June 2021 Newsletter
Our brief June newsletter includes twelve new and updated software titles. As a reminder, new software titles can be requested by sending email to help@biogrids.org or filling out our webform:
https://biogrids.org/help/?tab=software
New BioGrids Installation Manager
Our new graphical Installation Manager for macOS and Linux is now available for general use. You can find a quick link to download MacOS and Linux versions at the top of our wiki page:
https://biogrids.org/wiki/Home
We welcome any and all feedback from the community at help@biogrids.org.
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.
MacOS 10.15 Catalina
While we recommend not upgrading to 10.15 on any Mac with BioGrids already installed, we have implemented a workaround to install BioGrids and SBGrid on new machines. Two approaches are available.
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 290 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 Installer
The BioGrids Installer is an easy to use application that makes installing and managing life sciences software simple and quick.
A command line version is also available for Macs and Linux. Download using the link button above and register here for activation.
The BioGrids team provides support, infrastructure and testing for scientific software packages. We currently provide 335 titles in five categories and over 1,500 R, python and perl packages and modules. The collection grows weekly. Learn more here: About BioGrids 
BioGrids QuickStart
If you are new to BioGrids and would like to quickly get started with the command line version, follow the instructions below:
1: Download the BioGrids Installer command line version
Linux CLI
curl -kLO https://biogrids.org/wiki/downloads/biogrids-1.0.695-Linux.tgz
tar zxf biogrids-1.0.694-Linux.tgz
cd biogrids-1.0.694-Linux
OSX CLI
curl -kLO https://biogrids.org/wiki/downloads/biogrids-1.0.695-Darwin.tgz
tar zxf biogrids-1.0.694-Darwin.tgz
cd biogrids-1.0.694-Darwin
2: Activate biogrids
./biogrids activate biogrid-production jvinent1 70rYFTDnmCr93VUklfbf1s3M4jdyC9bFVYHew==
Replace the site name, user name and activation key with your own credentials.
3: Install software with BioGrids
./biogrids install fastqc trimmomatic samtools star subread igv
When finished, verify applications are installed:
./biogrids installed
Software Updates
pangolin
(Phylogenetic Assignment of Named Global Outbreak LINeages) software package for assigning SARS-CoV-2 genome sequences to global lineages.
Updated versions:3.1.5 | OS X INTEL 3.1.5 | Linux 64
gofasta
gofasta provides functions for working on alignments in fasta format.
Updated versions:0.0.4 | Linux 64 0.0.4 | OS X INTEL
DROP
(Detection of RNA Outlier Pipeline) pipeline to find aberrant gene expression events in RNA sequencing data.
Updated versions:1.0.5 | Linux 64 1.0.4 | Linux 64
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:6.0.1 | Linux 64
scan2
Genotyper for somatic SNV and indel discovery in PTA-amplified single cells.
Updated versions:2.0 | Linux 64
TreeTime
TreeTime provides routines for ancestral sequence reconstruction and inference of molecular-clock phylogenies.
Updated versions:0.8.1 | OS X INTEL 0.8.1 | Linux 64
PhaseDel
PhaseDel is a Java-based variant caller designed for detecting somatic deletions from high-coverage (~30x) single-cell whole-genome sequencing (scWGS) data.
Updated versions:1.0.0 | Linux 64 1.0.0 | OS X INTEL
FreeSurfer
is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies.
Updated versions:7.1.1 | Linux 64 7.1.1 | OS X INTEL
CRKIT
CRKIT (Computational Radiology Kit) is a collection of algorithms and image processing tools developed by the Computational Radiology Laboratory team
Updated versions:1.6.0 | Linux 64
LiRA
LiRA (Linked Read Analysis) is a computational tool for removing amplification artifacts from single-cell DNA sequencing data and estimating mutation rates in single cells.
Updated versions:1f4cab4 | Linux 64 1f4cab4 | OS X INTEL
AbundanceBin
AbundanceBin is an abundance-based tool for binning metagenomic sequences.
Updated versions:1.0.1 | OS X INTEL 1.0.1 | Linux 64
quip
Quip compresses next-generation sequencing data with extreme prejudice.
Updated versions:1.1.8 | Linux 64 1.1.8 | OS X INTEL
Software Training
Training sessions available to HMS trainees:
HMS Research Computing
Spring training courses have ended. Please see the HMS Research Computing Training Portal for the most current updates.
The Harvard Chan Bioinformatics Core
Courses for Summer 2021 are now open. See the Workshop Updates page for updates.
| Topic |
Category |
Date |
Duration |
Prerequisites |
| |
|
|
|
|
| R |
Basic |
July 9th, 13th, 16th & 20th |
Four 2h sessions |
-- |
| scRNA-seq |
Advanced |
July 30th, August 3rd & 6th |
Three 2.5h sessions |
R |
| Command-line Interface (Shell) and HPC |
Basic |
August 17th, 20th & 24th |
Three 2.5h sessions |
-- |
ChIP-seq Part 1
(Experimental design to Peak calling) |
Advanced |
September 21st, 24th & 28th |
Three 2.5h sessions |
Shell |
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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