Azab, UiO)</div><div>16:00 - 17:00 : NCGC somatic variant calling pipeline [Presentation & demo] (Daniel Vodak / Sigve Nakken, OUS-HF - Radium)</div><div><br /></div><div>19:00 : [http://www.mister-india.no Dinner]</div><div>------------------------------------------------------------------------</div><div><br /></div><div>Thursday 19th March, 2015</div><div>------------------------------------------------------------------------</div><div>09:00 - 09:30 : Introduction to Galaxy ([[Media:Galaxy introduction.pdf|Sveinung Gundersen]] / [[Media:pres19mar15 Elixir workshop.pdf|Geir Kjetil Sandve]], UiO)</div><div>09:30 - 09:45 : NSC germline variant calling pipeline (Ying Sheng)</div><div>09:45 - 10:45 : [[Media:Elixir-workshop-hands-on-2015.doc|Galaxy in TSD [Hands-on]]] with running of germline pipeline [Demo] (Abdulrahman Azab, UiO / Ghislain Fornous, OUS-HF - Radium)</div><div><br /></div><div>10:45 - 11:00 : Coffee Break</div><div><br /></div><div>11:00 - 11:20 : [[Media:034 - NeLS Oslo Kidane (general).pdf|Overview of National e-Infrastructure for Life Science (NeLS)]] (Kidane Tekle, UiB)</div><div>11:20 - 12:00 : [[Media:NeLS hands on.pdf|Handling data and storage in NeLS [Hands-on]]] (Sveinung Gundersen, UiO)</div><div><br /></div><div>12:00 - 13:00 : Lunch</div><div><br /></div><div>13:00 - 13:50 : [[Media:RNA-seq-hands-on.pdf|RNA-seq pipelines in NeLS [Hands-on]]] (Kjell Petersen, UiB)</div><div>13:50 - 14:20 : [[Media:meta-pipe-oslo-2015-03-19.pdf|MetaPipe - metagenomics pipeline in NeLS [Demo]]] (Alexander Raknes, UiT)</div><div><br /></div><div>14:20 - 14:30 : Coffee Break</div><div><br /></div><div>14:30 - 15:00 : [[Media:HyperBrowser.pdf|Statistical genomics with the HyperBrowser [Demo]]] (Sveinung Gundersen, UiO)</div><div>15:00 - 16:00 : Discussion / [https://nettskjema.uio.no/answer/65002.html feedback] session (Eivind Hovig, OUS-HF - Radium/UiO)</div><div>------------------------------------------------------------------------</div><div><br /></div><div><br /></div><div>'''Workshop for NCGC''' '''at the OUH-Radiumhospitalet'''</div><div><div>Monday 23rd March</div><div>-------------------------------------------------------------------------</div><div>10:00 - 10:15 : [[Media:Intro.pdf|Welcome & introduction]] (Eivind Hovig)</div><div>10:15 - 10:45 : [[Media:Seq Technology Meza-Zepeda.pdf|Sequencing lab workflow]] (Leonardo Meza-Zepeda)</div><div>10:45 - 11:00 : General data flow (Ghislain Fournous/Daniel vodák)</div><div>11:00 - 11:30 : [[Media:TSD2.pdf|Tjenester for Sensitive Data (TSD)]] - Overview and usage (Abdulrahman Azab)</div><div>11:30 - 12:15 : [[Media:Elixir-workshop-hands-on-2015.doc|TSD [Hands-on]]] (Abdulrahman Azab]</div><div><br /></div><div>12:15 - 13:00 : Lunch</div><div><br /></div><div>13:00 - 14:00 : [[Media:Somatic variant calling NCGC.pdf|NCGC pipeline]]/ICGC/[[Media:Cancer variant annotation Elixir.pdf|Annotation pipeline]] (Daniel Vodák, Ghislain Fournous, Sigve Nakken)</div><div>14:00 - 14:30 : Bash, Ruby pipeline (Ghislain Fournous, Daniel Vodák)</div><div>14:30 - 14:40 : Coffee break</div><div>14:40 - 15:30 : NCGC pipeline [Hands-on] (Daniel Vodák, Ghislain Fournous, Sigve Nakken)</div><div>15:30 - 16:30 : Downstream analysis options [Discussion] (Everybody, Sigve Nakken, Eivind Hovig)</div></div> | ||
+ | [[Category:Pages with broken file links|Pages_with_broken_file_links]] |
Latest revision as of 12:02, 15 December 2016
RNA-Seq workshop at Dept of Informatics, UiO
Wednesday 14th Dec, 2016
Materials can be found here:
https://etherpad.net/p/ELIXIR_Oslo_December
------------------------------------------------------------------------
RNA-Seq workshop at Dept of Informatics, UiO
Wednesday 5th Oct, 2016
------------------------------------------------------------------------
RNA-Seq workshop at Dept of Informatics, UiO
Wednesday 1st June, 2016
NeLS file handling (please see "Handling data and storage in NeLS" document below).
