Difference between revisions of "AllBio Forum"

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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 [http://www.allbioinformatics.eu/doku.php?id=public:hack4 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.
 +
This wiki was created after the first Hack-a-Thon Session for Test Cases [http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc9 #9] and [http://www.allbioinformatics.eu/doku.php?id=public:loadedtestcases:tc12 #12], held in Amsterdam, September 19-21, 2013. For general information about this Session please refer to the [http://www.allbioinformatics.eu/doku.php?id=public:hack4 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 ==
  
== What's new ==
  +
* Metastudent results are ready
  +
* OrthoMCL results are ready
  +
* '''new potato ITAG available for download in the [[#section Download|Download section]]'''
 
* New TODO list [Sept 29, 2013]
  
* New TODO list [Sept 29, 2013]
 
* First Hack-a-thon protocol and result slides added to Dropbox
  
* First Hack-a-thon protocol and result slides added to Dropbox
Line 10: Line 13:
   
 
== Annotation Pipelines ==
  
== Annotation Pipelines ==
  +
* Metastudent (Tanya) output: done | parsing : done.
−  
 
* Trinotate (Agnieszka + Didi+ Oren) output: done | parsing: done.
  
* Trinotate (Agnieszka + Didi+ Oren) output: done | parsing: done.
−
* Blast2GO (Estelle ??) output: done | parsing: done??.
 +
* Blast2GO (Estelle) output: done | parsing: done.
−
* PotatoCyc (Kate) output: done | parsing: MISSING??.
 +
* PotatoCyc (Kate) output: done | '''parsing: MISSING??.'''
−
* OrthoMCL (Tanya + Esstelle): output: MISSING for 52 proteomes | parsing: MISSING.
 +
* OrthoMCL (Tanya + Estelle): output: for 52 proteomes -> OrthoMCL crushes for 52 proteomes, therefore we took 18 instead: done | parsing: done.
 
* Phytozome (Itziar) output: done| parsing: done.
  
* Phytozome (Itziar) output: done| parsing: done.
−
* KEGG (Itziar contacted the KEGG people?) output: done?? | parsing: done??.
 +
* KEGG (Itziar contacted the KEGG people?) '''output: done??''' | '''parsing: done??.'''
   
   
 
== Protocol & Result Files ==
  
== Protocol & Result Files ==
   
−
All the result files, protocols, etc. can be found in ..\Dropbox\Hack-a-thon\protocols_results\.<br>
 +
All the power point point presentations, protocols, etc. can be found in ''../Dropbox/Hack-a-thon/protocols_results/''.<br>
 
Below is their short description.
  
Below is their short description.
   
−
* ''HackathonReport_09292013.docx'' - Hack-a-thon final report, Amsterdam Sept. 19-21, 2013
 +
* 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
 +
* workflow_09292013.pptx - annotation workflow and preliminary results on every flow performance & gene expression data
−
* ''4Greg_Hack-a-thon_Amsterdam_0913.pptx''
 +
* 4Greg_Hack-a-thon_Amsterdam_0913.pptx
   
  +
Result files are placed on VM in ''/virdir/Scratch/Oren/''
−
== Data Analysis and Integration ==
  
  +
−
Please put your data analysis results into this section [[Data Analysis and Integration]].
 
  +
* NEW_ORTHOMCL/ORTHOMCL_GO_PGSC.txt - OrthoMCL's GO terms for PGSC
  +
* NEW_ORTHOMCL/ORTHOMCL_GO_ITAG.txt - OrthoMCL's GO terms for ITAG
  +
* FLOWS_OUTPUTS/METASTUDENT_GO_PGSC.txt - Metastudent's GO terms for PGSC
  +
* FLOWS_OUTPUTS/METASTUDENT_GO_ITAG.txt - Metastudent's GO terms for ITAG
  +
* KO2GO - 8 files (2 ITAG "goldpairs", 2 PGSC "goldpairs", 2 ITAG "all", 2 PGSC "all" - see README file in same folder)
   
   
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===September 29, 2013===
  
===September 29, 2013===
  +
* Get GO terms from the Metastudent pipeline [Tanya: '''DONE''']
−
* Get GO for another KAAS output of PGSC and for 2 KAAS outputs for ITAG [Estelle]
  
−
* OrthoMCL 52 species flow output – calculate all measurement as above. [Estelle, Agnieszka, Didi, Tanya and Oren].
+
* Get GO for another KAAS output of PGSC and for 2 KAAS outputs for ITAG [Estelle, Tanya:'''DONE''']
  +
* Finish running OrthoMCL for 52 species -> For 52 species OrthoMCL crashed, so we took 18 representative species instead [Estelle, Tanya: '''DONE''']
−
* Calculate precision and recall to SG and the PotatoCyc output gene lists (after mapping from KEGG to GO IDs [Oren, Agnieszka, Didi].
  
