June 2024 Newsletter
Our June software updates include 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 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
metagenome-atlas - three commands to start analysing your metagenome data.
Updated versions:2.18.2 | Linux 64 2.18.2 | OS X INTEL
ensembl_vep - predicts the functional effects of genomic variants.
Updated versions:112.0 | Linux 64
perbase - Per-base metrics on BAM/CRAM files.
Updated versions:0.9.0 | Linux 64 0.9.0 | OS X INTEL
delly - an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data.
Updated versions:1.2.6 | Linux 64 1.2.6 | OS X INTEL
roary - takes annotated assemblies in GFF3 format and calculates the pan genome.
Updated versions:3.13.0 | OS X INTEL 3.13.0 | Linux 64
nextflow - a reactive workflow framework and programming DSL that ease writing computational pipelines with complex data.
Updated versions:23.04.1.5866 | Linux 64 23.04.1.5866 | OS X INTEL
cutadapt - finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
Updated versions:4.9 | Linux 64 4.9 | OS X INTEL
code-server - run VS Code on any machine anywhere and access it in the browser.
Updated versions:4.90.1 | Linux 64 4.90.1 | OS X INTEL
MMseqs2 - an ultra fast and sensitive sequence search and clustering suite.
Updated versions:15.6f452 | Linux 64 15.6f452 | OS X INTEL
raven - a de novo genome assembler for long uncorrected reads.
Updated versions:1.8.3 | Linux 64 1.8.3 | OS X INTEL
PCAone - Principal Component Analysis All in One.
Updated versions:0.4.4 | Linux 64 0.4.4 | OS X INTEL
ITK-SNAP - a software application used to segment structures in 3D medical images.
Updated versions:3.8.0 | OS X INTEL 4.2.0 | Linux 64 3.8.0 | Linux 64
bowtie2 - an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
Updated versions:2.5.4 | Linux 64 2.5.4 | OS X INTEL
AWS CLI - (Amazon Web Services Command Line Interface) a command line interface tool to manage multiple Amazon Web Services and automate them through scripts.
Updated versions:2.16.4 | Linux 64 2.16.4 | OS X INTEL
AFNI - (Analysis of Functional NeuroImages) is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity.
Updated versions:24.1.16 | OS X INTEL 24.1.16 | Linux 64
juicer - a one-click pipeline for processing terabase scale Hi-C datasets.
Updated versions:2.0.0-beta | Linux 64
OpenJDK - (Open Java Development Kit) is a free and open source implementation of the Java Platform, Standard Edition (Java SE).
Updated versions:zulu21 | Linux 64 zulu17 | Linux 64 zulu21 | OS X INTEL zulu17 | OS X INTEL
FreeSurfer - a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies.
Updated versions:7.4.1 | 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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