[Biopython-dev] Biomanycores, GPU bioinformatics with BioJava, BioPerl and Biopython

Mathieu Giraud mathieu.giraud at lifl.fr
Fri Jul 15 05:44:08 UTC 2011

Dear colleagues,

We are pleased to announce the last release of Biomanycores, a library of bioinformatics applications for GPU and other manycore processors. We gather some CUDA and OpenCL codes and provide interfaces with the latest versions of BioJava, BioPerl and Biopython, and we aim to provide soon benchmarks on GPU-accelerated applications through the Bio* frameworks.

                             ==> http://www.biomanycores.org/ <==

Currently, Biomanycores has codes for sequence alignment (Smith-Waterman), genome alignment (MUMmer), transcription factor lookup with position-weight matrices, and RNA secondary structure and pseudo-knot prediction. We plan to integrate other applications in the next months.

We invite you to try Biomanycores applications and interfaces. We welcome any feedback, most notably on the way we realised the integrations. The main developper of Biomanycores, Jean-Frédéric Berthelot, is full-time on the project and can provide help. In particular, we are willing to provide support on the following points:

1) you can propose other GPU applications for inclusion ;

2) if you have some computation time bottlenecks on a BioJava, BioPerl or Biopython pipeline, we can work together to see if some current or potential GPU applications could speed-up your scripts.

You can join us at <contact at biomanycores.org>. Moreover, we will be present this week in Wien at BOSC 2011.

Best regards,

The Biomanycores team

Mathieu Giraud - http://www.lifl.fr/~giraud
CNRS, LIFL, Université Lille 1, INRIA Lille, France

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