November 2023 Newsletter
Our November newsletter includes eleven 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:
macOS: Installation Manager 2.6.17
Linux: Installation Manager 2.6.17
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
3D Slicer is a free and open-source platform for analyzing and understanding medical image data.
Updated versions: 5.4.0 | Linux 64 5.6.0 | OS X INTEL
bids-validator Brain Imaging Data Structure (BIDS) validator.
Updated versions:1.13.1 | OS X INTEL 1.13.1 | Linux 64
R-pkgs-Biogrids contains common and requested R packages for BIOGRIDS. This title is dependent on R.
Updated versions: r4.1-20231122 r4.2.3-20231103
R a free software environment for statistical computing and graphics.
Updated versions:4.2.1 | Linux 64
origami a pipeline for processing and calling high-confidence chromatin loops associated with the ChIPped factor.
Updated versions:1.1 | Linux 64
whitematteranalysis (WMA) provides fiber clustering and tractography analysis tools.
Updated versions:0.3.0 | OS X INTEL 0.3.0 | Linux 64
CUDA redistributable software libraries to support CUDA applications for Linux.
Updated versions:12.1 | 12.1.1 | 12.2.2
hichip-peaks is a package that can be used to find enriched peak regions from HiChIP datasets that can then be used as an input to available loop calling tools or to do differential peak analysis.
Updated versions:0.1.2 | OS X INTEL 0.1.2 | Linux 64
Julia is a flexible dynamic language appropriate for scientific and numerical computing with performance comparable to traditional statically-typed languages.
Updated versions:1.9.3 | Linux 64 1.9.3 | OS X INTEL
mmquant RNA-Seq quantification tool, with special handling on multi-mapping reads.
Updated versions:1.0.7 | OS X INTEL 1.0.7 | Linux 64
scVelo is a scalable toolkit for RNA velocity analysis in single cells.
Updated versions:0.2.5 | Linux 64 0.2.5 | 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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