September 2024 Newsletter
Our September software updates include eleven 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
VSEARCH - an alternative to the USEARCH tool developed by Robert C. Edgar (2010) for which the source code is not publicly available, VSEARCH is an open source, multithreaded 64-bit tool for processing and preparing metagenomics, genomics, and population genomics nucleotide sequence data. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling, and sorting. It also supports FASTQ file analysis, filtering, conversion, and merging of paired-end reads.
Updated versions:2.29.0 | Linux 64 2.29.0 | OS X INTEL
RingMapper - Code for performing RING-MaP and PAIR-MaP analysis (RingMapper & PairMapper)
Updated versions:1.2 | Linux 64
Luna - an open-source C/C++ software package for manipulating and analyzing polysomnographic recordings, with a focus on the sleep EEG.
Updated versions:1.0.0 | Linux 64 1.0.0 | OS X INTEL
BCFtools - a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
Updated versions:1.21 | Linux 64 1.21 | 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:1.21 | Linux 64 1.21 | OS X INTEL
MDAnalysis - an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. It can write most of these formats, too, together with atom selections suitable for visualization or native analysis tools.
Updated versions:2.7.0, 2.4.2 | Linux 64 2.7.0 | OS X INTEL
Spyder - a powerful scientific environment written in Python, for Python, and designed by and for scientists, engineers and data analysts.
Updated versions:4.1.3 | OS X INTEL 5.3.2 | Linux 64 4.1.3 | Linux 64
R - a free software environment for statistical computing and graphics.
Updated versions:4.2.3 | OS X INTEL 4.2.3 | Linux 64
cas-offinder - an OpenCL based, ultrafast and versatile program that searches for potential off-target sites of CRISPR/Cas-derived RNA-guided endonucleases (RGEN).
Updated versions:2.4.1 | Linux 64 2.4.1 | OS X INTEL
BLAST+ - 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:2.6.0 | Linux 64 2.6.0 | OS X INTEL
Segment Anything 2 - (SAM2) produces high quality object masks from input prompts such as points or boxes, and it can be used to generate masks for all objects in an image.
Updated versions:7e1596c | 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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