January 2024 Newsletter
Our January newsletter includes 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
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: 1.19.2 | Linux 64 1.19.2 | OS X INTEL
Presto - A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.
Updated versions: 0.7.2 | OS X INTEL 0.7.2 | Linux 64
MOODS - a collection of algorithms used to match position weight matrices (PWM) with DNA sequences.
Updated versions: 1.9.4.2 | OS X INTEL 1.9.4.2 | Linux 64
Bowtie 2 - ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
Updated versions: 2.5.3 | Linux 64 2.5.3 | OS X INTEL
IGV - (Integrative Genomics Viewer) a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.
Updated versions: 2.17.0 | Linux 64 2.17.0 | OS X INTEL
Severus - somatic structural variation (SV) caller for long reads (both PacBio and ONT).
Updated versions: 0.1.2 | OS X INTEL 0.1.2 | Linux 64
fibertools-rs - CLI tool for interacting with fiberseq bam files.
Updated versions: 0.3.7 | Linux 64 0.3.7 | OS X INTEL
BLAST+ - a 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: 2.15.0 | Linux 64 2.15.0 | OS X INTEL
BCFtools - 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:1.19 | Linux 64 1.19 | OS X INTEL
rasusa - Randomly subsample sequencing reads to a specified coverage.
Updated versions:0.8.0 | OS X INTEL 0.8.0 | Linux 64
CellBender - software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.
Updated versions:0.3.0 | OS X INTEL 0.3.0 | 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.
|
|
|
|
|
