February 2025 Newsletter
Our February software update includes fifteen new and updated titles. Updates include the latest version of AlphaFold (3.0.1) and significant new package updates for R version 4.4.2.
New software titles 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 660 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
AlphaFold - an implementation of the inference pipeline of AlphaFold v2.0 using a completely new model that was entered in CASP14.
Updated versions: 3.0.1 | Linux 64
AmberTools24 - a suite of programs that allows users to carry out molecular dynamics simulations, particularly on biomolecules.
Updated versions: 24 | Linux 64 24 | OS X INTEL
DIAMOND - a high-throughput program for aligning a file of short DNA sequencing reads against a protein reference database such as NR, at 20,000 times the speed of BLASTX, with high sensitivity.
Updated versions: 2.1.11 | Linux 64 2.1.11 | OS X INTEL
GEDI - a software platform for working with genomic data such as sequencing reads, sequences, per-base numeric values or annotations written in Java.
Updated versions: 1.0.6a | OS X INTEL 1.0.6a | Linux 64
HTSlib - a C library for reading/writing high-throughput sequencing data.
Updated versions: 1.9 | OS X INTEL 1.9 | Linux 64 1.21 | Linux 64 1.21 | OS X INTEL
kma - a method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend.
Updated versions: 1.4.18 | Linux 64
pairtools - CLI tools to process mapped Hi-C data
Updated versions: 1.1.3 | Linux 64 1.1.3 | OS X INTEL
PlotHiC - is used to visualize whole genome-wide contact heatmaps after genome scaffolding.
Updated versions: 0.5.0 | OS X INTEL 0.5.0 | Linux 64
polychrom - a tool designed to build mechanistic models - i.e. models that simulates a biological process.
Updated versions: 0.1.1 | OS X INTEL 0.1.1 | Linux 64
PPanGGOLiN - a software suite used to create and manipulate prokaryotic pangenomes from a set of either genomic DNA sequences or provided genome annotations. It is designed to scale up to tens of thousands of genomes.
Updated versions: 2.2.1 | Linux 64 2.2.1 | OS X INTEL
R - a free software environment for statistical computing and graphics.
Updated versions: 4.4.2 | OS X INTEL 4.4.2 | Linux 64
SnpEff - genomic variant annotation and functional effect prediction toolbox.
Updated versions: 5.2e | Linux 64 5.2e | OS X INTEL
TRUST4 - a computational tool to analyze TCR and BCR sequences using unselected RNA sequencing data, profiled from fluid and solid tissues, including tumors.
Updated versions: 1.1.5 | Linux 64 1.1.5 | 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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