AllBio Forum

This wiki was created after the first Hack-a-Thon Session for Test Cases #9 and #12, held in Amsterdam, September 19-21, 2013. 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 + Estelle): 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 and 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]

Photos

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

Links

The files related to the PGSC latest version (v4.03) of pseudomolecules is now available at: http://solanaceae.plantbiology.msu.edu/pgsc_download.shtml

The article describing the construction of these reference pseudomolecules is available at: http://www.g3journal.org/content/early/2013/09/18/g3.113.007153.full.pdf+html

Contacts

For any question regarding this wiki page please contact Tatyana Goldberg