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Objective 2.2 Implementation Team Meeting 20110802

Minutes of the Implementation Team Teleconference (August 2, 2011)
Jean-Marcel Ribaut (at start with communication problems)
Scott Chapman
Alain Charcosset
Mark Dieters
Delphine Fleury (later due to time error, with communication problems)
Graham McLaren
Clarissa Pimentel
Arllet Portugal
Trushar Shar
Fabio Valente
Jiankang Wang
Guoyou Ye
Marcos Masoletti
Jose Crossa
Fred van Eeuwijk
The meeting started at 6am Mexico time but due to a scheduling error (missed daylight saving change) some people joined later. Some people also had communication problems – all seemed to be able to hear but some cold not speak (JM, Delphine and Marcos). However Marcos re-set his microphone and then was able to talk.
I sincerely apologise for the scheduling mix-up (I promise to use only GMT in future). I am also sorry about the microphone difficulties for some people, but I have no idea what to do about that.

  1. Annual report

Graham thanked everyone for their contribution to the annual report which will be posted on the Wiki. He asked everyone to review it, especially appendix B - for the group to check the milestones and the achieved targets and confirm that they are right. If there is other evidence for completed milestones please report it to Graham. Then revisit the workplan in the light of the milestone that are not yet done.
2. GDMS (Trushar)

  • It is installed in Chunlin's computer
  • There is a problem with duplicate datasets as there is not editing feature yet.
  • Documentation is being produces and will be posted on Cropforge
  • Trushar will also give the documentation to Graham who will post it to everyone.
  • The developers are loading the ICRISAT and sorghum for GRM.
  • For data analysis, GDMS is already able to export data in flapjack format.
  • Trushar to develop a workplan for the GDMS for 2011/12 estimating needed resources.
  • Trushar to review the definition of the Gene Catalogue and develop a strategic plan for the development of GDMS.
  • Trushar has thought about the design but not yet how should it evolve and how to handle the nextgen sequencing.
  • Graham suggested Trushar take advantage of the people coming to GRM organize a planning meeting after the GRM. (Jeffrey from IRRI may be available).

3.  OptiMas (Allain and Flavio)

  • The team is in communication with Jeff Ehlers and working with his data.
  • They use flapjack format for genotypic, QTL and phenotypic data.
  • Online help is being developed
  • Flavio confirmed that a new release would be available for GRM but no one from their group is presently scheduled to come to GRM.
  • Flavio can possibly come in GRM but needs to check
  • IF not, possibly Delphine can demo OptiMAS with Jeff Ehlers data.

4. Analytical Pipeline (Marcus)

  • WUR group is starting to work on QA with data from Jeff Ehlers
  • But no other dataset (Graham and Delphine to get datasets from users)
  • A QA tool to be made available by December 
  • R codes to be sent to Gouyou soon for inclusion in the menu interface
  • The QTL analysis code is being reorganized and should be ready by September
  • The phenotypic analysis code is available in the wiki site (calculations and GUI) - Graham to talk with Gouyou to check it.
  • Fred and Marcus have been discussing the use of ASREML with Brian Cullis and will use the R version in QTL analysis. However this will still require a licence so alternate free scripts will also be developed.
  • Training plans -  QTL course in Argentina in December
  • GSS recipients will soon have genotyping data and need the analysis, possibly coordinate a course in early 2012.

5. Selection indices (Pancho by email)
Jose Crossa sent the following report before the meeting describing on-going work on selection indices:

  • Document the R codes for phenotypic and molecular marker selection indices
  • Illustrate the use of the phenotypic and genomic selection indices implemented in R with real examples
  • Produce user manual(s) for these selections indices
  • Continue research on genomic selection indices.

6.  Simulation tools (Jiankang)

  • The group has updated the QU-Gene website (with updated versions of QuLine, QuHybrid and QuMARS with documentation and examples)
  • They are collecting datasets from Richard Trethowan.
  • Adrian from Scott's lab and Morris from Mark's lab will visit CASS – they should make a conference call with Alain's group to discuss simulated data for testing OptiMAS and the possibility of including some simulation in OptiMAS
  • Jiankang will visit CIMMYT in two weeks time and attend GRM.

7. Simulation Tools (Mark)
We discussed the action items for simulation from the June 4th meeting:

  • Clean the user interface - still in the process of getting developers
  • Breeding design program – not clear what the product should be. The idea came from the document about integrated breeding simulation tools in the San Diego documentation. Scott said that most of that was from the QuGene user guide. So much further discussion is needed to reach the action item "Mark and the simulation team will identify the most promising intervention points and options for use of simulation in the AP. They will also outline prospects for the generic simulation platform and highlight the resource implications of various options" from the June meeting.
  • There was no progress on adding simulation steps in OptiMAS. This further discussion between Alain, Laurence, Fabio, Mark, Scott and Jiakang – perhaps while the latter three are together in CAAS.
  • Scott has simulated several QTL populations but it is not clear if all elements required for optiMAS have been simulated. The group to discuss on how to proceed - Alain to discuss with Mark and Scott for needed dataset.
  • There is some progress in changing the output format of QuGene so that it can run on the iPlant infrastructure. The code needs to be optimized to run on LINUX also, but a version running on iPlant should be ready by September.
  • The MARS data for rice from Gouyou is not yet being sent since he has not received the dataset from users  (Arvind) but at the end of this year it will be sent. Guoyou will uset he datased for simulation work and share it with the rest of the simulation team for collaborative work.

8. R Cropstat (Gouyou)

  • R Cropstat is a TCL version of a menu interface to R scripts it will be released by the end of August to serve as a prototype for the Eclipse version of the AP>
  • Single site analysis is almost done using Eclipese RCP and the multi-site is being added.
  • Two or more developers will go to the GRM meeting to demonstrate the Eclipse prototype.
  • The Cropforge repository for R scripts should have been released. Guoyou to follow up whether it is being done and inform the group.
  • The new version of CropForge is set up but moving the projects to the new cropforge has not been done. This needs urgent attention with each project group. 
  • The review of R code for design generation has not been done as the code in RCropStat should be sufficient.
  • However, we need review of what is available in R-Cropstat and make it available in Cropforge and compare it to other design packages.

 9. ICIS  - technical support (Graham)

  • IRRI have resources  to recruit staff to replace Ching and provide support staff.
  • Guoyou could talk with HR to upgrade the positions to be able to hire fewere but better staff.
  • Guoyou is not planning to support ICIS lite which will not be released.
  • The Workbook part of the ICIS lite should be supported and Guoyou is planning to move the pedigree part to Java; Guoyou will checkthe IB Fieldbook for Workbook functionality.
  • ICIS mobile is being redeveloped under Android for Tablet PCs. We really need to know the specifications of the Mobile App and the tablet to avoid duplication the work at CIMMYT and in order to make the IB Fieldbook compatible with the Mobile. A summary of what is being done is to be documented by the developer  and send to Hector and Graham.
  • David Jordan's group is using voice recognition for data collection. Mark to follow up and see if a collaboration is possible.

10. Other matters
We have the morning of September 23 for developers meetings at ICRISAT. Anyone with agenda items please send them to Graham and Delphine ASAP.
Sept 27-28 – there is a workshop at ICRISAT for database developers (Workbench, Breeding Module, Phenotypic Data Management, Genotypic Data Management) and to review the Menu prototype for R. All working on these items should come, others welcome and other topics are welcome also.

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