February 2024 Newsletter
Our February newsletter includes ten new and updated titles for Mac and Linux. 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
Python - general-purpose, interpreted, object oriented, high-level dynamic programming language.
Updated versions: 3.9.16 | Linux 64 3.6.5 | Linux 64
Updated versions: 3.11.8 | Linux 64 3.11.8 | OS X INTEL
AlphaFold - an implementation of the inference pipeline of AlphaFold v2.0 using a completely new model that was entered in CASP14.
Updated versions: 2.3.2_202402b | Linux 64
humann3 - pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data.
Updated versions:3.8 | OS X INTEL 3.8 | Linux 64
MetaPhlAn - Metagenomic Phylogenetic Analysis
Updated versions:4.0.6 | OS X INTEL 4.0.6 | Linux 64
BLAST+ - suite of BLAST (Basic Local Alignment Search Tool) tools that utilizes the NCBI C++ Toolkit with a number of performance and feature improvements over the legacy BLAST applications.
Updated versions:2.15.0 | Linux 64
mbgc (Multiple Bacteria Genome Compressor) is a tool for compressing genomes in FASTA (or gzipped FASTA) input format.
Updated versions:2.0.1 | OS X INTEL 2.0.1 | Linux 64
LAST - finds & aligns related regions of sequences. LAST is designed for moderately large data (e.g. genomes, DNA reads, proteomes).
Updated versions:1541 | Linux 64 1541 | OS X INTEL
Juicer - one-click pipeline for processing terabase scale Hi-C datasets. Using Juicer, you can:
Updated versions:2.0.0-beta | Linux 64
HHsuite - open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).
Updated versions:3.3.0 | OS X INTEL 3.3.0 | Linux 64
hictk - Blazing fast toolkit to work with .hic and .cool files
Updated versions:0.0.7 | Linux 64 0.0.7 | 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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