Section: Software

Biomanycores.org – a community for bioinformatics on manycore processors

Actively developped in 2011.

Software self-assessment: A-3up4, SO-2, SM-2, EM-3, SDL-4up5, DA-4, CD-4, MS-4, TPM-4

Software web site : http://www.biomanycores.org/

Manycore architectures are an emerging field of research full of promises for parallel bioinformatics. However the usage of GPUs is not so widespread in the end-user bioinformatics community. The goal of the biomanycores.org project is to gather open-source CUDA and OpenCL parallel codes and to provide easy installation, benchmarking, and interoperability. The last point includes interfaces to popular frameworks such as Biopython, BioPerl and BioJava.

The development of Biomanycores is supported by a national ADT(ADT (Action for Technological Development) is an INRIA internal call) between Bonsai , Symbiose (CRI Rennes) and Dolphin (CRI Lille). This ADT started in October 2010 and led to the hiring of J.-F. Berthelot (IJD).

In the first year of the ADT, J.-F. Berthelot redesigned and rewrote almost all the existing code. The code base is now stable. He worked on the documentation and on various software engeneering aspects such as continuous integration. The second year of the ADT will focus on integrating more applications and targeting bioinformaticians users.