The following information has been graciously provided by The BioGrids Consortium. Please contact help@biogrids.org with questions about the contents of this page.
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Fig. 1. BioGrids applications are supported on a wide variety of computational platforms.
1. What are the benefits of using BioGrids compiled versions of applications?
An experienced team of software engineers, who complete over 200 software installations per year, professionally compile all BioGrids titles. The team (https://biogrids.org/about/staff/), which is embedded in the Department of Biological Chemistry and Molecular Pharmacology at Harvard Medical School, takes care of all software dependencies, completes extensive testing of each title, and preconfigures the execution environment for each application. All BioGrids applications are executed through the ASP environment, which ensures that there are no clashes in execution and library paths. Once an application is included in the BioGrids collection, all you have to do to launch the application is to call it by its name (Figure 2). No shell modifications, library inclusions or path modifications are needed.
2. What software titles are available?
As of March 2021, BioGrids supports 378 open source applications, with extensive coverage of bioinformatics, imaging, and scientific visualization. The full list of applications is always available on the BioGrids website at https://biogrids.org/software/.
Additional titles and new versions of the existing applications can be requested by completing the following form https://biogrids.org/help/?tab=software or by email to help@biogrids.org. |
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Human Gene Mutation Database (HGMD) - Tools For Variant Discovery software is available, as BioGrids coordinates a Longwood-wide license. Access is provided on a fiscal year basis, July-June of the following year. We grant complimentary access to users who submit requests within the current fiscal year, and ask those users to contribute to the shared license upon renewal (around $300/year/user for online access, and more for access to the downloadable database). To request access please complete the following form https://www.biogrids.org/hgmd/register. It typically takes ~5 business days to approve requests.
Schrodinger Drug Discovery platform (access limited to Harvard Medical School groups only). As part of our long-standing engagement with Schrodinger, SBGrid (Morin et al., 2013) offers access to an extensive collection of Schrodinger Drug Discovery platform software. In conjunction with software access, we provide additional services ranging from technical support and installation, dedicated computational resources, compound libraries, scientific advice, and collaborative projects. There is no additional fee for exploratory use of this special medicinal chemistry platform. For moderate and heavy use, we will assess an additional fee to offset license and infrastructure costs. Please contact insilico@sbgrid.org to inquire about our support for small molecule discovery projects.
3. How can I run BioGrids applications on HMS and BCH clusters?
All BioGrids applications are preinstalled on O2 at HMS and on E2 at BCH in the /programs directory. To use these applications, source the biogrids environment with the following command (Figure 2):
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Figure 2. BioGrids shell supports access to a stack of ~300 biomedical applications without further configuration.
4. Are applications supported as modules?
There are two ways to run BioGrids applications in a module environment (Figure S1). You can preload the entire BioGrids collection with ~350 applications as a single module with the following command:
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After this modification, the “module avail” command should display an additional 900 entries for all versions of BioGrids supported software.
5. Where can I find full documentation and tutorials?
The software page (https://biogrids.org/software/) on the BioGrids website provides an excellent starting point to explore functionality of individual applications (Figure S2). For each software title we meticulously curate the following information: a) a brief description and relevant keywords, b) Find Out More page with additional version and citation information, c) link to software website and d) link to relevant web forums.
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Additional documentation resource include:
Support wiki, at https://biogrids.org//wiki with information mostly focused on installation and configuration of the BioGrids environment
A YouTube Channel with training videos https://www.youtube.com/user/SBGridTV, which is currently mostly focused on structural biology software.
6. Are BioGrids titles available through Open OnDemand?
Open OnDemand (OOD) is an NSF-funded, open-source High Performance Computing (HPC) based project (Figure S3). It provides web-based graphical access to HPC compute nodes, enabling GUI-based applications, file management, and graphical desktops for compute clusters.
BioGrids has piloted Jupyter, RStudio, IGV and several other applications in OOD on HPC clusters at BCH and HMS. We provide templates for implementing other GUI-based BioGrids applications. No additional software installations are needed. The BioGrids environment greatly simplifies OOD templating, typically only requiring setting the name of the cluster, queue, and particular BioGrids application. Further customization can be made to provide additional resources.
