May 2019 Newsletter
Our May newsletter includes one new title and updates to three other widely used titles. Seven new workshops and classes are available on the Harvard Longwood campus.
Thanks to all who attended our May workshop: Using BioGrids for RNA-Seq on AWS and your Laptop.
We appreciate your feedback and hope to host more workshops in the future. Toward that end we ask for your input.
BioGrids is considering implementing a weekly rotating workshop series centered on using the Unix command line for bioinformatics. We envision a three part series comprising beginner, intermediate and more advanced topics. Please assist us in creating useful material by answering the one-click survey below.
How likely are you to attend a three part workshop consisting of one hour per week:
Introduction to bash and the Unix command line interface for bioinformatics.
*|SURVEY: Not likely|*
*|SURVEY: Maybe|*
*|SURVEY: Very likely|*
As a reminder, BioGrids is now available to all Harvard affiliates on a trial basis for the 2019 calendar year.
Register here to try out our software installer, which allows users to choose from 200+ bioinfomatics 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 over 200 titles in five categories and an additional 1,500 R, python and perl packages and modules. The collection grows weekly. Learn more here: About BioGrids 
Software Updates
Trimmomatic is a flexible read trimming tool for Illumina NGS data.
Version: 0.39
STAR (Spliced Transcripts Alignment to a Reference) is an ultrafast universal RNA-seq aligner.
Version: 2.7.0f
cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
Version: 2.3
fastp is a tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.
Version : 0.20.0
Software Training
Training sessions available to HMS trainees:
HMS Research Computing
Data Analysis and Visualization in MATLAB
06/04/2019 1-3p TMEC L-008
Please email: Alyssa Silverman <asilverm@mathworks.com>
Intro to R/Bioconductor
06/19/2019 3-5p Countway 403 Register
Demystifying deep learning: A practical approach in MATLAB
06/25/2019 1-3p TMEC106
Please email: Alyssa Silverman <asilverm@mathworks.com>
Intro to O2
06/26/2019 3-5p TMEC106 User Training github Register
The Harvard Chan Bioinformatics Core
Introduction to the command-line interface (shell)
June 4th 1 day Register
Introduction to bulk RNA-seq
June 24th & 25th 2 days
Introduction to R
July 1st & 2nd 1.5 days
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 the HMS TnT fund and based upon SBGrid.org
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