May 2023 Newsletter
Our May newsletter includes twenty five 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
Control-FREEC - copy number and genotype annotation from whole genome and whole exome sequencing data.
Updated versions:11.6 | OS X INTEL 11.6 | Linux 64
TakeABreak - a tool that can detect inversion breakpoints directly from raw NGS reads, without the need of any reference genome and without de novo assembling the genomes.
Updated versions:1.1.2 | Linux 64 1.1.2 | OS X INTEL
GSearch - an ultra-fast and scalable microbial genome search program based on MinHash-like metric and graph-based approximate nearest neighbor search.
Updated versions:0.1.2 | OS X INTEL 0.1.2 | Linux 64
unikmer - a toolkit for k-mer with taxonomic information.
Updated versions:0.19.1 | OS X INTEL 0.19.1 | Linux 64
medaka - a tool to create consensus sequences and variant calls from nanopore sequencing data.
Updated versions:1.8.0 | Linux 64
Metaphor - Metagenomic Pipeline for Short Reads
Updated versions:1.7.7 | OS X INTEL 1.7.7 | Linux 64
ChIPs - a tool for simulating ChIP-sequencing experiments.
Updated versions:2.4 | Linux 64 2.4 | OS X INTEL
MetaGraph - framework allows for indexing and analysis of very large biological sequence collections, producing compressed indexes that can represent several petabases of input data.
Updated versions:0.3.6 | Linux 64 0.3.6 | OS X INTEL
dEploid - deconvolutes mixed genomes with unknown proportions.
Updated versions:0.5 | Linux 64 0.5 | OS X INTEL
GCEN - a command-line toolkit that allows biologists to easily build gene co-expression network and predict gene function, especially in RNA-Seq research or lncRNAs annotation.
Updated versions:0.6.3 | OS X INTEL 0.6.3 | Linux 64
Captus - Assembly of Phylogenomic Datasets from High-Throughput Sequencing data.
Updated versions:0.9.91 | OS X INTEL 0.9.91 | Linux 64
SRA Toolkit - (Sequence Read Archive Toolkit) a collection of tools and libraries for using data in the INSDC Sequence Read Archives.
Updated versions:3.0.5 | Linux 64 3.0.5 | OS X INTEL
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
shark - Mapping-free filtering of useless RNA-Seq reads.
Updated versions:1.2.0 | OS X INTEL 1.2.0 | Linux 64
YaHS - yet another Hi-C scaffolding tool.
Updated versions:1.2a.2 | Linux 64 1.2a.2 | OS X INTEL
SpydrPick - Mutual information based detection of pairs of genomic loci co-evolving under a shared selective pressure.
Updated versions:1.2.0 | Linux 64 1.2.0 | OS X INTEL
umis - tools for processing UMI RNA-tag data.
Updated versions:1.0.9 | Linux 64 1.0.9 | OS X INTEL
CellProfiler - a cell image analysis software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.
Updated versions:4.2.5 | Linux 64 4.2.5 | OS X INTEL
bedtools - a swiss-army knife of tools for a wide-range of genomics analysis tasks.
Updated versions:2.31.0 | Linux 64 2.31.0 | OS X INTEL
LCA - Lowest Common Ancestor calculation tool.
Updated versions:0.24 | OS X INTEL 0.24 | Linux 64
fastq-dl - a tool to download FASTQs associated with Study, Experiment, or Run accessions.
Updated versions:2.0.1 | Linux 64
TreeTime - provides routines for ancestral sequence reconstruction and inference of molecular-clock phylogenies.
Updated versions:0.10.0 | Linux 64 0.10.0 | OS X INTEL
3D Slicer - a free and open-source platform for analyzing and understanding medical image data.
Updated versions:4.10.2 | OS X INTEL
Jellyfish - a tool for fast, memory-efficient counting of k-mers in DNA.
Updated versions:2.3.0 | Linux 64 2.3.0 | OS X INTEL
km - software for RNA-seq investigation using k-mer decomposition.
Updated versions:2.1.1 | 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 2023 Spring User Training is now open.
| Class |
Date |
Time |
| Intro to Git and GitHub |
Jun. 7, 2023 |
10am to 11am |
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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