September 2023 Newsletter
Our September newsletter includes eighteen 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
pixelator - commandline tool and library to process and analyze sequencing data from Molecular Pixelation (MPX) assays.
Updated versions:0.13.1 | OS X INTEL 0.13.1 | Linux 64
IQ-TREE - efficient and versatile phylogenomic software by maximum likelihood.
Updated versions:2.2.5 | Linux 64 2.2.5 | OS X INTEL
spaln - Map and align a set of cDNA/EST or protein sequences onto a genome
Updated versions:3.0.0 | Linux 64 3.0.0 | OS X INTEL
seq2science - Automated preprocessing of Next-Generation-Sequencing data.
Updated versions:1.1.0 | Linux 64 1.1.0 | OS X INTEL
allo - Multi-mapped read rescue strategy for gene regulatory analyses
Updated versions:1.0.5 | Linux 64 1.0.5 | OS X INTEL
Infernal - (INFERence of RNA ALignment) searches DNA sequence databases for RNA structure and sequence similarities and uses a special case of profile stochastic context-free grammars called covariance models (CMs). In many cases It is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.
Updated versions:1.1.4 | Linux 64 1.1.4 | OS X INTEL
Truvari - Structural variant comparison tool for VCFs
Updated versions:4.1.0 | Linux 64 4.1.0 | OS X INTEL
DROP - (Detection of RNA Outlier Pipeline) pipeline to find aberrant gene expression events in RNA sequencing data.
Updated versions:1.3.3 | Linux 64
R-pkgs-Biogrids - contains common and requested R packages for BIOGRIDS. This title is dependent on R.
Updated versions: r4.3.0-20230921 | Linux 64 | r4.2.3-20230807 | OS X INTEL
ninja-nj - Nearly Infinite Neighbor Joining Application
Updated versions:0.98 | OS X INTEL 0.98 | 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 2.0.0 | Linux 64
cellranger-arc - 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 2.0.0 | Linux 64
mmquant - RNA-Seq quantification tool, with special handling on multi-mapping reads.
Updated versions:1.0.6 | Linux 64
biobambam2 - tools for early stage NGS alignment file processing including fast sorting and duplicate marking.
Updated versions:2.0.183 | Linux 64
STAR - (Spliced Transcripts Alignment to a Reference) is an ultrafast universal RNA-seq aligner.
Updated versions:2.7.11a | Linux 64 2.7.11a | OS X INTEL
Python - a general-purpose, interpreted, object oriented, high-level dynamic programming language that emphasizes code readability. Its syntax allows programmers to express concepts in fewer lines of code than in C++ or Java, thus allowing programmers to work more quickly and integrate their systems more effectively.
Updated versions:3.9.16 | Linux 64
dRep - a python program for rapidly comparing large numbers of genomes, dRep can also "de-replicate" a genome set by identifying groups of highly similar genomes and choosing the best representative genome for each genome set.
Updated versions:3.4.4 | Linux 64 3.4.4 | OS X INTEL
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:7.1.0 | Linux 64 6.1.2 | Linux 64 6.0.1 | Linux 64 4.0.0 | Linux 64
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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