March 2020 Newsletter
Our March newsletter includes sixteen new and updated software titles as well as eighteen new R packages for R version 3.6.2.
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.
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:
Eagle software estimates haplotype phase  either within a genotyped cohort or using a phased reference panel.
EIGENSOFT is a package that combines functionality from population genetics methods (Patterson et al. 2006) and EIGENSTRAT stratification correction method (Price et al. 2006).
FASTA is a DNA and protein sequence alignment software package that searches for matching sequence patterns or words, called k-tuples.
FastQTL is a QTL mapper that is easy to set up for large deployment on compute clusters.
GORpipe is a tool based on a genomic ordered relational architecture and allows analysis of large sets of genomic and phenotypic tabular data using a declarative query language, in a parallel execution engine.
ImageJ a Java image processing program inspired by NIH Image that can display, edit, analyze, process, save and print 8-bit, 16-bit, and 32-bit images.
Minimac4 is a lower memory and more computationally efficient implementation of the genotype imputation algorithms in minimac/mininac2/minimac3.
Nextflow is a workflow framework and programming DSL that ease writing computational pipelines with complex data.
nilearn is a Python module for fast and easy statistical learning on NeuroImaging data.
ORFRATER (Open Reading Frame - Regression Algorithm for Translational Evaluation of Ribosome-protected footprints) comprises a series of scripts for coding sequence annotation based on ribosome profiling data.
PyRQA is a tool to conduct recurrence analysis in a massively parallel manner using the OpenCL framework.
pyunicorn (Unified Complex Network and RecurreNce analysis toolbox) is a fully object-oriented Python package for the advanced analysis and modeling of complex networks.
Qualimap is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.
STAR (Spliced Transcripts Alignment to a Reference) is an ultrafast universal RNA-seq aligner.
TeX Live cleans up raw data files and converts them to pdf format with LaTex.
TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files.
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.