August 2019 Newsletter
Our August newsletter includes seven software updates, including two new titles, and an additional eight R packages in the latest available version of R (3.5.1). Six new workshops are available on the Harvard Longwood campus.
As a reminder to all our new users, 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.
BioGrids is 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 over 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.
Software Highlight: WebLogo
WebLogo is a web based application designed to make the generation of sequence logos as easy and painless as possible.
Sequence logos are a graphical representation of an amino acid or nucleic acid multiple sequence alignment developed by Tom Schneider and Mike Stephens.
Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position.
In general, a sequence logo provides a richer and more precise description of, for example, a binding site, than would a consensus sequence.
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 
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-1.0.694-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-1.0.694-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
Cytoscape is a software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.
Version: 3.7.1
SaTScan is a free software that analyzes spatial, temporal and space-time data using the spatial, temporal, or space-time scan statistics.
Version: 9.6
MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <200 sequences), FFT-NS-2 (fast; for alignment of <30,000 sequences).
Version: 7.429
TensorFlow is an open source software library for high performance numerical computation. Its flexible architecture allows easy deployment of computation across a variety of platforms (CPUs, GPUs, TPUs), and from desktops to clusters of servers to mobile and edge devices. Originally developed by researchers and engineers from the Google Brain team within Google’s AI organization, it comes with strong support for machine learning and deep learning, and the flexible numerical computation core is used across many other scientific domains.
Version: 1.14.0
Python is a general-purpose, interpreted, object oriented, high-level dynamic programming language that emphasizes code readability.
Version: 3.7.4
FFmpeg is a complete, cross-platform solution to record, convert and stream audio and video.
Version: 3.2.4
WebLogo is a set of command line tools for sequence logo generation.
Version: 3.7.1
Software Training
Training sessions available to HMS trainees:
HMS Research Computing
Intro to O2 09/04/2019 3-5p Countway 506 Minot Room
Intro to Matlab 09/11/2019 2-4p Countway 506 Minot Room
Intro to Python 09/18/2019 3-5p TMEC 106
Intro to Perl 09/25/2019 3-5p Countway 403
The Harvard Chan Bioinformatics Core
Introduction to the command-line interface 09/17/2019 1 day
Introduction to bulk RNA-seq 09/23/2019 - 09/24/2019 2 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
BioGirds is supported by Harvard Medical School and Boston Children's Hospital and relies on a framework that was developed by SGBGrid.
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