------------------------------------------------------------------------
Wednesday 20th April, 2016
Elixir presentation (Ståle Nygård, OUS-Radium/UiO)
NeLS presentation (David Fredman, CBU, UiB)
RNA-Seq background (Ståle Nygård, OUS-Radium/UiO)
Please also see relevant material from previous workshops below, e.g the RNA-seq hands-on by Kjell Petersen.
------------------------------------------------------------------------
10:00 - 10:15 : Welcome & introduction to Elixir (Eivind Hovig, OUS-HF - Radium/UiO)
10:15 - 10:30 : Overview of Elixir.no infrastructure and resources (Kjell Petersen, UiB)
10:30 - 11:00 : Sensitive data (Gard O. Thomassen, USIT)
11:00 - 12:00 : Tjenester for Sensitive Data (TSD) - Architecture and services (Gard O. Thomassen, USIT)
12:00 - 13:00 : Lunch
13:00 - 14:10 : TSD - Login [Hands-on] (Abdulrahman Azab, UiO)
14:10 - 14:50 : TSD - Data transfer [Hands-on] (Abdulrahman Azab, UiO)
14:50 - 15:00 : Coffee break
15:00 - 16:00 : TSD - Running software on the command line [Hands-on] (Abdulrahman Azab, UiO)
16:00 - 17:00 : NCGC somatic variant calling pipeline [Presentation & demo] (Daniel Vodak / Sigve Nakken, OUS-HF - Radium)
19:00 : Dinner
------------------------------------------------------------------------
Thursday 19th March, 2015
------------------------------------------------------------------------
09:00 - 09:30 : Introduction to Galaxy (Sveinung Gundersen / Geir Kjetil Sandve, UiO)
09:30 - 09:45 : NSC germline variant calling pipeline (Ying Sheng)
09:45 - 10:45 : Galaxy in TSD [Hands-on] with running of germline pipeline [Demo] (Abdulrahman Azab, UiO / Ghislain Fornous, OUS-HF - Radium)
10:45 - 11:00 : Coffee Break
11:00 - 11:20 : Overview of National e-Infrastructure for Life Science (NeLS) (Kidane Tekle, UiB)
11:20 - 12:00 : Handling data and storage in NeLS [Hands-on] (Sveinung Gundersen, UiO)
12:00 - 13:00 : Lunch
13:00 - 13:50 : RNA-seq pipelines in NeLS [Hands-on] (Kjell Petersen, UiB)
13:50 - 14:20 : MetaPipe - metagenomics pipeline in NeLS [Demo] (Alexander Raknes, UiT)
14:20 - 14:30 : Coffee Break
14:30 - 15:00 : Statistical genomics with the HyperBrowser [Demo] (Sveinung Gundersen, UiO)
15:00 - 16:00 : Discussion / feedback session (Eivind Hovig, OUS-HF - Radium/UiO)
------------------------------------------------------------------------
Workshop for NCGC at the OUH-Radiumhospitalet
Monday 23rd March
-------------------------------------------------------------------------
10:00 - 10:15 : Welcome & introduction (Eivind Hovig)
10:15 - 10:45 : Sequencing lab workflow (Leonardo Meza-Zepeda)
10:45 - 11:00 : General data flow (Ghislain Fournous/Daniel vodák)
11:00 - 11:30 : Tjenester for Sensitive Data (TSD) - Overview and usage (Abdulrahman Azab)
11:30 - 12:15 : TSD [Hands-on] (Abdulrahman Azab]
12:15 - 13:00 : Lunch
13:00 - 14:00 : NCGC pipeline/ICGC/Annotation pipeline (Daniel Vodák, Ghislain Fournous, Sigve Nakken)
14:00 - 14:30 : Bash, Ruby pipeline (Ghislain Fournous, Daniel Vodák)
14:30 - 14:40 : Coffee break
14:40 - 15:30 : NCGC pipeline [Hands-on] (Daniel Vodák, Ghislain Fournous, Sigve Nakken)
15:30 - 16:30 : Downstream analysis options [Discussion] (Everybody, Sigve Nakken, Eivind Hovig)