795 Open Source Applications on O2 [BioGrids]

Effective July 1, 2025 HMS is no longer subscribing to institution-wide access to BioGrids. BioGrids is extending support on O2 through the end of July for continuity. If your lab would like to subscribe for continued access to the BioGrids software collection on O2 and other resources after July 31st, please email help@biogrids.org.

QuickStart

BioGrids provides biomedical software titles on O2, e.g. AlphaFold, samtools and R. The full list of titles is available on the BioGrids Website. BioGrids curated R versions come with many R packages already installed. Search for packages across all R versions here:

BioGrids R Package Search

All applications in the collections are curated daily by software engineers who are embedded at Harvard Medical School in BCMP. The collection utilizes the capsules technology that has been developed at Harvard. This allows end users to use all applications in the collection without further configuration. BioGrids can also be installed on Linux workstations and Mac computers. 

To start using BioGrids on O2 immediately use the following command:

All BioGrids applications are now available in your current shell as if they were natively installed on the system.

Obtain detailed information on all titles and available versions with these easy steps:

ace2sam                maq2sam-long plot-bamstats soap2sam.pl
blast2sam.pl           maq2sam-short psl2sam.pl wgsim
bowtie2sam.pl          md5fa sam2vcf.pl wgsim_eval.pl
export2sam.pl          md5sum-lite samtools zoom2sam.pl
fasta-sanitize.pl      novo2sam.pl samtools.pl
interpolate_sam.pl    plot-ampliconstats seq_cache_populate.pl

Version information for: /programs/x86_64-linux/samtools

Default version:                    1.20
In-use version:                     1.20

Installed versions:                 1.20 1.19.2 1.18 1.17 1.16.1 1.16 1.15.1 1.15 1.14 1.13 1.12 1.10 1.9 1.8 1.7 1.6 1.5 1.4.1 1.3.1 1.3 0.1.19
Other available versions:           1.19.2 1.18 1.17 1.16.1 1.16 1.15.1 1.15 1.14 1.13 1.12 1.10 1.9 1.8 1.7 1.6 1.5 1.4.1 1.3.1 1.3 0.1.19
Overrides use this shell variable:  SAMTOOLS_X

You can list all installed titles and versions with the biogrids-cli command. 

BioGrids can be installed on Linux and Mac computers for both single and multi-user systems. See https://biogrids.org for more information.

For inquiries about SBGrid, please contact help@sbgrid.org (and see the section on SBGrid below).

BioGrids Details

Overview

Academic Software Platform (ASP) integrates two major stacks of scientific software: BioGrids stack of ~700 biomedical applications (https://biogrids.org/software/) as well as SBGrid stack of ~500 structural biology applications. The BioGrids stack is ready for execution on the O2 cluster at Harvard Medical School and on the E3 cluster at Boston Children’s Hospital. Multiple versions of applications are maintained, and users can also easily install the same stack of software on laptops, research workstations or cloud resources, under Linux or Mac OS X operating systems (Fig. 1). Access to BioGrids is offered to all research groups at Harvard and affiliated institutions.

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 2025, BioGrids supports 795 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/.

Based on the user requests, applications and new versions of the existing applications are added to the collection on a monthly basis, or potentially more often on as-needed basis. Please note that server-based software (web servers, database servers, docker containers, etc) are generally not supported.

Notably, we also provide access to two commercial applications: 

• 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 E3 at BCH in the /programs directory. To use these applications, source the biogrids environment with the following command (Figure 2): 

   $  source /programs/biogrids.shrc

Afterwards, users can execute all BioGrids applications without further configuration. E.g. to run bowtie, just type bowtie in your command prompt. Alternatively the applications can be also installed as modules (see below), but the advantage of our native environment is the ability to mix and match any application from the BioGrids with simple calls to binaries.

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 ~700 applications as a single module with the following command:

   $ module load biogrids/latest