User:Doughertye/SBGrid Consortium

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The SBGrid Consortium ^[1] is a non-profit, National Institutes of Health-compliant Service Center that operates out of Harvard Medical School. SBGrid provides the global structural biology community with support for research computing.

SBGrid’s primary service is the collection, deployment and maintenance of a comprehensive set of software and computational tools that are useful in structural biology research. The SBGrid software library acts as a scientific "app store" that allows users to access a wide range of up-to-date applications without having to download, compile, configure, maintain or update software. Members also benefit from access to SBGrid-supported high performance computing (HPC) resources and training opportunities.

Members of the SBGrid Consortium fund SBGrid’s ongoing operations through an annual membership fee. The resulting organization is a user-supported and user-directed community resource.

SBGrid Background

SBGrid was first created by Piotr Sliz as an in-house effort to support and maintain a few dozen X-ray crystallography in the laboratory of Stephen C. Harrison and the late Don Craig Wiley, then at Harvard University and Boston Children’s Hospital. After adding support for additional labs, SBGrid began charging user fees to recover operational costs in 2002. It also expanded software support to include electron microscopy (EM), nuclear magnetic resonance (NMR) and other structural biology techniques. In response to requests from users for support for Macintosh computers, SBGrid recompiled most of its applications to run on the OSX platform in 2004. By 2006, the SBGrid consortium included 37 laboratories at 14 different institutions.

SBGrid’s user-oriented community began to solidify in 2008 with its first user meeting: Quo Vadis Structural Biology (“Where is structural biology heading?”). The meeting attracted approximately 300 participants and incorporated a structural biology symposium and three workshops: scientific programming with Python; molecular visualization with Maya; and OSX programming. SBGrid held subsequent meetings in Boston (2009, 2013, 2014). In 2011 SBGrid hosted the Open Science Grid All-Hands Meeting at Harvard Medical School after having established a Virtual Organization (SBGrid VO) within the Open Science Grid (OSG) and deployed a grid computing portal in 2010. SBGrid has become one of the top OSG users (outside of high-energy physics users) and utilizes ~5,000,000 CPU hours per year.

In 2012, SBGrid launched a webinar program featuring software tutorials from a different developer each month. Recordings are publicly available on the YouTube.org/SBGridTV channel. SBGrid team members have also published a guide to software licensing ^[2], an editorial that advocates for better disclosure of source code^[3], and recommendations for optimizing peer review of software source code.^[4]

By 2014, SBGrid had 245 member laboratories around the world. The consortium supports more than 270 scientific software applications.

SBGrid Membership

Laboratories interested in joining SBGrid may request a membership packet or apply through the SBGrid Consortium Registration process. SBGrid has developed an end-user licensing agreement (EULA) in cooperation with the Harvard University Office of Technology Development (OTD) to formalize its relationships with Consortium laboratories.

During the registration process, an SBGrid associate with advise new labs regarding hardware and computing requirements to deploy SBGrid support onsite. Once a new member laboratory’s hardware is in place, most new members are fully operational with SBGrid within two weeks of joining.

SBGrid Software Services for Members

The SBGrid team installs and maintains a collection of 270+ structural biology applications on Linux and OS X computers in member laboratories, 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.

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

Training for SBGrid Members

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 YouTube.org/SBGridTV channel.

Resources for SBGrid Members

The SBGrid technical team offers guidance to new members in setting up an adequate computing infrastructure. Members also benefit from access to a number of other specialized computing resources, including:

The Wide-Search Molecular Replacement (WSMR) computing portal,^[5] a service for determining crystallographic phase using the Phaser program.^[6]

The Deformable Elastic Network (DEN) portal,^[7] a service for refining low-resolution electron density data.

A dedicated server to host the SHARP application.^[8]

A Discovery Server for Small Molecule Docking Computations with Schrodinger Glide, which is available to SBGrid members in North America. A library of 400,000 compounds are available from the ICCB-Longwood Screening Facility has been preprocessed with Schrodinger’s ligprep and can be incorporated in the virtual screening workflow.

SBGrid provides European WeNMR Grid Certificates to the North American Structural Biology Community. WeNMR is a grid-based platform that integrates and streamlines the computational approaches necessary for NMR and SAXS data analysis and structural modeling.

XSEDE is a virtual cyberinfrastructure in the U.S. that is supported by the National Science Foundation that provides access to High Performance Computing (HPC) by combining resources from several HPC sites.

SBGrid operates an OpenScienceGrid (OSG) Virtual Organization and utilizes OSG opportunistic resources to support WSMR and DEN workflows. The OSG is a US-based, NSF-supported multi-disciplinary partnership to federate local, regional, community, and national cyberinfrastructures to meet high throughput computing needs for researchers.

SBGrid Resources for Software Developers

SBGrid provides developers of SBGrid-supported applications with access to the SBGrid build-test computing network at Harvard Medical for building and testing software on a range of operating systems.

References

^ Morin, A. "Cutting edge: Collaboration gets the most out of software". eLife 2013;2:e01456.
^ Morin, A. "A quick guide to software licensing for the scientist-programmer". PLOS Computational Biology July 2012.
^ Morin, A. "Shining Light into Black Boxes". Science 336:159-60(2012).
^ Morin, A. "Optimizing Peer Review of Software Code". Science 341:236-237(2013). {{cite web}}: Missing or empty |url= (help)
^ Stokes-Rees, I. "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).
^ McCoy, AJ. "Phaser crystallographic software". J Appl Cryst 40:658–74.
^ O’Donovan, DJ. "A grid-enabled web service for low-resolution crystal structure refinement". Acta Crystallographica D68: 261-267 (2012).
^ Bricogne, G. "Generation, representation and flow of phase information in structure determination: recent developments in and around SHARP 2.0". Acta Crystallogr D Biol Crystallogr. 2003; 59:2023-30).

External links

www.example.com

[1] Morin, A. "Cutting edge: Collaboration gets the most out of software". eLife 2013;2:e01456.

[plos2012-2] Morin, A. "A quick guide to software licensing for the scientist-programmer". PLOS Computational Biology July 2012.

[science2012-3] Morin, A. "Shining Light into Black Boxes". Science 336:159-60(2012).

[science2013-4] Morin, A. "Optimizing Peer Review of Software Code". Science 341:236-237(2013). {{cite web}}: Missing or empty |url= (help)

[5] Stokes-Rees, I. "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).

[6] McCoy, AJ. "Phaser crystallographic software". J Appl Cryst 40:658–74.

[7] O’Donovan, DJ. "A grid-enabled web service for low-resolution crystal structure refinement". Acta Crystallographica D68: 261-267 (2012).

[8] Bricogne, G. "Generation, representation and flow of phase information in structure determination: recent developments in and around SHARP 2.0". Acta Crystallogr D Biol Crystallogr. 2003; 59:2023-30).

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