April 2020 Newsletter
Our April newsletter includes ten new and updated software titles as well as nine new R packages. We include a short tip on using BioGrids to enhance reproducibility in workflows.
Training schedules have been modified, with many classes cancelled. Please see the updated schedules at the end of this newsletter. The Countway Library has moved a number of classes online already.
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 email@example.com. 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.
Workflow Reproducibility with BioGrids
Reproducible computational research is not only important for science but is critical as a time saver for individual researchers. Reproducibility allows previously developed methodologies to be applied to new data without substantial investment of time.
See Ten Simple Rules for Reproducible Computational Research for more on the importance of replication and reproducibility in computational research.
Part of making reproducible workflows is to develop good habits and employ technologies that make the process efficient.
Enhance the reproducibility of your workflows by making software versions explicit.
BioGrids makes this task simple.
Specify software versions using a BioGrids shell variable. They have the form: TITLE_M (for Mac) or TITLE_X ( for Linux)
Use the variable in a shell script like this:
The line above enforces version 1.9 for samtools on a Mac. When calling 'samtools' in a BioGrids environment, version 1.9 will be used.
Print this version specifier in your output:
echo " BioGrids samtools version: $SAMTOOLS_M "
Collect detailed information about versions with the biogrids-info command:
$ biogrids-info -l samtools
Version information for: /programs/i386-mac/samtools
Default version: 1.10
Installed versions: 1.10
Other available versions: 1.9 1.8 1.7 1.6 1.5 1.4.1 1.3.1 1.3 0.1.19
Overrides use this shell variable: SAMTOOLS_M
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: firstname.lastname@example.org.
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 290 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
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
curl -kLO https://biogrids.org/wiki/downloads/biogrids-1.0.694-Linux.tgz
tar zxf biogrids-1.0.694-Linux.tgz
curl -kLO https://biogrids.org/wiki/downloads/biogrids-1.0.694-Darwin.tgz
tar zxf biogrids-1.0.694-Darwin.tgz
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:
R packages for version 3.6.2 have been updated. To update packages for an existing R installation update R with the BioGrids CLI: biogrids update r
or update with the BioGrids GUI Installer by selecting the Rebuild Installation menu item.
RStudio is an integrated development environment (IDE) for R that includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.
jq is a lightweight and flexible command-line JSON processor.
jo is a small utility to create JSON objects.
AmberTools is a suite of programs that allows users to carry out molecular dynamics simulations, particularly on biomolecules. The suite can be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB) with either explicit water or generalized Born solvent models. The independently developed packages work well by themselves, and with Amber itself.
BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
pycudadecon is a package that provides a python wrapper and convenience functions for cudaDeconv, which is a CUDA/C++ implementation of an accelerated Richardson Lucy Deconvolution algorithm1, suitable for general applications, but designed particularly for stage-scanning light sheet applications such as Lattice Light Sheet.
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.
SimpleITK is a simplified layer built on top of ITK, intended to facilitate its use in rapid prototyping, education, interpreted languages.
BioGrids Installer - Installation Client for the BioGrids software collection.
Velocyto is a library for the analysis of RNA velocity.
wot is a software package for analyzing snapshots of developmental processes in scRNA-seq data.
Training sessions available to HMS trainees:
HMS Research Computing
As part of Harvard Medical School's response to COVID-19, HMS Research Computing is now working remotely.
All training classes will be held online until further notice, via Zoom meetings.
More details will be posted here soon, and we will notify enrollees with more details on how to use Zoom to attend class.
The Harvard Chan Bioinformatics Core
Workshops for HSCI and on-quad HMS researchers:
Previously scheduled classes for April have been cancelled.
Interactive Data Visualization with Shiny in R
May 13th 1 PM HSPH Kresge G1 Introduction to R
Countway Library of Medicine
Online Short-Seminar: The Research Data Lifecycle
Monday, April 6, 2020
12:00pm - 12:30pm
Online Seminar: Writing a Data Management Plan
Friday, April 10, 2020
12:00pm - 1:00pm
Online Short-Seminar: Data Management in Action
Tuesday, April 14, 2020
2:00pm - 2:30pm
Online Short-Seminar: Let’s Make Research Data FAIR
Wednesday, April 22, 2020
10:00am - 10:30am
Online Short-Seminar: Get Your Data Organized
Thursday, April 30, 2020
1:00pm - 1:30pm
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: email@example.com
BioGrids is supported by Harvard Medical School and Boston Children's Hospital and relies on a framework that was developed by SGBGrid.