January 2021 Newsletter
Our January newsletter includes fifteen new and updated software titles and fifteen new R packages. Spring workshop and training registrations are open for both The Harvard Chan Bioinformatics Core and HMS Research Computing.
Testing is underway with Apple's new M1 "apple silicon" ARM64 based macs. We expect to support M1 based Macs in early 2021. This may include a combination of direct support with OS11 and the Apple Rosetta compatibility environment.
New BioGrids Install Client
We have updated our command-line installation manager, "sbgrid-cli", to version 2.1.3 (2.1.4 is coming soon). This new version, available for Mac and Linux, has many improvements including multithreaded rsync transfer, selectable installation target path, and network diagnostics for troubleshooting.
For details on how to access this new version, see our wiki at https://sbgrid.org//wiki/sbgrid-cli.
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 Updates
Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis.
Versions: 2.1.1 | Linux 64
DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3/4 to other formats such as MaCH or PLINK.
Versions: 1.0.4 | OS X INTEL 1.0.4 | Linux 64
emacs is an extensible, customizable, free/libre text editor.
Versions: 26.3 | Linux 64 26.3 | OS X INTEL
Google Cloud SDK is a set of tools and libraries for interacting with Google Cloud products and services.
Versions: 316.0.0 | OS X INTEL 316.0.0 | Linux 64
IGV (Integrative Genomics Viewer) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.
Versions: 2.8.13 | Linux 64 2.8.13 | OS X INTEL
Julia The Julia programming language is a flexible dynamic language appropriate for scientific and numerical computing with performance comparable to traditional statically-typed languages.
Versions:1.4.2 | Linux 64 1.3.1 | Linux 64 1.4.2 | OS X INTEL 1.3.1 | OS X INTEL 1.5.3 | OS X INTEL 1.5.3 | Linux 64
MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <200 sequences), FFT-NS-2 (fast; for alignment of <30,000 sequences).
Versions:7.475 | Linux 64 7.475 | OS X INTEL
NanoPack is a set of tools developed for visualization and processing of long-read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences.
Versions: 1.1.1 | Linux 64 1.1.1 | OS X INTEL
PyRQA is a tool to conduct recurrence analysis in a massively parallel manner using the OpenCL framework.
Versions: 7.0.1 | OS X INTEL 7.0.1 | Linux 64
Python is a general-purpose, interpreted, object oriented, high-level dynamic programming language that emphasizes code readability.
Versions: 3.6.5 | Linux 64
R is a free software environment for statistical computing and graphics.
Versions: 3.6.2 | OS X INTEL
R-pkgs-Biogrids contains common and requested R packages for BIOGRIDS. This title is dependent on R.
Versions: r3.6.2-latest | Linux 64 r3.6.2-20210125 | Linux 64
scvi-tools (single-cell variational inference tools) is a package for end-to-end analysis of single-cell omics data.
Versions: 0.8.1 | Linux 64
sniffles is a structural variation caller using third generation sequencing.
Versions: 1.0.12b | Linux 64
tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data.
Versions: 1.5.1 | OS X INTEL 1.5.1 | Linux 64
Software Training
Training sessions available to HMS trainees:
HMS Research Computing
New courses and registrations for Spring 2021 are now open.
See the HMS Research Computing Training Portal for the most current updates.
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Date
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Venue
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February 3rd
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Introduction to MATLAB
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Register |
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February 17th
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Using MATLAB with Python
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Register
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March 3rd
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21 MATLAB Features You Need Now
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Register
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March 24th
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Machine Learning with MATLAB
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Register
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April 7th
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Systems Modeling and Controls with Simulink & Simscape
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Register
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April 21st
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What’s New in MATLAB for Research
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Register |
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May 5th
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Distance Learning and Virtual Labs
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Register |
The Harvard Chan Bioinformatics Core
Courses for Spring 2021 are now open. See the Workshop Updates page for updates.
| Topic |
Category |
Date |
Duration |
Prerequisites |
| R |
Basic |
January 26th, 29th & February 2nd, 5th |
Four 2h sessions |
None |
| scRNA-seq |
Advanced |
February 16th, 19th, 23rd |
Three 2.5h sessions |
R |
| Command-line interface and the O2 cluster (shell/Unix/Linux) |
Basic |
March 5th, 9th, 12th |
Three 2.5h sessions |
None |
| Bulk RNA-seq (Part I - FASTQ to counts) |
Advanced |
March 23rd, 26th, 30th & April 2nd |
Four 2.5h sessions |
Command-line interface |
| R |
Basic |
April 13th, 16th, 20th, 23rd |
Four 2h sessions |
None |
| Bulk RNA-seq (Part II - Differential gene expression) |
Advanced |
May 4th, 7th, 11th, 14th |
Four 2h sessions |
R |
| scRNA-seq |
Advanced |
May 25th, 28th & June 1st |
Three 2.5h sessions |
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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