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.
- 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]
- 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
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]
Potato itag potato dm v403 File:Potato itag potato dm v403.gff3.zip
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
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