February 2021 Newsletter
Our February newsletter includes five new and updated software titles. Spring workshop and training registrations are open for both The Harvard Chan Bioinformatics Core and HMS Research Computing.
macOS 11 Big Sur support
We've been testing new application installations on macOS 11 Big Sur. The majority of applications appear to work normally on both x86_64 and Apple Silicon hardware, with a few exceptions. If you have a new Big Sur M1 mac, you should be able to install software with the BioGrids installation manager. Be sure to install XQuartz, and let us know if you encounter any problems
Installation Manager Beta Testing
Our new graphical Installation Manager for macOS and Linux is nearly ready to go and we are looking for some beta testers! Internal testing is going well and we would now like feedback from the community. Email help@biogrids.org and we'll get you set up.
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
R a free software environment for statistical computing and graphics.
Updated versions: 4.0.2 | Linux 64 4.0.2 | OS X INTEL 3.6.2 | OS X INTEL 3.6.2 | Linux 64
R-pkgs-Biogrids contains common and requested R packages for BIOGRIDS. This title is dependent on R.
Updated versions: r4.0.2-latest | OS X INTEL r4.0.2-20201112 | OS X INTEL r3.6.2-latest | OS X INTEL r3.6.2-20210224 | OS X INTEL r4.0.2-latest | Linux 64 r4.0.2-20210224 | Linux 64 r3.6.2-latest | Linux 64 r3.6.2-20210224 | Linux 64
OSGenome is an Open Source Web Application for Genetic Data (SNPs) using 23AndMe and Data Crawling Technologies.
Updated versions:b05eae4 | OS X INTEL b05eae4 | Linux 64
nanodoc provides RNA modification detection using Nanopore raw reads with Deep One Class classification.
Updated versions:2021-01-21 | OS X INTEL 2021-01-21 | Linux 64
PyRQA is a tool to conduct recurrence analysis in a massively parallel manner using the OpenCL framework.
Updated versions:7.0.1 | OS X INTEL 7.0.1 | Linux 64
Software Training
Training sessions available to HMS trainees:
HMS Research Computing
New courses and registrations for Spring 2021 are now open.
See the HMS Research Computing Training Portal for the most current updates.
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Date
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Venue
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March 3rd
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21 MATLAB Features You Need Now
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Register
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March 24th
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Machine Learning with MATLAB
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Register
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April 7th
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Systems Modeling and Controls with Simulink & Simscape
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Register
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April 21st
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What’s New in MATLAB for Research
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Register |
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May 5th
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Distance Learning and Virtual Labs
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Register |
The Harvard Chan Bioinformatics Core
Courses for Spring 2021 are now open. See the Workshop Updates page for updates.
| Topic |
Category |
Date |
Duration |
Prerequisites |
| Command-line interface and the O2 cluster (shell/Unix/Linux) |
Basic |
March 5th, 9th, 12th |
Three 2.5h sessions |
None |
| Bulk RNA-seq (Part I - FASTQ to counts) |
Advanced |
March 23rd, 26th, 30th & April 2nd |
Four 2.5h sessions |
Command-line interface |
| R |
Basic |
April 13th, 16th, 20th, 23rd |
Four 2h sessions |
None |
| Bulk RNA-seq (Part II - Differential gene expression) |
Advanced |
May 4th, 7th, 11th, 14th |
Four 2h sessions |
R |
| scRNA-seq |
Advanced |
May 25th, 28th & June 1st |
Three 2.5h sessions |
R |
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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