July 2020 Newsletter
Our July newsletter includes eleven new and updated software titles. HMS Research Computing has updated their Summer Part 2 workshops. All online workshops are open for registration and are detailed at the end of the newsletter.
If you have not already done so, please upgrade the BioGrids install client
Upgrade Your BioGrids Install Client
BioGrids Installer version 1.0.694 and earlier will display a message: "Missing Internet connection". This is due to an expired certificate.
All users must upgrade the install client to continue using it.
The issue has been corrected in the latest version (695), available here:
https://biogrids.org/wiki/client_install
Activated users can download the new version and use it without additional activation or registration steps.
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 314 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
scMatch is a single-cell gene expression profile annotation tool using reference datasets.
Version: 20200722
ANTs (Advanced Normalization Tools) extracts information from complex datasets that include imaging (Word Cloud). Paired with ANTsR (answer), ANTs is useful for managing, interpreting and visualizing multidimensional data. ANTs is popularly considered a state-of-the-art medical image registration and segmentation toolkit. ANTsR is an emerging tool supporting standardized multimodality image analysis.
Version: 2.3.4
Spyder is a powerful scientific environment written in Python, for Python, and designed by and for scientists, engineers and data analysts.
Version: 4.1.3
cartopy is a Python package designed to make drawing maps for data analysis and visualisation easy.
Version: 0.17.0 | OS X INTEL 0.17.0 | Linux 64
Entrez Edirect Utilities provides access to the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.
Version: 13.7.20200713
luna is an open-source C/C++ software package for manipulating and analyzing polysomnographic recordings, with a focus on the sleep EEG.
Version: 0.23
lftp is a file transfer program that allows sophisticated FTP, HTTP and other connections to other hosts. If site is specified then lftp will connect to that site otherwise a connection has to be established with the open command.
Version: 4.8.1
RGT is an open source python library for analysis of regulatory genomics. RGT is programmed in an oriented object fashion and its core classes provide functionality for handling regulatory genomics data.
Version: 0.13.0
datalad provides joint management of analysis code and data. This enables you to comprehensively track the exact state of any analysis inputs that produced your results — across the entire lifetime of a project, and across multiple datasets.
Version: 0.13
OpenMPI is an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available.
Version: 3.1.0 , 3.1.6_compat
jo is a small utility to create JSON objects.
Version: 1.3
Software Training
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.
See the HMS Research Computing Training Portal for the most current updates and registration.
| MATLAB for Medical Imaging Applications |
August 4th |
| Using MATLAB with Python |
August 11th |
| Text Analytics and Machine Learning with MATLAB |
August 18th |
| Data Science using MATLAB |
August 25th |
| Big Data: Scale Up to the Cloud with MATLAB |
September 1st |
| Machine Learning with MATLAB |
September 8th |
| Automated Image Labeling and Iterative Learning |
September 15th |
| Deep Learning for Neuroscience |
September 22nd |
The Harvard Chan Bioinformatics Core
See the Workshop Updates page for recent changes.
Introduction to single-cell RNA-seq data analysis (online) Advanced
August 27th, September 1st & 3rd
Three 2.5h sessions
Prerequisites Introduction to 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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