July 2025 Newsletter
Our July software update includes ten new and updated titles. Our new R package search tool lets you easily find packages of interest and shows which versions of BioGrids R already contain that package.
New software titles and R packages can be requested by sending email to help@biogrids.org or filling out our Software Request Form.
About BioGrids
BioGrids is a core facility at Harvard Medical School that provides an integrated and tested suite of ~ 800 applications (https://www.biogrids.org/software/) used in biomedical sciences for installation on Mac and Linux operating systems, including collections for high-throughput sequencing, genomics, proteomics, and visualization. These collections are available for members to install on individual laptops or workstations, as a site installation shared to users through a network, and on HPC or cloud resources, provided that such access is limited to BioGrids members.
We maintain multiple versions for many applications, including more than 1500 R packages (https://biogrids.org/wiki/R_packages.html), and roll out updates a couple times each month. BioGrids members can help shape the software collection and are encouraged to submit requests for new titles and updates to existing titles, which our curation team will prioritize based on demand from the wider community.
We have institutional or lab-based subscription options. Contact us at help@biogrids.org for a quote.
Remote Working Help
The BioGrids Wiki provides step by step instructions for installing BioGrids software on a local laptop or desktop machine. If you prefer a live demonstration, or run into trouble, please contact help@biogrids.org. We can set up a Zoom meeting to assist you.
Cite BioGrids
If your use of BioGrids supplied software was an important element in your publication, please include the following statement in your work:
"Software used in the project was installed and configured by BioGrids
(cite: eLife 2013;2:e01456, Collaboration gets the most out of software.)"
See our Grant Support page for additional details.
Register here to try out our software installer, which allows users to choose from over 770 bioinformatics and life sciences tools that can be installed as ready-to-run applications on Mac or Linux machines with the click of a button or a short command from the CLI. No need to worry about dependencies or compilation.
BioGrids is supported by a team of scientists and engineers at HMS. We provide direct support to BioGrids members. This includes all aspects of software installation and management. If you need assistance of any kind please send a note to: help@biogrids.org.
BioGrids Quickstart
The latest version of the BioGrids Installation Manager is available for Linux and MacOS computers from the BioGrids Wiki QuickStart page.
Start the BioGrids environment:
source /programs/biogrids.shrc
List available titles (Linux):
cat /programs/x86_64-linux/biogrids_x86_64-linux
List available titles (Mac):
cat /programs/i386-mac/biogrids_i386-mac
Get version and override info:
biogrids-info -l star
Get list of executables for a title:
biogrids-list star
Need more help? Send mail to: help@biogrids.org
Software Updates
R - a free software environment for statistical computing and graphics.
Updated versions:4.4.2 | OS X INTEL 4.4.2 | Linux 64
Cell Ranger
a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis.
Updated versions:9.0.1 | Linux 64
UGENE a free open-source bioinformatics software for macOS, and Linux.
Updated versions:52.1 | OS X INTEL 52.1 | Linux 64
SAIGE - is an R package developed with Rcpp for genome-wide association tests in large-scale data sets and biobanks.
Updated versions:1.4.7 | Linux 64
Julia - a flexible dynamic language appropriate for scientific and numerical computing with performance comparable to traditional statically-typed languages.
Updated versions:1.11.6 | Linux 64 1.11.6_arm | OS X INTEL 1.11.6_intel | OS X INTEL
regenie - a C++ program for whole genome regression modelling of large genome-wide association studies.
Updated versions:4.1.1 | OS X INTEL 4.1.1 | Linux 64
BCFtools - a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
Updated versions:1.22 | Linux 64 1.22 | OS X INTEL
SAMtools - (Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.
Updated versions:1.22.1 | Linux 64 1.22.1 | OS X INTEL
Cactus - a reference-free whole-genome multiple alignment program based upon notion of Cactus graphs.
Updated versions:2.9.9 | Linux 64
GATK - (Genome Analysis Toolkit) a software package developed to analyze high-throughput sequencing data capable of taking on projects of any size with a primary focus on variant discovery, genotyping, and data quality assurance.
Updated versions:4.6.2.0 | Linux 64 4.6.2.0 | OS X INTEL
Software Training
Center for Computational Biomedicine
The Center for Computational Biomedicine (CCB) Fall newsletter contains training and collaboration opportunities.
HMS Research Computing
HMS Research Computing User Training
Bioinformatics Support
Need help getting software installed on new machines? Have you been planning to try Amazon Web Services (AWS) cloud computing?
BioGrids can help you get started. We have expertise in bioinformatics, programming, workflow development and high performance computing.
We improve the collection with feedback from the community.
Want to see a new application in BioGrids?
Let us know: help@biogrids.org
BioGrids is supported by Boston Children's Hospital and relies on a framework that was developed by SBGrid.
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