The second phase of this project extends the existing software based on gc3pie to run the Selectome workflow in a full production environment.

See also Selectome Phase 1

Goals

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:

• provide an efficient solution to satisfy the computational needs imposed by the Selectome application.
• further develop and deploy in production mode existing code from the first phase of the project that has resulted from a very successful collaboration between UNIL, SIB and UZH (GC3). Additionally, this application can be considered as one of the few Swiss life science applications that are already well established and make true use of a Grid environment.
• make regular full Selectome releases possible, which will be of value for the life science community working in the domain of evolutionary biology and phylogenetics.

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.

Steps

The project includes two technical work packages:

• Enhancements of Grid-enabled workflow for Selectome and Codeml: command line-based, fault-tolerant gridification of Codeml as the computational back-end to Selectome.
  1. Improvements of current gc3pie-based submission system for Codeml (gcodeml)
  2. Extending the existing submission system to EGI's middleware
  3. Software testing and evaluation (incl. scalability tests)
• Full production runs of Selectome/Codeml: full Selectome releases will be run on both SMSCG and EGI.
  1. Extension and improvements of the Grid-based workflow for Selectome using Codeml
  2. Prepare and run Selectome releases based on the existing and developed software