November 2022 Newsletter
Our November newsletter includes thirty six 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 webform:
https://biogrids.org/help/?tab=software
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 630 bioinfomatics 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
AlphaFold an implementation of the inference pipeline of AlphaFold v2.0 using a completely new model that was entered in CASP14.
Updated versions:2.2.4 | Linux 64 2.2.3 | Linux 64
Anaconda a Python distribution that includes more than 400 of the most popular Python packages for science, math, engineering, and data analysis.
Updated versions:2022.10 | Linux 64 2022.10 | OS X INTEL
arcs scaffolding genome sequence assemblies using linked or long reads.
Updated versions:1.2.4 | OS X INTEL 1.2.4 | Linux 64
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:1.27.13 | Linux 64 1.27.13 | OS X INTEL
FASTA a DNA and protein sequence alignment software package that searches for matching sequence patterns or words, called k-tuples.
Updated versions:36.3.8i | Linux 64 36.3.8i | OS X INTEL
BamToCov extract coverage information from BAM files, supporting stranded and physical coverage and streams.
Updated versions:2.7.0 | OS X INTEL 2.7.0 | Linux 64
BLAST+ (BLAST Plus) 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:2.13.0 | Linux 64 2.12.0 | Linux 64 2.13.0 | OS X INTEL 2.12.0 | OS X INTEL
cas-offinder Cas-OFFinder is 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 | Linux 64 2.4 | OS X INTEL
CellProfiler is 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:4.2.1 | Linux 64
cellsnp-lite efficient genotyping bi-allelic SNPs on single cells.
Updated versions:1.2.2 | OS X INTEL 1.2.2 | Linux 64
cooler is a support library for a sparse, compressed, binary persistent storage format, also called cooler, used to store genomic interaction data, such as Hi-C contact matrices.
Updated versions:0.8.11 | Linux 64 0.8.11 | OS X INTEL 0.8.9 | OS X INTEL 0.8.9 | Linux 64
crimson bioinformatics tool outputs converter to JSON or YAML.
Updated versions:1.1.0 | Linux 64 1.1.0 | OS X INTEL
Deblur is a greedy deconvolution algorithm for amplicon sequencing based on Illumina Miseq/Hiseq error profiles.
Updated versions:1.1.1 | OS X INTEL 1.1.1 | Linux 64
dnaio is a Python 3.7+ library for very efficient parsing and writing of FASTQ and also FASTA files.
Updated versions:0.9.1 | OS X INTEL 0.9.1 | Linux 64
fibertools-rs a CLI tool for interacting with fiberseq bam files.
Updated versions:0.0.8 | OS X INTEL 0.0.8 | Linux 64
GATK (Genome Analysis Toolkit) a software package developed to analyze high-throughput sequencing data capable of taking on projects of any size with a primary focus on variant discovery, genotyping, and data quality assurance.
Updated versions:4.3.0.0 | Linux 64 4.3.0.0 | OS X INTEL
ghostz is a highly efficient remote homologue detection tool.
Updated versions:1.0.2 | Linux 64 1.0.0 | OS X INTEL
mbg minimizer based sparse de Bruijn graph constructor.
Updated versions:1.0.12 | OS X INTEL 1.0.12 | Linux 64
mmquant RNA-Seq quantification tool, with special handling on multi-mapping reads.
Updated versions:1.0.4 | OS X INTEL 1.0.4 | Linux 64
MMseqs2 ultra fast and sensitive sequence search and clustering suite.
Updated versions:14-7e284 | Linux 64 14.7e284 | OS X INTEL
poppunk (POPulation Partitioning Using Nucleotide Kmers) Calculate core and accessory distances, cluster genomes, assign new genomes to clusters, make visualisations
Updated versions:2.5.0 | OS X INTEL 2.5.0 | Linux 64
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:3.7.0 | Linux 64 | OS X INTEL
rfdesign protein hallucination and inpainting with RoseTTAFold.
Updated versions:c882ab0 | Linux 64
R-pkgs-Biogrids contains common and requested R packages for BIOGRIDS. This title is dependent on R.
Updated versions:r4.1-20221114 | OS X INTEL r4.1-20221114 | Linux 64
rustybam bioinformatics toolkit written in the rust programing language focused around manipulation of alignment (bam and PAF), annotation (bed), and sequence (fasta and fastq) files.
Updated versions:0.1.31 | OS X INTEL 0.1.31 | Linux 64
sdm simple demultiplex tool for FASTQ demultiplexing and dereplication.
Updated versions:2.05 | OS X INTEL 2.05 | Linux 64
spoa SIMD partial order alignment tool/library.
Updated versions:4.0.7 | OS X INTEL 4.0.7 | Linux 64
srnaMapper mapping small RNA data to a genome.
Updated versions:1.0.8 | Linux 64 1.0.8 | OS X INTEL
sscocaller haplotyping single-cell DNA sequenced gamete cells.
Updated versions:0.2.2 | OS X INTEL 0.2.2 | Linux 64
staramr scan genome contigs against the ResFinder and PointFinder databases.
Updated versions:0.9.0 | OS X INTEL 0.9.0 | Linux 64
stark a tool for bluntifying a bidirected de bruijn graph by removing overlaps.
Updated versions:0.1.1 | Linux 64 0.1.1 | OS X INTEL
strike a program to evaluate protein multiple sequence alignments using a single protein structure.
Updated versions:1.2 | Linux 64 1.2 | OS X INTEL
tantan masks simple regions (low complexity & short-period tandem repeats) in biological sequences.
Updated versions:40 | Linux 64 40 | OS X INTEL
UniFrac fast phylogenetic diversity calculations.
Updated versions:1.1.3 | Linux 64 1.1.3 | OS X INTEL
Vienna RNA RNA secondary structure prediction and comparison.
Updated versions:2.5.1 | Linux 64 2.5.1 | OS X INTEL
Wise2 key programs are genewise, a program for aligning proteins or protein HMMs to DNA, and dynamite a macro language which automates the production of dynamic programming.
Updated versions:2.4.1 | OS X INTEL 2.4.1 | Linux 64
Software Training
Center for Computational Biomedicine
The Center for Computational Biomedicine (CCB) Fall newsletter contains training and collaboration opportunities.
HMS Research Computing
User Training Fall 2022 has now ended. Stay tuned for Spring 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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