September 2020 Newsletter
Our September newsletter includes eighteen new and updated software titles. We present two new utilities for BioGrids users: biogrids-info and biogrids-list. These utilities provide an easy way to find the names of executables and version details for any BioGrids title.
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
BioGrids Utilities
biogrids-info and biogrids-list are two new utilities available in the BioGrids environment.
They are called after activating BioGrids. We use the title] samtools below to demonstrate.
$ source /programs/biogrids.shrc
$ biogrids-list samtools
ace2sam interpolate_sam.pl md5sum-lite sam2vcf.pl soap2sam.pl
blast2sam.pl maq2sam-long novo2sam.pl samtools wgsim
bowtie2sam.pl maq2sam-short plot-bamstats samtools.pl wgsim_eval.pl
export2sam.pl md5fa psl2sam.pl seq_cache_populate.pl zoom2sam.pl
The output of biogrids-list is a list of all executables associated with that title. Most titles have more than one executable available. Any executable in this list can be called directly.
The biogrids-list command takes a single argument - the name of a BioGrids title. This name must be all lower case. If you don't know the proper name for a title you can search for it on the BioGrids website:
https://biogrids.org/software/
The search field will autocomplete, giving you matching title names as you type. When you find the title the information presented will include an example command for installing with the BioGrids CLI tool. This command contains the proper lower case name for the title. For example:
biogrids install samtools
The biogrds-info command has several options. You can view these by typing the command with no arguments. The most useful command for end users is the -l option which lists version information for a title.
[ch199734@e2 ~]$ biogrids-info -l samtools
Version information for: /programs/x86_64-linux/samtools
Default version: 1.10
In-use version: 1.10
Installed versions: 1.10 1.9 1.8 1.7 1.6 1.5 1.4.1 1.3.1 1.3 0.1.19
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_X
The information displayed shows the default version and the in-iuse version. The default version will be used when there are no version overrides active. The in-use version will specify which version is active when the override variable has been set. The last line of the information display gives the name of the override variable.
The installed versions are also listed. These are versions available through the use of the override variable.
For example, the default version of samtools is 1.10. To use version 1.9 instead the override variable is set:
$ export SAMTOOLS_X=1.9
Now when samtools is called version 1.9 will be used.
If you have any questions about using these utilities please send a note to help@biogrids.org.
Software Updates
c3d is a command-line tool for converting 3D images between common file formats.
Version: 1.0.0
CellPhoneDB is a publicly available repository of curated receptors, ligands and their interactions.
Version: 2.1.4
CNVkit is a command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from high-throughput sequencing.
Version: 0.9.7
cooler is a support library for a sparse, compressed, binary persistent storage format, also called cooler, used to store genomic interaction data, such as Hi-C contact matrices.
Version: 0.8.9
CoNIFER uses exome sequencing data to find copy number variants (CNVs) and genotype the copy-number of duplicated genes.
Version: 0.2.2
GATK (Genome Analysis Toolkit) is 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
HUMAnN2 is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads).
Version: 2.8.2
ImageMagick is a software suite to create, edit, compose, or convert bitmap images.
Version: 7.0.8-7
kneaddata is a tool designed to perform quality control on metagenomic sequencing data, especially data from microbiome experiments
Version: 0.7.10
MetaPhlAn2 is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
Version: 2.96.1
MRtrix3 provides a set of tools to perform various types of diffusion MRI analyses, from various forms of tractography through to next-generation group-level analyses.
Version: 3.0.1
NiftySeg contains programs to perform EM based segmentation of images in nifti or analyse format.
Version: 1.0.0
piranha is a peak-caller for CLIP- and RIP-Seq data. It takes input in BED or BAM format and identifies regions of statistically significant read enrichment.
Version: 1.2.1
R is a free software environment for statistical computing and graphics.
Versions: 3.6.2, 4.0.2
ROBEX is an automatic whole-brain extraction tool for T1-weighted MRI data (commonly known as skull stripping).
Version: 1.2
TractSeg is a tool for fast and accurate white matter bundle segmentation from Diffusion MRI. It can create bundle segmentations, segmentations of the endregions of bundles and Tract Orientation Maps (TOMs).
Version: 2.1.1
TrimGalore is a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data.
Version: 0.6.6
triodenovo implements a Bayesian framework for calling de novo mutations in trios for next-generation sequencing data.
Version: 0.06
Software Training
Training sessions available to HMS trainees:
HMS Research Computing
Fall 2020 registration is now open.
See the HMS Research Computing Training Portal for the most current updates.
| Intro to R/Bioconductor |
Wednesday, October 7, 2020 |
3-5p |
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link |
| Intro to Matlab |
Wednesday, October 14, 2020 |
3-5p |
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link |
| Intermediate O2 |
Wednesday, October 21, 2020 |
3-5p |
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link |
| Intro to O2 |
Wednesday, October 28, 2020 |
3-5p |
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link |
| Intro to Git/Github |
Wednesday, November 4, 2020 |
3-5p |
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link |
| Intro to Parallel Computing |
Thursday, November 12, 2020 |
3-5p |
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link |
| Intro to Python |
Wednesday, November 18, 2020 |
3-5p |
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link |
| Intro to O2 |
Wednesday, November 25, 2020 |
3-5p |
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link |
| Intro to Python |
Wednesday, December 2, 2020 |
3-5p |
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link |
| Intro to R/Bioconductor |
Wednesday, December 9, 2020 |
3-5p |
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link |
The Harvard Chan Bioinformatics Core
See the Workshop Updates page for recent changes.
| Introduction to single-cell RNA-seq data analysis |
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October 20th, 23rd, 27th |
Three 2.5h sessions |
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| Introduction to the command-line interface (Shell, bash, Linux) and HMS-RC’s O2 cluster |
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November 3rd, 6th, 10th |
Three 2.5h sessions |
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| Introduction to bulk RNA-seq (raw data to counts) |
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November 20th, 24th, 27th, December 1st |
Four 2.5h sessions |
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| Reproducible research with Git/Github and RMarkdown |
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December 8th, 11th, 15th |
Three 2.5h sessions |
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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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