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SBGridTV

What We Do

We provide 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.

Built-to-run software and advanced training

SBGrid Consortium members access a complete execution environment that includes a suite 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 400+ structural biology applications on Linux and OS X computers in more than 300. 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 simple SBGrid installation client. 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.

We add new titles and provide first-level technical support in response to your software requests and bug reports. Our team reports member feedback to developers,recommending new features and describing bugs encountered, and also work closely with many developers to beta test new software versions.

Training

The monthly live webinars that we host feature contributing developers demonstrating their software and highlighting recent improvements. These tutorials offer members the opportunity to ask the developer questions directly relevant to their research. The SBGrid webinar collection is available on our website and published on theSBGridTV YouTube channel. Through occasional hands-on workshops and local computing schools, we also offer more intensive training opportunities to members.

Primary Publication

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

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 subset of chemical compounds that are used for screening at the ICCB-Longwood Screening Facility.

    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

    The SBGrid Software Suite contains 400+ scientific software applications for Linux and Mac, and is available as a site installation or using our software installation client, with a graphical user interface for Mac or command line versions for Mac and Linux. To fully benefit from the built-to-run software environment, member laboratories must maintain an adequate computing infrastructure. Regular updates to your operating system (at least once every few years!) are essential for both Linux and Mac computers. We encourage users to report software problems and request new software titles using the Support Form. Please don’t forget to cite the software tools that you rely on for your research - including our eLife paper.

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