June 2020 Newsletter
Our June newsletter includes twenty three new and updated software titles. Please note that an upgrade of the BioGrids install client is required for all users.
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
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.
Versions: 3.6.2
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
HiCExplorer is a set of programs to process, normalize, analyze and visualize Hi-C and cHi-C data.
Version: 3.4.3
GATK (Genome Analysis Toolkit) a software package developed to analyze high-throughput sequencing data capable of taking on projects of any size with a primary focus on variant discovery, genotyping, and data quality assurance.
Version: 3.8.1.0
Canvas is a tool for calling copy number variants (CNVs) from human DNA sequencing data.
Version: 1.40.0.1613 | Linux 64
SRA Toolkit is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.
Version: 2.10.7
luna is an open-source C/C++ software package for manipulating and analyzing polysomnographic recordings, with a focus on the sleep EEG.
Version: 0.22
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.
Versions: 3.1.6 | OS X INTEL 3.1.6_slurm-20.02.03 | Linux 64
tig is an ncurses-based text-mode interface for git.
Version: 2.5.1
htop is an interactive process viewer.
Version: 2.2.0
dcm2niix is designed to convert neuroimaging data from the DICOM format to the NIfTI format.
Version: 1.0.20200331
AWS CLI (Amazon Web Services Command Line Interface) a command line interface tool to manage multiple Amazon Web Services and automate them through scripts.
Version: 2.0.24
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.
Version: 1.10.2
prottest3 is a bioinformatic tool for the selection of best-fit models of aminoacid replacement for the data at hand. ProtTest makes this selection by finding the model in the candidate list with the smallest Akaike Information Criterion (AIC), Bayesian Information Criterion (BIC) score or Decision Theory Criterion (DT).
Version: 3.4.2 | Linux 64
CUDA is redistributable software libraries to support CUDA applications for Linux.
Version :9.2.148 | Linux 64 9.1.85 | Linux 64 9.0.176 | Linux 64 8.0.61 | Linux 64 8.0.44 | Linux 64 7.5.18 | Linux 64 10.2.89 | Linux 64 10.1.105 | Linux 64 10.0.130 | Linux 64
PyRQA is a tool to conduct recurrence analysis in a massively parallel manner using the OpenCL framework.
Version: 7.0.1 | OS X INTEL 7.0.1 | Linux 64
intervene is a tool for intersection and visualization of multiple genomic region and gene sets (or lists of items).
Version: 0.6.4 | OS X INTEL 0.6.4 | Linux 64
FastQTL is a fast, flexible, user-friendly, cluster-friendly QTL mapper.
Version: 2.0 | OS X INTEL
LUMPY is a probabilistic framework for structural variant discovery.
Version: 0.2.13
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: 0.12.6
Perl is a highly capable, feature-rich programming language with over 30 years of development. Perl runs on over 100 platforms from portables to mainframes and is suitable for both rapid prototyping and large scale development projects.
Version: 5.30.1 | Linux 64 5.30.1 | OS X INTEL
vg (Variation Graphs) provide a succinct encoding of the sequences of many genomes. A variation graph (in particular as implemented in vg) is composed of:
nodes, which are labeled by sequences and ids
edges, which connect two nodes via either of their respective ends
paths, describe genomes, sequence alignments, and annotations (such as gene models and transcripts) as walks through nodes connected by edges
Version: 1.24.0 | Linux 64
BLAST+ is a suite of BLAST (Basic Local Alignment Search Tool) tools that utilizes the NCBI C++ Toolkit with a number of performance and feature improvements over the legacy BLAST applications.
Version: 2.10.0
BioGrids Installer
Installation Client for the BioGrids software collection.
Version: 1.0.695
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.
The Harvard Chan Bioinformatics Core
Workshops for HSCI and on-quad HMS researchers:
See the Workshop Updates page for recent changes.
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 SGBGrid.
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