March 2024 Newsletter
Important Update
The default python in the BioGrids software collection is changing from version 2.7 to version 3. For those still using version 2.7 to run their own python scripts, that version will not be removed - it will just no longer be the default in the shell. You can restore it with a version override. We don’t expect this change to impact BioGrids applications as their python versions are defined explicitly.
Our software updates include twelve 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
AmberTools - suite of programs that allows users to carry out molecular dynamics simulations.
Updated versions:23 | Linux 64 23 | OS X INTEL
Python - general-purpose, interpreted, object oriented, high-level dynamic programming language.
Updated versions:3.9.16 | OS X INTEL 3.8.8 | OS X INTEL 3.7.0 | OS X INTEL 3.6.5 | OS X INTEL 3.12.2 | OS X INTEL 3.11.8 | OS X INTEL 2.7.5 | OS X INTEL 2.7.18 | OS X INTEL 2.7.10 | OS X INTEL 3.9.16 | Linux 64 3.8.8 | Linux 64 3.7.0 | Linux 64 3.6.5 | Linux 64 3.12.2 | Linux 64 3.11.8 | Linux 64 2.7.2 | Linux 64 2.7.18 | Linux 64 2.7.15 | Linux 64
DIAMOND - 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:2.1.9 | Linux 64 2.1.9 | OS X INTEL
gdcm - Grassroots DiCoM is a C++ library for DICOM medical files.
Updated versions:3.0.23 | Linux 64 3.0.23 | OS X INTEL
MAFFT - multiple sequence alignment program for unix-like operating systems.
Updated versions:7.525 | Linux 64 7.525 | OS X INTEL
hictk - Blazing fast toolkit to work with .hic and .cool files
Updated versions:0.0.11 | Linux 64 0.0.11 | OS X INTEL
BCFtools - 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:1.19 | OS X INTEL 1.19 | 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:4.5.0.0 | Linux 64 4.5.0.0 | OS X INTEL
SRA Toolkit - (Sequence Read Archive Toolkit) a collection of tools and libraries for using data in the INSDC Sequence Read Archives.
Updated versions:3.1.0 | Linux 64 3.1.0 | OS X INTEL
SpliceAI - deep learning-based tool to identify splice variants.
Updated versions:1.3.1 | OS X INTEL 1.3.1 | Linux 64
Fasten - Perform random operations on fastq files, using unix streaming. Secure your analysis with Fasten!
Updated versions:0.8.3 | Linux 64 0.8.3 | OS X INTEL
ANTs - (Advanced Normalization Tools) extracts information from complex datasets that include imaging.
Updated versions:2.5.1 | Linux 64 2.5.1 | 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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