Built-to-run software

BioGrids Consortium members access a complete execution environment that includes a suite of of structural biology applications preconfigured to run without any additional settings. Applications are invoked from the shell prompt; there is no need to set up additional variables, change your path environment, or install supporting applications. Members find savings in time, money, and the frustration associated with managing software licensing, updates, conflicts, and bug fixes.

The Consortium team installs and maintains a comprehensive collection of these 700+ biomedical software applications on Linux and macOS computers. These applications are remotely curated with updates made available each month and recompiled versions pushed out for newer releases of supported operating systems. Consortium members can self-manage access to individual applications on their personal Mac or Linux workstations using a modular BioGrids installation manager powered by our new capsules environment, which also ensures consistent operation across various platforms without requiring system administration access.

The BioGrids collection is also available to Harvard Medical School users on the HMS O2 cluster and has been optimized for the O2 environment.

Primary Publications

The BioGrids collection is an extension of SBGrid 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" and cite the following publications:

• Andrew Morin, Ben Eisenbraun, Jason Key, Paul C Sanschagrin, Michael A Timony, Michelle Ottaviano, Piotr Sliz. Cutting edge: Collaboration gets the most out of software. Read more in eLife
• Carol Herre et al. Introduction of the Capsules environment to support further growth of the SBGrid structural biology software collection (2024). Read more in Acta Cryst D

History

BioGrids was conceived as a project to build on the success of SBGrid Consortium, a community-based consortium that curates installs and maintains scientific software for structural biologists, and extend that model to other biological disciplines that rely on computing and scientific software. SBGrid 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 500 labs and research institutions at over 180 institutions in 22 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. Utilizing 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 curate the software, and compiling an initial collection of approximately 100 software titles.