SBGridTV

What We Do for Structural Biologists

We support structural biologists by providing structural biology laboratories with a tested and refined software infrastructure that includes a large library of scientific applications. Members also benefit from access to SBGrid-supported high performance computing (HPC) resources and training opportunities.

Software Support

The SBGrid team installs and maintains a collection of 270+ structural biology applications on Linux and OS X computers in your laboratory (including laptops). A few commercial applications are also supported, including Geneious for cloning and bioinformatics, incentive builds for PyMOL, and for North American labs, the Schrodinger Small-Molecule Drug Discovery Suite. Members access a complete execution environment that includes the suite of structural biology 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.

SBGrid will monitor all software websites for updates and install major software upgrades on a monthly basis. We also recompile existing software for newer releases of supported operating systems and respond to your bug reports and new software requests.

Members find savings in time, money, and the frustration associated with managing software licensing, updates, conflicts, and bug fixes.

Training

SBGrid hosts monthly live webinars that feature tutorials by contributing developers and offer members the opportunity to ask the developer questions directly. This collection of tutorials is also published on the SBGridTV YouTube channel and made publicly available. More intensive training opportunities are provided to members through occasional hands-on workshops and local computing schools.

Publications

You can find out more about ongoing and completed activities and projects related to SBGrid by reading these publications:

Primary Publication:

  • 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. Journal | PDF

Structure determination portal and grid computing:

  • Ian Stokes-Rees and Piotr Sliz. Protein Structure Determination by exhaustive search of Protein Data Bank derived databases. PNAS (2010). Journal | PDF
  • Daniel J O'Donovan, Ian Stokes-Rees, Yunsun Nam, Stephen Blacklow, Gunnar F Schroder, Axel T Brunger and Piotr Sliz. A grid-enabled web service for low-resolution crystal structure refinement. Acta Crystallographica D68: 261-267 (2012). Django-condor code | Journal | PDF
  • Ian Stokes-Rees, Ian Levesque, Frank V. Murphy IV, Wei Yang, Ashley Deacon and Piotr Sliz. Adapting federated cyberinfrastructure for shared data collection facilities in structural biology. Journal of Synchrotron Radiation 19:462-467 (2012). Journal | PDF
  • Ian Stokes-Rees and Piotr Sliz. Compute and data management strategies for grid deployment of high throughput protein structure studies. 3rd IEEE workshop on Many-Task Computing on Grids and Supercomputers. (2010). PDF

Software Licensing and Open Source:

  • Andrew Morin and Piotr Sliz. Optimizing Peer Review of Software Code. Science 341: 236-237 (2013). Journal | PDF
  • Andrew Morin, Jennifer Urban, Paul D Adams, Ian Foster, Andrej Sali, David Baker and Piotr Sliz. Shining Light into Black Boxes. Science 6078: 159-160 (2012). Letter from Yale | Journal | PDF
  • Andrew Morin, Jennifer Urban and Piotr Sliz. A quick guide to software licensing for the scientist-programmer. PLoS Computational Biology 8: e1002598 (2012). Journal | PDF

Structural Biology Software:

  • Andrew Morin and Piotr Sliz. Structural biology computing: Lessons for the biomedical research sciences. Biopolymers (2013). Journal | PDF
  • Amber L McConahy, Ben Eisenbraun, James Howison, James D Herbsleb and Piotr Sliz. Techniques for Monitoring Runtime Architectures of Socio-technical Ecosystems. 2012 ACM Conference on Computer Supported Cooperative Work: Data-Intensive Collaboration in Science and Engineering Workshop. (2012). Journal | PDF

Special Resources

Our technical team can offer guidance for setting up an adequate computing infrastructure in your own laboratory. We also facilitate access to the Open Science Grid Cyberinfrastructure through the SBGrid OSG Virtual Organization and the US XSEDE Cyberinfrastructure through the SBGrid Campus Champion program. The XSEDE program is especially useful for EM computations. See our Additional Resources page for more information.

Members also benefit from access to a number of other specialized computing resources, including:

    • the Wide-Search Molecular Replacement (WSMR) computing portal, a service for determining crystallographic phase using the Phaser program.
    • the Deformable Elastic Network (DEN) portal, a service for refining low-resolution electron density data.
    • a dedicated server to host the SHARP application.
    • a subset of chemical compounds that are used for screening at the ICCB-Longwood Screening Facility.
    • for labs in North America, a dedicated SBGrid cluster at Harvard Medical School to run docking jobs using a limited version of the Schrodinger Suite for molecular modeling and small molecule docking.

    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. Our monthly webinars and occasional workshops also support developer training initiatives.

    Developers, please see our Deploy Your Software page for more information on our developer program.

    Cost

    The SBGrid Consortium is a non-profit, NIH-compliant Service Center that operates out of Harvard Medical School. We view the Consortium as a user-supported and user-directed community resource and rely on annual membership fees to support our community operation. Please visit our Join Us page to request a membership packet and a detailed quote.

    Your Responsibilities

    To fully benefit from SBGrid support, Consortium members must maintain an adequate computing infrastructure. Most labs operate a central server to host structural biology applications, share the software directory to individual workstations, configure individual workstations with one of our supported Linux operating systems (e.g. Red Hat, CentOS, or Scientific Linux), and install NVIDIA drivers and other required system components. 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 the SBGrid monthly newsletter, where software changes and updates as well as community events are announced.

    Effective communication with the SBGrid support team is another important component of membership. We encourage users to report software problems and request new software titles using the SBGrid 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 SBGrid (see our eLife paper). We are actively applying for grant support to improve SBGrid and your acknowledgement directly helps this effort.