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Wednesday 18th March
 
Wednesday 18th March
<div>------------------------------------------------------------------------</div><div>10:00 - 10:15 &nbsp;: &nbsp;[[Media:Intro.pdf|Welcome & introduction to Elixir]]<font face="monospace, Courier">'''&nbsp;'''</font>(Eivind Hovig, OUS-HF - Radium/UiO)&nbsp;</div><div>10:15 - 10:30 &nbsp;: &nbsp;[[Media:NeLS-incl-TSD-overview.pdf|Overview of Elixir.no infrastructure and resources]] (Kjell Petersen, UiB)</div><div>10:30 - 11:00 &nbsp;: &nbsp;Sensitive data (Gard O. Thomassen, USIT)</div><div>11:00 - 12:00 &nbsp;: &nbsp;Tjenester for Sensitive Data (TSD) - Architecture and services (Gard O. Thomassen, USIT)</div><div><br/></div><div>12:00 - 13:00 &nbsp;: &nbsp;Lunch</div><div><br/></div><div>13:00 - 14:10 &nbsp;: &nbsp;[[Media:Elixir-workshop-hands-on-2015.doc|TSD - Login [Hands-on]]] (Abdulrahman Azab, UiO)</div><div>14:10 - 14:50 &nbsp;: &nbsp;[[Media:Elixir-workshop-hands-on-2015.doc|TSD - Data transfer [Hands-on] ]](Abdulrahman Azab, UiO)</div><div><br/></div><div>14:50 - 15:00 &nbsp;: &nbsp;Coffee break</div><div><br/></div><div>15:00 - 16:00 &nbsp;: &nbsp;[[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 &nbsp;: &nbsp;NCGC somatic variant calling pipeline [Presentation & demo] (Daniel Vodak / Sigve Nakken, OUS-HF - Radium)</div><div><br/></div><div>19:00&nbsp;: &nbsp;[http://www.mister-india.no Dinner]</div><div>------------------------------------------------------------------------</div><div><br/></div><div>Thursday 19th March</div><div>------------------------------------------------------------------------</div><div>09:00 - 09:30 &nbsp;: &nbsp;Introduction to Galaxy ([[Media:Galaxy introduction.pdf|Sveinung Gundersen]] / [[Media:pres19mar15 Elixir workshop.pdf|Geir Kjetil Sandve]],&nbsp;UiO)</div><div>09:30 - 09:45 &nbsp;: &nbsp;NSC germline variant calling pipeline (Ying Sheng)</div><div>09:45 - 10:45 &nbsp;: &nbsp;[[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 &nbsp;: &nbsp;Coffee Break</div><div><br/></div><div>11:00 - 11:20 &nbsp;: [[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 &nbsp;: [[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 &nbsp;: &nbsp;Lunch</div><div><br/></div><div>13:00 - 13:50 &nbsp;: &nbsp;[[Media:RNA-seq-hands-on.pdf|RNA-seq pipelines in NeLS [Hands-on]]] (Kjell Petersen, UiB)</div><div>13:50 - 14:20 &nbsp;: &nbsp;[[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 &nbsp;: &nbsp;Coffee Break</div><div><br/></div><div>14:30 - 15:00 &nbsp;: &nbsp;[[Media:HyperBrowser.pdf|Statistical genomics with the HyperBrowser [Demo]]] (Sveinung Gundersen, UiO)</div><div>15:00 - 16:00 &nbsp;: &nbsp;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'''&nbsp;'''at the OUH-Radiumhospitalet'''</div><div><div>Monday 23rd March</div><div>-------------------------------------------------------------------------</div><div>10:00 - 10:15 &nbsp;: &nbsp;[[Media:Intro.pdf|Welcome & introduction]] (Eivind Hovig)</div><div>10:15 - 10:45 &nbsp;: &nbsp;[[Media:Seq Technology Meza-Zepeda.pdf|Sequencing lab workflow]] (Leonardo Meza-Zepeda)</div><div>10:45 - 11:00 &nbsp;: &nbsp;General data flow (Ghislain Fournous/Daniel vodák)</div><div>11:00 - 11:30 &nbsp;: &nbsp;[[Media:TSD2.pdf|Tjenester for Sensitive Data (TSD)]] - Overview and usage (Abdulrahman Azab)</div><div>11:30 - 12:15 &nbsp;: &nbsp;[[Media:Elixir-workshop-hands-on-2015.doc|TSD [Hands-on] ]](Abdulrahman Azab]</div><div><br/></div><div>12:15 - 13:00 &nbsp;: &nbsp;Lunch</div><div><br/></div><div>13:00 - 14:00 &nbsp;: &nbsp;[[Media:Somatic_variant_calling_NCGC.pdf|NCGC pipeline]]/ICGC/[[Media:cancer variant annotation Elixir|Annotation pipeline]] (Daniel Vodák, Ghislain Fournous, Sigve Nakken)</div><div>14:00 - 14:30 &nbsp;: &nbsp;Bash, Ruby pipeline (Ghislain Fournous, Daniel Vodák)</div><div>14:30 - 14:40 &nbsp;: &nbsp;Coffee break</div><div>14:40 - 15:30 &nbsp;: &nbsp;NCGC pipeline [Hands-on] (Daniel Vodák, Ghislain Fournous, Sigve Nakken)</div><div>15:30 - 16:30 &nbsp;: &nbsp;Downstream analysis options [Discussion] (Everybody, Sigve Nakken, Eivind Hovig)</div></div>
+
