October 2020 Newsletter
Our October newsletter includes eight new and updated software titles. We present a Software Spotlight on the program jq - a json parsing utility. If you have not done so already, please update your BioGrids install client to the latest version - 695.
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 335 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 Spotlight - jq
jq is a lightweight and flexible command-line JSON processor. From the jq website (https://stedolan.github.io/jq/):
jq is like sed for JSON data - you can use it to slice and filter and map and transform structured data with the same ease that sed, awk, grep and friends let you play with text.
Documentation is complete and includes an excellent progressive tutorial:
https://stedolan.github.io/jq/tutorial/
NCBI provides a tutorial for downloading gene sets that includes an example of using jq to convert downloaded json data: https://www.ncbi.nlm.nih.gov/datasets/docs/command-line-gene/
The website https://jqplay.org/ provides an online interactive interface for jq. You can use this to learn about jq without installing.
Software Updates
bcbio-nextgen provides best-practice pipelines for automated analysis of high throughput sequencing data with the goal of being quantifiable, analyzable, scalable and reproducible.
Updated versions:1.2.4 | Linux 64
Dask is a flexible library for parallel computing in Python.
Updated versions:2.30.0 | OS X INTEL 2.30.0 | Linux 64
H2O is a scalable machine learning and predictive analytics platform.
Updated versions:3.30.1.2 | OS X INTEL 3.30.1.2 | Linux 64
jq is a lightweight and flexible command-line JSON processor.
Updated versions:1.6 | OS X INTEL 1.6 | Linux 64
Python is a general-purpose, interpreted, object oriented, high-level dynamic programming language that emphasizes code readability.
Updated versions:3.6.5 | Linux 64
R is a free software environment for statistical computing and graphics.
Updated versions:4.0.2 | Linux 64
scvi-tools (single-cell variational inference tools) is a package for end-to-end analysis of single-cell omics data.
Updated versions:0.6.8 | Linux 64 0.6.8 | OS X INTEL
TractSeg is tool for fast and accurate white matter bundle segmentation from Diffusion MRI.
Updated versions:2.1.1 | Linux 64
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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