7. How can I run BioGrids applications on other computers/AWS?
In order to access BioGrids applications outside of O2/E2, you will need a Linux or Mac computer preconfigured with BioGrids software. You can complete this installation yourself (Figure S4), on a single computer or laptop, using our Installation Manager (https://biogrids.org/wiki/client_install), or work with your local system administrator to install the software on your network. Installation in cloud environments is also supported.
8. Can I run a particular version of a BioGrids application?
Definitely. The ASP environment supports access to multiple versions of each application. By default, you have access to the most recent, stable version of an application. To change the version in use, simply set a single environment variable, for example: $ export SAMTOOLS_X=1.9. Please visit the BioGrids wiki for full documentation: https://biogrids.org/wiki/versions. If you would like to use a version not currently available at your site, please contact help@biogrids.org.
9. I urgently need access to a software title/version which is not included in BioGrids. What to do?
Please email help@biogrids.org immediately and indicate that your request is urgent. We will review your request and provide an installation timeline within 1 business day. In the meantime, you can always install the application on your own in your home directory. We recommend that you transition to the BioGrids version once the application becomes available.
10. Can Research Computing advise me on the use of BioGrids software?
All Research Computing consultants at HMS and at BCH are familiar with BioGrids setup, and utilize BioGrids software. In additional the following HMS and BCH staff are involved with the project:
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Bill Barnett - Harvard Medical School
Shira Rockowitz - Boston Children’s Hospital
11. BioGrids Updates and Newsletter
The BioGrids newsletter is distributed on a monthly basis in conjunction with the monthly software upgrade cycle. Information on recently added or updated software is available at https://biogrids.org/software/recent/archive/.
12. What is BioGrids and how is it supported?
BioGrids is a part of larger Academic Software Initiative (ASI, formerly SBGrid) - a non-profit, academic effort by the Sliz Group in the Department of Biological Chemistry and Molecular Pharmacology at Harvard Medical School to develop a distributed research computing infrastructure, with focus on scientific software. The key elements of the initiative include:
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The focus of BioGrids is to specifically maintain a stack of biomedical research applications. Its efforts support BioGrids Consortium - a community of academics that utilize BioGrids software stack.
13. Is the Academic Software Platform utilized more broadly? How is SBGrid related to BioGrids?
The ASP provides a general software execution platform that can support various collections of scientific applications. It was developed at Harvard Medical School in 2001, initially specifically to support the structural biology community with the SBGrid stack of applications. The ASP SBGrid stack of 453 applications (https://sbgrid.org/software/) includes software collection such as X-ray Crystallography, Electron Microscopy, NMR, Computational Chemistry, Structure Visualization and Structure Analysis. The SBGrid stack is now used globally in 22 countries by 395 research groups (https://sbgrid.org/members/). Access to the SBGrid stack of applications is available to structural biologists who are SBGrid Consortium members. The BioGrids stack of applications, utilizing the same ASP infrastructure, was established in 2016, and is now utilized by research groups at Harvard Medical School and Boston Children’s Hospital.
14. How is the software licensed?
Please note that use of BioGrids software is subject to the terms of the end-user-licenses of all individual titles. In particular commercial use might be limited. A full copy of corresponding licenses is typically available at individual software websites - for your reference we provide links to software websites on the BioGrids page https://biogrids.org/software/. SBGrid support is limited to technical guidance, and unless additional written arrangements are in place, all intellectual rights are retained by the users.
15. How to Acknowledge and Cite BioGrids?
In all publications which rely on the use of BioGrids-compiled software, please reference the primary SBGrid citation URL (Morin et al., 2013). Users can also include the BioGrids logo in the acknowledgement slides of their presentations
References:
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Fig. S2. Listing of all BioGrids applications is available on http://biogrids.org website. Information about each software title includes brief description, link to the software website, citation information and links to relevant software forums.
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Fig. S3. RStudio application available through HMS O2 Open OnDemand system.
Fig. S4. BioGrids software installer running on OS X operating system.
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