December 2020 Newsletter
Our December newsletter includes nine new and updated software titles. We remind users that OSX Big Sur is not yet supported by BioGrids.
Testing is underway with Apple's new M1 "apple silicon" ARM64 based macs. We expect to support M1 based Macs in early 2021. This may include a combination of direct support with OS11 and the Apple Rosetta compatibility environment.
Upgrade Your BioGrids Install Client
BioGrids Installer version 1.0.694 and earlier will display a message: "Missing Internet connection". This is due to an expired certificate.
All users must upgrade the install client to continue using it.
The issue has been corrected in the latest version (695), available here:
https://biogrids.org/wiki/client_install
Activated users can download the new version and use it without additional activation or registration steps.
As always, please let us know if you have any questions or problems upgrading - 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
DANPOS3 is a toolkit for Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing.
Versions: 3.1.1 | Linux 64
ExpansionHunterDenovo (EHdn) is a suite of tools for detecting novel expansions of short tandem repeats (STRs).
Versions: 0.9.0 | 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.
Versions: 4.1.7.0 | Linux 64
hic_breakfinder is a framework that integrates optical mapping, high-throughput chromosome conformation capture (Hi-C), and whole genome sequencing to systematically detect SVs in a variety of normal or cancer samples and cell lines.
Versions:1.0 | Linux 64
ITK is an open-source, cross-platform library that provides developers with an extensive suite of software tools for image analysis
Versions: 5.1.1 | OS X INTEL 5.1.1 | Linux 64
Peakachu is an acronym that standands for Unveil Hi-C Anchors and Peaks. It takes genome-wide contact data as input and returns coordinates of likely interactions such as chromatin loops.
Versions:1.1.4 | OS X INTEL 1.1.4 | Linux 64
Python is a general-purpose, interpreted, object oriented, high-level dynamic programming language that emphasizes code readability.
Versions:3.6.5 | OS X INTEL 3.6.5 | Linux 64
R-pkgs-Biogrids contains common and requested R packages for BIOGRIDS. This title is dependent on R.
Versions: r3.5.1-latest | OS X INTEL r3.5.1-20191216 | OS X INTEL r3.5.1-20191018 | OS X INTEL r4.0.2-latest | OS X INTEL r3.6.2-latest | OS X INTEL r3.6.2-20200714 | OS X INTEL r3.6.2-20200915 | OS X INTEL r3.6.2-20201112 | OS X INTEL r4.0.2-20200805 | OS X INTEL r4.0.2-20200909 | OS X INTEL r4.0.2-20201112 | OS X INTEL r4.0.2-20201112 | Linux 64 r4.0.2-20200909 | Linux 64 r4.0.2-20200805 | Linux 64 r3.6.2-latest | Linux 64 r3.6.2-20201112 | Linux 64 r3.6.2-20201007 | Linux 64 r3.6.2-20200909 | Linux 64 r3.6.2-20200714 | Linux 64 r3.5.1-latest | Linux 64 r3.5.1-20191216 | Linux 64 r3.5.1-20191018 | Linux 64 r4.0.2-latest | Linux 64
scvi-tools (single-cell variational inference tools) is a package for end-to-end analysis of single-cell omics data.
Versions: 0.7.0-beta.0 | Linux 64
Software Training
Training sessions available to HMS trainees:
HMS Research Computing
New course and registrations for Spring 2021 not announced yet..
See the HMS Research Computing Training Portal for the most current updates.
The Harvard Chan Bioinformatics Core
New courses not yet announced. See the Workshop Updates page for updates.
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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