August 2025 Newsletter
Our August software update includes nine 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
Trimmomatic - a flexible read trimming tool for Illumina NGS data.
Updated versions: 0.40
FreeSurfer - a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies.
Updated versions: dev_08202025
Python - a general-purpose, interpreted, object oriented, high-level dynamic programming language.
Updated versions: 3.11.8
StringTie - a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.
Updated versions: 3.0.1
dnarrange - Find rearrangements in "long" DNA reads relative to a genome sequence.
Updated versions: 1.6.3
RNAnorm - RNA-seq data normalization in Python.
Updated versions: 2.2.0
metaMDBG - a fast, low-memory assembler designed for long and accurate metagenomic reads, such as those produced by PacBio HiFi and Nanopore sequencing.
Updated versions: 1.2
MDAnalysis - an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations.
Updated versions: 2.9.0
tensorQTL - a GPU-enabled QTL mapper, achieving ~200-300 fold faster cis- and trans-QTL mapping compared to CPU-based implementations.
Updated versions: 1.0.10
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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