Difference between revisions of "AllBio Forum"
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===September 29, 2013=== |
===September 29, 2013=== |
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| − | * Get GO for another KAAS output of PGSC and for 2 KAAS outputs for ITAG [Estelle] |
+ | * Get GO for another KAAS output of PGSC and for 2 KAAS outputs for ITAG ['''Estelle'''] |
| − | * Finish running OrthoMCL for 52 species [Estelle, Tanya] |
+ | * Finish running OrthoMCL for 52 species ['''Estelle''', '''Tanya'''] |
| − | * OrthoMCL 52 species flow output – calculate all measurement as above. [Estelle, Agnieszka, Didi, Tanya and Oren]. |
+ | * 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]. |
+ | * 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]. |
+ | * 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]. |
+ | * 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 all expression based analyses on 3 GE data sets: a) all tisues; b) tubers; c) leaves.['''Oren''', '''Didi''' '''Itziar''']. |
* Run co-expression simulations |
* Run co-expression simulations |
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* 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. |
* 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]. |
+ | * Plot GO similarity analysis [semsim package – '''Didi''']. |
* Get input from Kate and write discussion. |
* Get input from Kate and write discussion. |
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| − | * Inspect manually the GO prediction made by flows for the carotenoid pathway genes. [Oren]. |
+ | * 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] |
+ | * 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] |
+ | * reults and scirpts QA ['''All'''] |
| − | * Documentation of scripts and writing MS [All] |
+ | * Documentation of scripts and writing MS ['''All'''] |
| − | |||
== Photos == |
== Photos == |
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Revision as of 11:46, 29 September 2013
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.
Contents
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]
Photos
New photos from the hack-a-thon in AMS are in ..\Dropbox\Hack-a-thon\photos-Amsterdam\
Contacts
For any question regarding this wiki page please contact Tatyana Goldberg
