January 2020 Newsletter
Our January newsletter includes thirteen new and updated software titles and fifty four new R packages available in R 3.6.2. This new release of R is also available for use with Jupyter notebooks. Spring training schedules include sixteen workshops and classes available to HMS researchers.
We remind readers that BioGrids is not compatible with MacOS 10.15 at this time.
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.
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 over 290 titles in five categories and an additional 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-1.0.694-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-1.0.694-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
Anvi'o is an open-source, community-driven analysis and visualization platform for ‘omics data. It brings together many aspects of today’s cutting-edge genomic, metagenomic, metatranscriptomic, pangenomic, and phylogenomic analysis practices to address a wide array of needs.
Version: 6.1
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
gffread validates, filters, converts and performs various other operations on GFF files (use gffread -h to see the various usage options).
Version: 0.11.6
GFOLD computes a generalized fold change for ranking differentially expressed genes from RNA-seq data.
Version: 1.1.4
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.
Version: 2.7.2
MAGeCK Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens (or GeCKO) technology.
Version: 0.5.9.2
MAGeCK-VISPR is a comprehensive quality control, analysis and visualization workflow for CRISPR/Cas9 screens.
Version: 0.5.3
Mono is an open source implementation of Microsoft's .NET Framework based on the ECMA standards for C# and the Common Language Runtime.
Version: 6.8.0.96
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
R is a free software environment for statistical computing and graphics. BioGrids R includes 434 packages.
Version: 3.6.2
PyCharm is a dedicated Python Integrated Development Environment (IDE) providing a wide range of essential tools for Python developers, tightly integrated together to create a convenient environment for productive Python, web, and data science development.
Version: 2019.3.1
StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus.
Version: 2.0.6
TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.
Version: 5.5.0
New packages in R version 3.6.2
| acidbase |
bookdown |
ggbeeswarm |
mutoss |
Rhtslib |
sf |
| batchelor |
boot |
goalie |
nnet |
rjson |
SingleR |
| beachmat |
brio |
inline |
pinp |
RUnit |
sn |
| beeswarm |
edgeR |
jpeg |
pkgKitten |
sandwich |
spdep |
| BiocFileCache |
enrichR |
leiden |
plotrix |
scater |
syntactic |
| BiocNeighbors |
ExperimentHub |
mnormt |
pROC |
scran |
TFisher |
| BiocSingular |
foreign |
monocle3 |
rappdirs |
scRNAseq |
TH.data |
| BiocStyle |
FRASER |
multcomp |
rbenchmark |
SeuratData |
transformer |
| bioverbs |
freerange |
multtest |
RcppHNSW |
SeuratWrappers |
vipor |
Software Training
Training sessions available to HMS trainees:
HMS Research Computing
Intro to O2 (K) 2/5/2020 3-5p Countway 506 Minot Room
Intro to O2 (G) 2/12/2020 3-5p Countway 506 Minot Room
Intro to Python 3/4/2020 3-5p Countway 506 Minot Room
Intro to MATLAB 3/18/2020 2-4p TMEC 328 Learning studio (Cannon)
The Harvard Chan Bioinformatics Core
Workshops for HSCI and on-quad HMS researchers:
Introduction to R Basic February 3rd & 4th 1.5 days
Introduction to single-cell RNA-seq Analysis Advanced February 27th & 28th
Introduction to the command-line interface (shell/bash/Unix) Basic March 6th
Introduction to bulk RNA-seq Analysis Advanced March 16th & 17th
Introduction to R Basic April 1st & 2nd 1.5 days
Introduction to Differential Gene Expression Analysis Advanced May 19th & 20th
Workshops for all researchers at Harvard University and affiliated institutions:
Introduction to R January 15th 1 PM HSPH Kresge G1
Introduction to tidyverse and Data Visualization with ggplot2 February 12th 1 PM HSPH Kresge G1
Gene Annotations and Functional Analysis of Gene Lists March 18th 1 PM HSPH Kresge G1
Generating Data Analysis Reports with RMarkdown April 15th 1 PM HSPH Kresge G1
Countway Library of Medicine
Practical Presentation Skills
Meets Wednesdays, Jan 29 - Jun 17, from 5:30pm - 7:00pm, Countway L2: Room 025, Harvard Longwood Campus
Introduction to the New PubMed Interface Feb 11, 2020 1pm - 2pm Countway L2: Room 025, Harvard Longwood Campus
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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