Difference between revisions of "Main Page"
From projects.elixir-workshop
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Wednesday 20th April, 2016 | Wednesday 20th April, 2016 | ||
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| − | [[ | + | [[Media: Elixir-pres.pptx|Elixir presentation]] (Ståle Nygård, OUS-Radium/UiO) |
[[Media: HI-13-April-2016.pdf|NeLS presentation]] (David Fredman, UiB) | [[Media: HI-13-April-2016.pdf|NeLS presentation]] (David Fredman, UiB) | ||
| − | RNA-Seq background (Ståle Nygård, OUS-Radium/UiO) | + | [[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. | Please also see relevant material from previous workshops below, e.g the RNA-seq hands-on by Kjell Petersen. | ||
Revision as of 13:02, 19 May 2016
RNA-Seq workshop at Dept of Informatics, UiO
Wednesday 20th April, 2016
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Workshop for NSC/NGC/NCGC at Dept of Informatics, UiO
Elixir presentation (Ståle Nygård, OUS-Radium/UiO)
NeLS presentation (David Fredman, 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.
Wednesday 18th March, 2015
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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
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Thursday 19th March, 2015
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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)
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Workshop for NCGC at the OUH-Radiumhospitalet
Monday 23rd March
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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)
