The BioGrids team installs and maintains a collection of biomedical applications for Harvard Medical School and Boston Children's Hospital. Members access a complete execution environment that includes a suite of applications preconfigured to run without any additional settings. Applications can be invoked from the shell prompt; there is no need to set up additional variables, change your path environment, or install supporting applications.
All applications in the BioGrids collection are maintained with multiple versions and are available for desktop or laptop installation using our software installation manager. The collection is also available to Harvard Medical School users on the HMS Orchestra cluster and has been optimized for the Orchestra environment. New applications and updates are released on a monthly basis. Users can report bugs and request installation of additional applications through the Get Help section of this website.
The BioGrids collection is an extension of the SBGrid.org project and was developed with support from the Harvard Medical School Tools and Technologies committee. To recognize this generous funding support all users should include the following statement in publications and presentations: "Software used in the project was installed and configured by BioGrids (cite: eLife 2013;2:e01456, Collaboration gets the most out of software).
Research computing providers interested in deploying BioGrids on their resources should contact BioGrids Principal Investigator, Piotr Sliz for more information.
BioGrids is a non-profit, NIH-compliant Service Center that operates out of Harvard Medical School that is currently operating as a beta project. We are in the midst of developing a pricing model to make the project available to the community at large.
BioGrids was conceived as a project to build on the success of the SBGrid Consortium, a community-based software curation, installation, and maintenance service, and extend that model to other biological disciplines that rely on computing and scientific software. The SBGrid Consortium was founded by Dr. Sliz in 2001 to support a dozen software applications for a handful of labs in the New England area. It has grown organically to include 300 labs at over 100 institutions in 21 countries around the world.
SBGrid now maintains a collection of over 350 software applications and supports the structural biology community by hosting workshops, a monthly webinar series, and supporting a variety of computing resources. Relying on seed funding from the Harvard Medical School Tools and Technologies Committee and the existing SBGrid infrastructure, we began work on the BioGrids in 2013, further developing infrastructure, identifying domain specialists to help curate the software, and compiling a collection of approximately 100 software titles.
Partner with Developers
Our team reports member feedback to developers to help identify bugs and promote features and works closely with many developers to beta test new software versions. We recompile and install popular applications on new operating systems, when developers can no longer provide support, and provide guidance on software licensing to streamline the licensing process for our members.
To fully benefit from BioGrids support, users must maintain an adequate computing infrastructure. Regular updates to your operating system (at least once every few years!) are essential for both Linux and OS X computers. And be sure to subscribe to and read ourmonthly newsletter, where software changes and updates as well as community events are announced.
Effective communication with the BioGrids support team is another important component of membership. We encourage users to report software problems and request new software titles using the BioGrids Support Form. When submitting a request, be sure to include the information necessary to properly troubleshoot your problem.
Please don't forget to cite the software tools that you rely on for your research - including BioGrids (see our eLife paper). We are actively applying for grant support to improve BioGrids and your acknowledgement directly supports our efforts.