May 2022 Newsletter
Our May newsletter includes seven new and updated titles for Mac and Linux as well as 47 new R packages for R version 4.1.
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
R-pkgs-Biogrids contains common and requested R packages for BIOGRIDS. This title is dependent on R.
Updated versions:r4.1-20220506 | OS X INTEL r4.1-20220506 | Linux 64
PyMOL Open Source open source version of the widely used molecular visualization package developed by Warren DeLano.
Updated versions:2.5.0 | Linux 64
pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
Updated versions:0.11.2 | Linux 64
scDRS (single-cell disease-relevance score) is a method for associating individual cells in scRNA-seq data with disease GWASs, built on top of AnnData and Scanpy.
Updated versions:1.0.0 | Linux 64
Cell Ranger ATAC a set of analysis pipelines that perform identification of open chromatin regions, motif annotation, and differential accessibility analysis for Single Cell ATAC data.
Updated versions:2.1.0 | Linux 64
cellranger-arc a set of analysis pipelines in this suite perform sample demultiplexing, barcode processing, identification of open chromatin regions, and simultaneous counting of transcripts and peak accessibility in single cells.
Updated versions:2.0.1 | Linux 64
Cell Ranger a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis.
Updated versions:6.1.2 | Linux 64
R a free software environment for statistical computing and graphics.
Updated versions:4.1.3 | Linux 64 4.1.3 | 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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