June 2025 Newsletter
Our June software update includes eight new and updated titles. Our new R package search tool lets you easily find packages of interest and shows which versions of BioGrids R already contain that package.
New software titles and R packages 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 770 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
Cellpose -Cellpose-SAM: cell and nucleus segmentation with superhuman generalization. It can be optimized for your own data, applied in 3D, works on images with shot noise, (an)isotropic blur, undersampling, contrast inversions, regardless of channel order and object sizes.
Updated versions:4.0.4 | Linux 64 4.0.4 | OS X INTEL
scanpy - a scalable toolkit for analyzing single-cell gene expression data built jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.
Updated versions:1.11.2 | OS X INTEL 1.11.2 | Linux 64
ColabFold - an easy-to-use Notebook based environment for fast and convenient protein structure predictions.
Updated versions:1.5.5_2 | Linux 64
R - a free software environment for statistical computing and graphics.
Updated versions:4.4.2 | Linux 64 | OS X INTEL
BLAST+ - a 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:2.16.0 | Linux 64 2.16.0 | OS X INTEL
PyTorch - an open source deep learning platform that provides a seamless path from research prototyping to production deployment.
Updated versions:2.6.0 | OS X INTEL 1.8.1 | OS X INTEL 1.7.0 | OS X INTEL 1.6.0 | OS X INTEL 0.4.1 | OS X INTEL 1.8.1 | Linux 64 1.7.0 | Linux 64 1.6.0 | Linux 64 0.4.1 | Linux 64
nextclade - SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks
Updated versions:3.14.3 | Linux 64 3.14.3 | OS X INTEL
SAMtools - (Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.
Updated versions:1.22 | Linux 64 1.22 | 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 Boston Children's Hospital and relies on a framework that was developed by SBGrid.
|
|
|
|
|