  +
* OrthoMCL 18 species flow output – calculate all measurement as above. ['''Estelle''', '''Agnieszka''', '''Didi''', '''Tanya''' and '''Oren'''].
−
* 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].
  
  +
* Calculate precision and recall to SG and the PotatoCyc output gene lists (after mapping from KEGG to GO IDs ['''Oren''', '''Agnieszka''', '''Didi'''].
−
* Searching for the 'SanjeevGold' gene IDs in all outputs separately and collecting some statistics and comparisons. [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: '''DONE'''].
−
* Run all expression based analyses on 3 GE data sets: a) all tisues; b) tubers; c) leaves.[Oren, Didi Itziar].
  
  +
* Searching for the 'SanjeevGold' gene IDs in all outputs separately and collecting some statistics and comparisons. [Agnieszka: '''DONE'''].
  +
* 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
  
* 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.
  
* 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.
−
* 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: '''DONE'''].
−
* 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''']
  +
  +
==Download==
  +
'''Potato itag potato dm v403''' [[File:Potato_itag_potato_dm_v403.gff3.zip]] <br>
  +
(click on the file name to get to the download page, there click on the .zip file to initiate the download)
  +
  +
  +
== 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
   
   
 
== Photos ==
  
== Photos ==
 
New photos from the hack-a-thon in AMS are in ..\Dropbox\Hack-a-thon\photos-Amsterdam\
  
New photos from the hack-a-thon in AMS are in ..\Dropbox\Hack-a-thon\photos-Amsterdam\
  +
   
 
== Contacts ==
  
== Contacts ==

Latest revision as of 17:08, 29 November 2013

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

  • Metastudent results are ready
  • OrthoMCL results are ready
  • new potato ITAG available for download in the Download section
  • 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

  • Metastudent (Tanya) output: done | parsing : done.
  • Trinotate (Agnieszka + Didi+ Oren) output: done | parsing: done.
  • Blast2GO (Estelle) output: done | parsing: done.
  • PotatoCyc (Kate) output: done | parsing: MISSING??.
  • OrthoMCL (Tanya + Estelle): output: for 52 proteomes -> OrthoMCL crushes for 52 proteomes, therefore we took 18 instead: done | parsing: done.
  • Phytozome (Itziar) output: done| parsing: done.
  • KEGG (Itziar contacted the KEGG people?) output: done?? | parsing: done??.


Protocol & Result Files

All the power point point presentations, 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

Result files are placed on VM in /virdir/Scratch/Oren/

  • NEW_ORTHOMCL/ORTHOMCL_GO_PGSC.txt - OrthoMCL's GO terms for PGSC
  • NEW_ORTHOMCL/ORTHOMCL_GO_ITAG.txt - OrthoMCL's GO terms for ITAG
  • FLOWS_OUTPUTS/METASTUDENT_GO_PGSC.txt - Metastudent's GO terms for PGSC
  • FLOWS_OUTPUTS/METASTUDENT_GO_ITAG.txt - Metastudent's GO terms for ITAG
  • KO2GO - 8 files (2 ITAG "goldpairs", 2 PGSC "goldpairs", 2 ITAG "all", 2 PGSC "all" - see README file in same folder)


TO DO Lists

September 29, 2013

  • Get GO terms from the Metastudent pipeline [Tanya: DONE]
  • Get GO for another KAAS output of PGSC and for 2 KAAS outputs for ITAG [Estelle, Tanya:DONE]
  • Finish running OrthoMCL for 52 species -> For 52 species OrthoMCL crashed, so we took 18 representative species instead [Estelle, Tanya: DONE]
  • OrthoMCL 18 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: DONE].
  • Searching for the 'SanjeevGold' gene IDs in all outputs separately and collecting some statistics and comparisons. [Agnieszka: DONE].
  • 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: DONE].
  • 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]

Download

Potato itag potato dm v403 File:Potato itag potato dm v403.gff3.zip
(click on the file name to get to the download page, there click on the .zip file to initiate the download)


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


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

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