ICRISAT Archival Report 2006 - The seedlings of success in the ...

functionality and user interfaces continue to be modified to suit user requirements. The LIMS application has
also been extended and adapted for use at ICRISAT/IITA/ILRI - Nairobi and IITA-Ibadan. A workshop was
conducted at ICRISAT-Nairobi to demonstrate the software to potential users and obtain feedback. The software
has also been shared with several universities and private partners under the terms of the GNU general public
license.
B Jayashree, DA Hoisington, S Senthilvel, RK Varshney,
DKiambi and S de Villiers
Activity C.10.2: Integrated database development with web interfaces and interoperability requirements.
Milestone C.10.2.1: Development of database and middleware with GUI (JB/DH/ and others, 2007)
The LIMS –ICRIS adaptor allows the flow of genotyping data from the LIMS application into the ICRIS
database. The database is expected to integrate genotyping information with genetic resource and phenotype
information. Progress was made this year in coding for generic middleware to this database to bring it in
compliance with the GCP(generation challenge program) platform. This will allow for the database to become
interoperable with other databases and repositories available in the public domain. A GCP platform compliant
data source API (application program interface) is also being developed that will allow data consumers such as
publicly available analytical or visualization tools to access data within the database.
B Jayashree and DA Hoisington
Milestone C.10.2.2: Alpha and beta testing of database by users (CTH/SS/RKV/HDU/RB/VV/and others)
Milestone C.10.2.3: Curation of data with involvement of data providers.
Output target C.11: Development of data analysis tools
Activity C.11.1: iMAS a decision support system for marker aided breeding.
Milestone C.11.1.1: Further development and testing of application (SC/DH/JB, 2007).
The goal of this two-year project (2005-06) was to develop an integrated decision support system, called iMAS,
to seamlessly facilitate marker-assisted plant breeding by integrating freely available quality software involved
in the journey from phenotyping-and-genotyping of genetic entities to the identification and application of traitlinked
markers, and providing simple-to-understand-and-use online decision guidelines to correctly use these
software, interpret and use their outputs. The project was structured into nine activities, namely: A1: Analyze
potentially useful free software, A2: Select software for inclusion in iMAS, A3: Develop iMAS system, A4:
Develop & incorporate online decision guidelines, A5: Test iMAS system, A6: Refine iMAS system, A7:
Develop iMAS user manual/tutorial, A8: Release of and Training in iMAS, A9: Consultation and support.
Five different software have been integrated in this pipeline along with online decision support and the
integration of two more software is in progress in 2006. Integrated software include IRRISTAT, Gmendel,
PlabQTL, POPMIN and GGT while the integration of WinQTLCartographer and TASSEL is in progress. The
pipeline has been modified to incorporate user comments, two major workshops were conducted
accommodating over 40 scientists from the NARS besides ICRISAT staff and interested private partners to test
the application. Besides, project partners reviewed the application and their suggestions are being incorporated.
S Chandra, DA Hoisington and B Jayashree
Activity C.11.2: High performance computing toolbox.
Milestone C.11.2.1: Extension of existing tools with user friendly interfaces (JB/RKV/DH/SC and others).
The pipelines and standalone software available within the comparative genomics and population genetics
toolboxes on the high performance computer have been extended through 2006. The comparative genomics
toolbox now includes a suite of parallelized programs for marker mining and detection from large public
datasets and open source software for comparative sequence analysis and phylogeny. The population genetics
toolkit includes a parallelized version of the program ‘structure’ with user interfaces and visualization software
along with format conversion tools for a variety of popularly used analysis software.
B Jayashree, RK Varshney, DA Hoisington, AG Sylvester,
S Chandra, MS Hanspal,and VT Jagdesh
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