January 2023 Newsletter
Our January newsletter includes thirteen 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.
HMS Research Computing 2023 Spring User Training courses are now open for registration. See the list of classes and registration link at the end of this newsletter.
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
plastid - a Python library designed specifically for nucleotide-resolution analysis of genomics and NGS data.
Updated versions: 0.6.1 | Linux 64 0.6.1 | OS X INTEL
Cell Ranger - a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis.
Updated versions: 7.1.0 | Linux 64
ASCIIGenome - a command-line genome browser running from terminal window and solely based on ASCII characters.
Updated versions: 1.17.0 | Linux 64 1.16.0 | Linux 64 1.17.0 | OS X INTEL 1.16.0 | OS X INTEL
DCMTK - a collection of libraries and applications implementing large parts the DICOM standard.
Updated versions: 3.6.7 | OS X INTEL 3.6.7 | Linux 64
Wally - Plotting of aligned sequencing reads, assembled contigs or pan-genome graphs in BAM/CRAM/GFA format and visualization of genomic variants.
Updated versions: 0.5.8 | Linux 64 0.5.8 | OS X INTEL
prodigal-gv - a fork of Prodigal meant to improve gene calling for giant viruses and viruses that use alternative genetic codes.
Updated versions: 2.10.0 | OS X INTEL 2.10.0 | Linux 64
gfastats - a single fast and exhaustive tool for summary statistics and simultaneous fa (fasta, fastq, gfa [.gz]) genome assembly file manipulation. gfastats also allows seamless fasta<>fastq<>gfa[.gz] conversion. It has been tested in genomes even >100Gbp.
Updated versions: 1.3.6 | OS X INTEL 1.3.6 | Linux 64
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: 2.4.2 | Linux 64 2.4.2 | OS X INTEL
AlphaFold - an implementation of the inference pipeline of AlphaFold v2.0 using a completely new model that was entered in CASP14.
Updated versions: 2.3.1 | Linux 64
R - a free software environment for statistical computing and graphics.
Updated versions: 4.2.1 | Linux 64
R-pkgs-Biogrids - contains common and requested R packages for BIOGRIDS. This title is dependent on R.
Updated versions: r4.1-20230111 | r4.2.1-20230105
chopper - Rust implementation of NanoFilt+NanoLyse, both originally written in Python. This tool, intended for long read sequencing such as PacBio or ONT, filters and trims a fastq file.
Updated versions: 0.2.0 | Linux 64 0.2.0 | OS X INTEL
AmberTools - a suite of programs that allows users to carry out molecular dynamics simulations, particularly on biomolecules.
Updated versions: 22 | Linux 64 22 | OS X INTEL
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 O2 |
Feb. 8, 2023 |
10am to 12pm |
| Intro to MATLAB |
Feb. 15, 2023 |
10am to 12pm |
| Intro to O2 Portal |
Mar. 1, 2023 |
10am to 11am |
| Intro to Parallel Computing |
Mar. 8, 2023 |
10am to 12pm |
| Optimizing O2 Jobs |
Mar. 22, 2023 |
10am to 11am |
| Intro to Python |
Mar. 29, 2023 |
10am to 12pm |
| Intro to O2 |
Apr. 12, 2023 |
10am to 12pm |
| Intro to O2 Portal |
May 3, 2023 |
10am to 11pm |
Where Should I Put My Data?
Understanding Data Storage at HMS |
May 10, 2023 |
10am to 11am |
| Intermediate O2 |
May 17, 2023 |
10am to 12pm |
| Intro to Python |
May 24, 2023 |
10am to 12pm |
RCBio: Easy and Quick HPC Pipeline
Builder and Runner |
May 31, 2023 |
10am to 11am |
| 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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