March 2019 Newsletter
Our March update includes 7 new software titles and four updates, as well as seven new workshops and classes available on the Harvard Longwood campus.
Please help guide future workshops by taking our survey. Just click below and you're done!
How likely are you to attend the workshop: RNA-Seq on AWS Using The BioGrids Installer
This feedback helps us plan future workshops. Feel free to suggest other workshop topics with a note to: help@biogrids.org
As a reminder, BioGrids is now available to all Harvard affiliates on a trial basis for the 2019 calendar year.
Register here (https://biogrids.org/registration/register/) to try out our software installer, which allows users to choose from 200+ bioinfomatics 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 (mailto: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.
https://biogrids.org/wiki/client_install A command line version is also available for Macs and Linux. Download using the link button above and register here (https://biogrids.org/registration/register/) for activation.
The BioGrids team provides support, infrastructure and testing for scientific software packages. We currently provide over 200 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
Software Updates
Bloocoo is a k-mer spectrum-based read error corrector, designed to correct large datasets with a very low memory footprint. It uses the disk streaming k-mer counting algorithm contained in the GATB library, and inserts solid k-mers in a bloom-filter. Version: 1.0.6
IMSEQ is a fast, PCR and sequencing error aware tool to analyze high throughput data from recombined T-cell receptor or immunoglobolin gene sequencing experiments. It derives immune repertoires from sequencing data in FASTA / FASTQ format. Version: 1.2.0
lorikeet is a tool for digital spoligotyping of MTB strains from Illumina read data. Version: 20
Python is a general-purpose, interpreted, object oriented, high-level dynamic programming language that emphasizes code readability. Version: 3.7.0
PyMOL Open Source is the open source version of the widely used molecular visualization package developed by Warren DeLano. Version : 2.3.0
regtools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context. Version: 0.5.1
SpliceMap is a de novo splice junction discovery and alignment tool. It offers high sensitivity and support for arbitrary RNA-seq read lengths. Version: 3.3.5.2
Subread comprises a suite of software programs for processing next-gen sequencing read data. Version: 1.6.3
VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. Version : 2.4.2
VSEARCH is an alternative to the USEARCH tool developed by Robert C. Edgar (2010) for which the source code is not publicly available. VSEARCH is an open source, multithreaded 64-bit tool for processing and preparing metagenomics, genomics, and population genomics nucleotide sequence data. Version: 2.11.1
Zerone discretizes several ChIP-seq replicates simultaneously and resolves conflicts between them. Zerone checks the results and tells you whether it passes the quality control. Version: 1.0
Software Training
Training sessions available to HMS trainees:
Registration for HMS Research Computing's User Training Spring 2019 courses is now open. Space is limited, and registrations are first-come, first-served.
Intro to Python 04/10/2019 3-5p TMEC 106 Register Here
Intro to R/Bioconductor 04/17/2019 3-5p TMEC 106 Register Here
R/Biostatistics Part I 04/24/2019 3-5p TMEC 106 Register Here
The Harvard Chan Bioinformatics Core
For HSCI and on-quad HMS researchers:
Introduction to differential gene expression analysis (bulk RNA-seq) Advanced April 1st and 2nd 2 days
Introduction to the command-line interface (shell) Basic April 11th 1 day
Introduction to ChIP-seq analysis Advanced April 29th and 30th 2 days
For all researchers at Harvard University and affiliated institutions:
Generating research analysis reports with RMarkdown April 3rd 1 PM FXB (HSPH), room G12
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 the HMS TnT fund and based upon SBGrid.org