April 2025 Newsletter
Our April software update includes thirteen 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.
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
HMMER - is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).
Updated versions:3.4 | Linux 64 | OS X INTEL
simpleaf - is a rust framework to make using alevin-fry even simpler.
Updated versions:0.19.5 | Linux 64
dREG - Detection of Regulatory DNA Sequences using GRO-seq Data.
Updated versions:4a1643a | Linux 64
Predictosaurus - a command-line tool designed for uncertainty-aware haplotype-based genomic variant effect prediction. It provides comprehensive functionality for building variant graphs, processing genomic features, and extracting peptide sequences. The tool integrates various bioinformatics processes to support efficient data analysis and visualization.
Updated versions:0.3.0 | OS X INTEL 0.3.0 | Linux 64
vireosnp - Variational Inference for Reconstructing Ensemble Origin by expressed SNPs in multiplexed scRNA-seq data.
Updated versions:0.5.9 | Linux 64 0.5.9 | OS X INTEL
skDER - efficient & high-resolution dereplication of microbial genomes
Updated versions:1.3.0 | Linux 64 1.3.0 | OS X INTEL
R - a free software environment for statistical computing and graphics. This update includes the R package RMariaDB.
Updated versions:4.4.2 | OS X INTEL 4.4.2 | Linux 64
GMAP - Genomic mapping and alignment program for mRNA and EST sequences.
Updated versions:2025.04.18 | Linux 64 2025.04.18 | OS X INTEL
UniFrac - Fast phylogenetic diversity calculations
Updated versions:1.3.2 | Linux 64 1.3.2 | OS X INTEL
ensembl_vep - predicts the functional effects of genomic variants
Updated versions:113.4 | Linux 64 113.4 | OS X INTEL
JupyterLab - a program for the next-generation web-based user interface for Project Jupyter. JupyterLab enables you to work with documents and activities such as Jupyter notebooks, text editors, terminals, and custom components in a flexible, integrated, and extensible manner.
Updated versions:4.4.0 | Linux 64 4.4.0 | OS X INTEL
PyMOL Open Source - open source version of the widely used molecular visualization package developed by Warren DeLano.
Updated versions:3.1.0 | Linux 64 3.1.0 | OS X INTEL
Bakta - rapid and standardized annotation of bacterial genomes & plasmids.
Updated versions:1.11.0 | Linux 64 1.11.0 | 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 Harvard Medical School and Boston Children's Hospital and relies on a framework that was developed by SBGrid.
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