February 2023 Newsletter
Our February newsletter includes fourteen 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
NanoQC Create fastQC-like plots for Oxford Nanopore sequencing data
Updated versions:0.9.4 | OS X INTEL 0.9.4 | Linux 64
Nanopolish software package for signal-level analysis of Oxford Nanopore sequencing data.
Updated versions:0.14.0 | Linux 64 0.14.0 | OS X INTEL
NanoPlot Plotting tool for long read sequencing data and alignments.
Updated versions:1.41.0 | OS X INTEL
NanoComp Comparing runs of Oxford Nanopore sequencing data and alignments
Updated versions:1.21.0 | Linux 64 1.21.0 | 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:1.17 | Linux 64 1.17 | OS X INTEL
HD-BET Automated brain extraction of multi-sequence MRI using artificial neural networks.
Updated versions:1.0 | OS X INTEL 1.0 | Linux 64
Foldseek enables fast and sensitive comparisons of large structure sets.
Updated versions:5-53465f0 | Linux 64 5-53465f0 | OS X INTEL
Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
Updated versions:1.18 | Linux 64 1.18 | OS X INTEL
rna-map An open-source tool for rapid analysis of RNA mutational profiling (MaP) experiments.
Updated versions:e4ff4ec | Linux 64 e4ff4ec | OS X INTEL
Python a general-purpose, interpreted, object oriented, high-level dynamic programming language that emphasizes code readability.
Updated versions:3.9.16 | Linux 64 3.9.16 | OS X INTEL
R a free software environment for statistical computing and graphics.
Updated versions:4.2.0 | Linux 64
bedtools a swiss-army knife of tools for a wide-range of genomics analysis tasks.
Updated versions:2.30.0 | Linux 64 2.30.0 | OS X INTEL
IGV Reports Creates self-contained html pages for visual variant review with IGV (igv.js).
Updated versions:1.7.0 | Linux 64 1.7.0 | OS X INTEL
Infant FreeSurfer An open source neuroimaging toolkit for processing, analyzing, and visualizing human brain MR images
Updated versions:4a14499 | OS X INTEL 4a14499 | 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 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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