May 2021 Newsletter
Our May newsletter includes twenty eight new and updated software titles. HMS Research Computing spring workshops and training courses have completed. The Harvard Chan Bioinformatics Core has listed five new summer workshops. See the Training section at the end of this newsletter.
New BioGrids Installation Manager
Our new graphical Installation Manager for macOS and Linux is now available for general use. You can find a quick link to download MacOS and Linux versions at the top of our wiki page:
https://biogrids.org/wiki/Home
We welcome any and all feedback from the community at 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
Alfred is an efficient and versatile command-line application that computes multi-sample quality control metrics in a read-group aware manner.
Version: 0.2.3
Comet-ms searches uninterpreted tandem mass spectra of peptides against sequence databases.
Version: 2019012
elPrep is a high-performance tool for analyzing .sam/.bam files (up to and including variant calling) in sequencing pipelines.
Version: 5.0.1
ENANO is a FASTQ lossless compression algorithm especially designed for nanopore sequencing FASTQ files.
Version: 1.0
FusionCatcher finds somatic fusion-genes in RNA-seq data.
Version: 1.33
GSAlign is an ultra-fast sequence alignment algorithm for intra-species genome comparison.
Version: 1.0.22
gsort is a tool to sort genomic files according to a genomefile.
Version: 0.1.4
HyPhy is an open-source software package for comparative sequence analysis using stochastic evolutionary models.
Version: 2.5.31
iqtree - Efficient and versatile phylogenomic software by maximum likelihood.
Version: 2.1.2
mosdepth - Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
Version: 0.3.1
MultiQC aggregates results from bioinformatics analyses across many samples into a single report.
Version: 1.10.1
nanoplexer is a standard tool to demultiplex Nanopore long read sequencing data.
Version: 0.1.2
NanoVar is a genomic structural variant (SV) caller that utilizes low-depth long-read sequencing such as Oxford Nanopore Technologies (ONT).
Version: 1.3.9
Nextstrain - Real-time tracking of pathogen evolution
Version: 20200304
ngless enables creation of a pipeline of work for all the first phase of NGS analysis until the point (inclusive) of annotation.
Version: 1.3.0
PopDel - Fast structural deletion calling on population-scale short read paired-end germline WGS data.
Version: 1.5.0
PyMOL Open Source is the open source version of the widely used molecular visualization package developed by Warren DeLano.
Version: 2.5.0
razers3 - Faster, fully sensitive read mapping.
Version: 3.5.8
sansa - Structural variant (SV) annotation.
Version: 0.0.8
segemehl is a software to map short sequencer reads to reference genomes.
Version: 0.3.4
SeqKit is a cross-platform ultrafast comprehensive toolkit for FASTA/Q processing.
Updated version: 0.16.0
sickle-trim - Windowed Adaptive Trimming for fastq files.
Version: 1.33
somalier: extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF
Version: 0.2.13
SViCT is a computational tool for detecting structural variations from cell free DNA (cfDNA) containing low dilutions of circulating tumor DNA (ctDNA).
Version: 1.0.1
SURVIVOR is a tool set for simulating/evaluating SVs, merging and comparing SVs within and among samples, and includes various methods to reformat or summarize SVs.
Version: 1.0.7
TaxonKit is a command-line toolkit for rapid manipulation of NCBI taxonomy data.
Version: 0.8.0
trf - Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences.
Version: 4.09.1
Software Training
Training sessions available to HMS trainees:
HMS Research Computing
Spring training courses have ended. Please see the HMS Research Computing Training Portal for the most current updates.
The Harvard Chan Bioinformatics Core
Courses for Summer 2021 are now open. See the Workshop Updates page for updates.
| Topic |
Category |
Date |
Duration |
Prerequisites |
Reproducibility Tools
(RMarkdown and Git/Github) |
Advanced |
June 22nd, 25th & 29th |
Three 2.5h sessions |
R |
| R |
Basic |
July 9th, 13th, 16th & 20th |
Four 2h sessions |
-- |
| scRNA-seq |
Advanced |
July 30th, August 3rd & 6th |
Three 2.5h sessions |
R |
| Command-line Interface (Shell) and HPC |
Basic |
August 17th, 20th & 24th |
Three 2.5h sessions |
-- |
ChIP-seq Part 1
(Experimental design to Peak calling) |
Advanced |
September 21st, 24th & 28th |
Three 2.5h sessions |
Shell |
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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