AllBio Forum

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Revision as of 10:45, 29 September 2013 by Allbio13 (talk | contribs)

This wiki was created after the first Hack-a-Thon Session for Test Cases #9 and #12, held in Amsterdam, September 19-21. For general information about this Session please refer to the AllBio website. The discussion board will be used by all members of the Hack-a-thon team for a regular update on project's status.

What's new

  • New TODO list [Sept 29, 2013]
  • First Hack-a-thon protocol and result slides added to Dropbox
  • Photos added to Dropbox
  • Wiki is up! [Sept 23, 2013]

Annotation Pipelines

  • Trinotate (Agnieszka + Didi+ Oren) output: done | parsing: done.
  • Blast2GO (Estelle ??) output: done | parsing: done??.
  • PotatoCyc (Kate) output: done | parsing: MISSING??.
  • OrthoMCL (Tanya + Esstelle): output: MISSING for 52 proteomes | parsing: MISSING.
  • Phytozome (Itziar) output: done| parsing: done.
  • KEGG (Itziar contacted the KEGG people?) output: done?? | parsing: done??.

Protocol & Result Files

All the result files, protocols, etc. can be found in ..\Dropbox\Hack-a-thon\protocols_results\.
Below is their short description.

  • HackathonReport_09292013.docx - Hack-a-thon final report, Amsterdam Sept. 19-21, 2013
  • workflow_09292013.pptx - annotation workflow and preliminary results on every flow performance & gene expression data
  • 4Greg_Hack-a-thon_Amsterdam_0913.pptx

TO DO Lists

September 29, 2013

  • Get GO for another KAAS output of PGSC and for 2 KAAS outputs for ITAG [Estelle]
  • Finish running OrthoMCL for 52 species [Estelle, Tanya]
  • OrthoMCL 52 species flow output – calculate all measurement as above. [Estelle, Agnieszka, Didi, Tanya and Oren].
  • Calculate precision and recall to SG and the PotatoCyc output gene lists (after mapping from KEGG to GO IDs [Oren, Agnieszka, Didi].
  • Assigning weights done by Erik and Sanjeev on PGSC to combined results from ITAG (based on corresponding pairs of GO and PGSC_id), so they don't have to do it again manually. [Agnieszka].
  • Searching for the 'SanjeevGold' gene IDs in all outputs separately and collecting some statistics and comparisons. [Agnieszka].
  • Run all expression based analyses on 3 GE data sets: a) all tisues; b) tubers; c) leaves.[Oren, Didi Itziar].
  • Run co-expression simulations
  • Inspected manually modules that averaged r-value scores <0.9.These should help us to get an insights of GO term that highly validated in expression data sets.
  • Plot GO similarity analysis [semsim package – Didi].
  • Get input from Kate and write discussion.
  • Inspect manually the GO prediction made by flows for the carotenoid pathway genes. [Oren].
  • Make annotations available for biologists to use. Communicate with Lukas Mueller involved with Solgenomics site to do this [Oren and Erik]
  • reults and scirpts QA [All]
  • Documentation of scripts and writing MS [All]


New photos from the hack-a-thon in AMS are in ..\Dropbox\Hack-a-thon\photos-Amsterdam\


For any question regarding this wiki page please contact Tatyana Goldberg