June 2022 Newsletter
Our June newsletter includes nine new and updated titles for Mac and Linux as well as new R packages. New titles include OpenFold, a complete PyTorch implementation of AlphaFold, as well as the latest version of AlphaFold itself.
New software titles can be requested by sending email to help@biogrids.org or filling out our webform:
https://biogrids.org/help/?tab=software
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.
MacOS 10.15 Catalina
Due to new security measures in OSX, installation under MacOS 10.15 requires an additional step. We have detailed a workaround to install BioGrids and SBGrid on new machines. Two approaches are available.
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 530 bioinfomatics 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 2.5.12
Linux: Installation Manager 2.5.12
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:2.2.2 | Linux 64 2.2.0 | Linux 64 2.1.2 | Linux 64 2.1.1 | Linux 64
globuscli a standalone application that can be installed on the user’s machine and used to access the Globus service.
Updated versions:3.6.0 | Linux 64
SomaticSeq is an ensemble somatic SNV/indel caller that has the ability to use machine learning to filter out false positives from other callers.
Updated versions:3.7.3 | OS X INTEL 3.7.3 | Linux 64
R-pkgs-Biogrids contains common and requested R packages for BIOGRIDS. This title is dependent on R.
Updated versions:r4.1-20220610 | OS X INTEL r4.1-20220610 | Linux 64
fqgrep is an approximate sequence pattern matcher for FASTQ/FASTA files.
Updated versions:0.4.4 | OS X INTEL 0.4.4 | Linux 64
scAllele is a versatile tool to detect and analyze nucleotide variants in scRNA-seq.
Updated versions:0.0.9.1 | Linux 64 0.0.9.1 | OS X INTEL
CUDA redistributable software libraries to support CUDA applications for Linux.
Updated versions:11.6 | Linux 64 11.6.2 | Linux 64
OpenFold A faithful PyTorch reproduction of DeepMind's AlphaFold 2.
Updated versions:0.1.0 | Linux 64
EVcouplings a tool to predict protein structure, function, and mutations using evolutionary sequence covariation.
Updated versions:0.1.1 | Linux 64 0.1.1 | OS X INTEL
Software Training
HMS Research Computing Spring 2022 sessions have ended.
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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