<div>------------------------------------------------------------------------</div><div>10:00 - 10:15 &nbsp;: &nbsp;[[Media:Intro.pdf|Welcome & introduction to Elixir]]<font face="monospace, Courier">'''&nbsp;'''</font>(Eivind Hovig, OUS-HF - Radium/UiO)&nbsp;</div><div>10:15 - 10:30 &nbsp;: &nbsp;[[Media:NeLS-incl-TSD-overview.pdf|Overview of Elixir.no infrastructure and resources]] (Kjell Petersen, UiB)</div><div>10:30 - 11:00 &nbsp;: &nbsp;Sensitive data (Gard O. Thomassen, USIT)</div><div>11:00 - 12:00 &nbsp;: &nbsp;Tjenester for Sensitive Data (TSD) - Architecture and services (Gard O. Thomassen, USIT)</div><div><br/></div><div>12:00 - 13:00 &nbsp;: &nbsp;Lunch</div><div><br/></div><div>13:00 - 14:10 &nbsp;: &nbsp;[[Media:Elixir-workshop-hands-on-2015.doc|TSD - Login [Hands-on]]] (Abdulrahman Azab, UiO)</div><div>14:10 - 14:50 &nbsp;: &nbsp;[[Media:Elixir-workshop-hands-on-2015.doc|TSD - Data transfer [Hands-on] ]](Abdulrahman Azab, UiO)</div><div><br/></div><div>14:50 - 15:00 &nbsp;: &nbsp;Coffee break</div><div><br/></div><div>15:00 - 16:00 &nbsp;: &nbsp;[[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 &nbsp;: &nbsp;NCGC somatic variant calling pipeline [Presentation & demo] (Daniel Vodak / Sigve Nakken, OUS-HF - Radium)</div><div><br/></div><div>19:00&nbsp;: &nbsp;[http://www.mister-india.no Dinner]</div><div>------------------------------------------------------------------------</div><div><br/></div><div>Thursday 19th March</div><div>------------------------------------------------------------------------</div><div>09:00 - 09:30 &nbsp;: &nbsp;Introduction to Galaxy ([[Media:Galaxy introduction.pdf|Sveinung Gundersen]] / [[Media:pres19mar15 Elixir workshop.pdf|Geir Kjetil Sandve]],&nbsp;UiO)</div><div>09:30 - 09:45 &nbsp;: &nbsp;NSC germline variant calling pipeline (Ying Sheng)</div><div>09:45 - 10:45 &nbsp;: &nbsp;[[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 &nbsp;: &nbsp;Coffee Break</div><div><br/></div><div>11:00 - 11:20 &nbsp;: [[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 &nbsp;: [[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 &nbsp;: &nbsp;Lunch</div><div><br/></div><div>13:00 - 13:50 &nbsp;: &nbsp;[[Media:RNA-seq-hands-on.pdf|RNA-seq pipelines in NeLS [Hands-on]]] (Kjell Petersen, UiB)</div><div>13:50 - 14:20 &nbsp;: &nbsp;[[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 &nbsp;: &nbsp;Coffee Break</div><div><br/></div><div>14:30 - 15:00 &nbsp;: &nbsp;[[Media:HyperBrowser.pdf|Statistical genomics with the HyperBrowser [Demo]]] (Sveinung Gundersen, UiO)</div><div>15:00 - 16:00 &nbsp;: &nbsp;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'''&nbsp;'''at the OUH-Radiumhospitalet'''</div><div><div>Monday 23rd March</div><div>-------------------------------------------------------------------------</div><div>10:00 - 10:15 &nbsp;: &nbsp;[[Media:Intro.pdf|Welcome & introduction]] (Eivind Hovig)</div><div>10:15 - 10:45 &nbsp;: &nbsp;[[Media:Seq Technology Meza-Zepeda.pdf|Sequencing lab workflow]] (Leonardo Meza-Zepeda)</div><div>10:45 - 11:00 &nbsp;: &nbsp;General data flow (Ghislain Fournous/Daniel vodák)</div><div>11:00 - 11:30 &nbsp;: &nbsp;[[Media:TSD2.pdf|Tjenester for Sensitive Data (TSD)]] - Overview and usage (Abdulrahman Azab)</div><div>11:30 - 12:15 &nbsp;: &nbsp;[[Media:Elixir-workshop-hands-on-2015.doc|TSD [Hands-on] ]](Abdulrahman Azab]</div><div><br/></div><div>12:15 - 13:00 &nbsp;: &nbsp;Lunch</div><div><br/></div><div>13:00 - 14:00 &nbsp;: &nbsp;[[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 &nbsp;: &nbsp;Bash, Ruby pipeline (Ghislain Fournous, Daniel Vodák)</div><div>14:30 - 14:40 &nbsp;: &nbsp;Coffee break</div><div>14:40 - 15:30 &nbsp;: &nbsp;NCGC pipeline [Hands-on] (Daniel Vodák, Ghislain Fournous, Sigve Nakken)</div><div>15:30 - 16:30 &nbsp;: &nbsp;Downstream analysis options [Discussion] (Everybody, Sigve Nakken, Eivind Hovig)</div></div>
 
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Revision as of 20:26, 7 April 2015

Workshop for NSC/NGC/NCGC at Dept of Informatics, UiO

Wednesday 18th March

------------------------------------------------------------------------
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
------------------------------------------------------------------------
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)