Biomanycores

contact [at] biomanycores.org

Biomanycores

open source manycores bioinformatics

biomanycores is a repository of open-source parallel bioinformatics code in OpenCL and in CUDA. We would like to bridge the gap between researches in high-performance-computing and platforms of usual bioinformaticians and biologists, in particular by giving access to high-performance prototypes through Bio* frameworks.

  • open-source – All projects and interfaces must be licensed under one open-source license recognized by OSI.
  • interoperability – The projects should, as far as possible, be integrated with Open Bioinformatics Foundation Bio* frameworks (BioJava, BioPerl, Biopython…).
  • portability – The recommended language is the OpenCL standard, whose specification has been released in December 2008. However, CUDA projects can be included too.
  • benchmarking – Projects should include elements of benchmarking or research papers. Benchmarking results should be reproducible by others.

News

  • 24 October 2012: New release 1.1210 for BioPerl, Biopython and BioJava.
  • 11 June 2012: New release 1.1206 for BioPerl and Biopython.
  • 2 March 2012: New release 1.1203 for Biopython.
  • 29 Febrary 2012: New release 1.1202 for BioPerl.
    Biomanycores now supports GPUBlast
  • 29 November 2011: New release 1.1111 for BioJava.
  • 12 July 2011: New biomanycores release 1.1107
    Many software quality improvements in this new release of biomanycores interfaces for BioPerl and Biopython. More work on BioJava should be done in the coming months.
  • This summer, Biomanycores has been presented at JOBIM 2011 as well as at BOSC 2011.

Older news

Download and install Biomanycores

  1. Install some GPU applications. All applications have been tested on CUDA 3.2 and 4.0 (see GPU compilation troubleshooting)
  2. Download and install biomanycores interfaces for your favourite framework:
  3. Read the README provided in each interface for detailed instructions and examples.

Get involved

Public git repository is at git clone git://scm.gforge.inria.fr/biomanycores/biomanycores.git, and the software documentation is available online. Developers can be reached through contact at biomanycores.org. We search for help in the following domains:

  • Bio* integration: improve exisiting interfaces, include a new Bio* framework..…
  • New project integration: integrate a CUDA/OpenCL project, improve a CUDA/OpenCL code to production quality…

About

biomanycores is a project of Bonsai bioinformatics group (LIFL, CNRS, Université Lille 1, INRIA Lille), in collaboration with Dolphin and Symbiose groups. We are funded by the INRIA ADT campaign 2010-2012.

If you use biomanycores, please cite: Mathieu Giraud, Stéphane Janot, Jean-Frédéric Berthelot, Charles Deltel, Laetitia Jourdan, Dominique Lavenier, Hélène Touzet, Jean-Stéphane Varré, Biomanycores, open-source parallel code for many-core bioinformatics, BOSC 2011.

Inria CNRS LIFL Université Lille 1