Selectome (phase 2)
|Long Title:||Selectome: positive Darwinian selection on the Grid - Phase 2|
|Université de Lausanne|
Swiss Institute of Bioinformatics
|Project Leader:||H. Stockinger|
|Deputy Project Leader:||S. Maffioletti|
See also Selectome Phase 1
|Software package: gcodeml||Source code of gcodeml|
|gcodeml: A Grid-enabled Tool for Detecting Positive Selection in Biological Evolution||Publication by Sébastien Moretti, Riccardo Murri, Sergio Maffioletti, Arnold Kuzniar, Briseis Castella, Nicolas Salamin, Marc Robinson-Rechavi and Heinz Stockinger in Biological Evolution. HealthGrid Conference, Amsterdam, The Netherlands, May 21-23, 2012|
The project provides a software tool (called gcodeml) that taps into the power of a computational Grid
(particularly Switzerland's SMSCG infrastructure and related ARC-based systems) to run CPU intensive
calculations that support the study of evolution of species. In this way, life scientists will have
an up-to-date Selectome database (http://selectome.unil.ch) which provides an easy-to-use web interface
to biological knowledge.
Life science researchers will have access to much more knowledge about evolution of genes than now. Given the modularity of the gcodeml applications, similar bioinformatics applications can also be enabled on the same infrastructure with minimal modification of the code.
The project objectives have been met to provide a computational engine for the Selectome database. This will enable the Selectome team at UNIL to create future versions of Selectome using computational Grid resources of Swiss scientific and academic partners. The main results of the project are:
A new Selectome database is planned to be made available in the first semester of 2013. Many of the required codeml calculations will be on on SMSCG using gcodeml.
The project will work in collaboration with NGI-CH to take advantage of additional computational resources by extending the software to use the Grid infrastructure operated by the EGI project. This will considerably improve the previous work. The second phase will:
Given that life science applications are major drivers in Grid computing, the proposed project will both help to promote the Swiss Grid infrastructure, and provide dedicated support to life scientists.
The project includes two technical work packages: