October 2018 Newsletter
Our October update brings 20 new software titles and 2 updates, the addition fo 3 popular scientific workflow tools, 9 new workshops and classes available on the Harvard Longwood campus, a reminder to connect with us during our weekly BioGrids office hours, and details on how to download BioGrids Software Installer and get started today.
BioGrids Office Hours
BioGrids office hours are held on Wednesdays from 9:00am - 10:00am via Zoom meeting. Want to see what BioGrids is and how it works? Join us for a quick demo. If you prefer to meet in person feel free to stop in 202 LHRRB.
Zoom Meeting URL: https://zoom.us/j/653421485 Wednesdays, 9:00 AM Eastern Time
BioGrids is supported by a team of scientists and engineers at HMS. We provide direct support to BioGrids members that includes all aspects of software installation and management.
Software Updates
This month we include three popular scientific workflow tools: Cromwell, NextFlow and Snakemake. Workflow management systems help replace fragile ad hoc analysis scripts with robust, documented, reproducible workflows.
bcbio-nextgen provides best-practice pipelines for automated analysis of high throughput sequencing data with the goal of being quantifiable, analyzable, scalable and reproducible. Versions: 1.1.1 | OS X INTEL
BEAST2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. Versions: 2.5.1 | OS X INTEL 2.5.1 | Linux 64
Bismark is a set of tools for the time-efficient analysis of Bisulfite-Seq (BS-Seq) data. Versions: 0.20.0 | OS X INTEL 0.20.0 | Linux 64
bmtagger removes human reads from metagenomics datasets. Versions: 3.101 | OS X INTEL 3.101 | Linux 64
Cromwell is a Workflow Management System geared towards scientific workflows. Versions: 35 | OS X INTEL 35 | Linux 64
Goalign is a set of command line tools to manipulate multiple alignments. It is implemented in Go language. Versions: 0.2.9 | Linux 64 0.2.9 | OS X INTEL
Gotree is a set of command line tools to manipulate phylogenetic trees. It is implemented in Go language. Versions: 0.3.0 | Linux 64 0.3.0 | OS X INTEL
HHsuite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs). Versions: 3.0.3 | OS X INTEL
inDrops is a pipeline for processing inDrops sequencing data. Versions: 3088992 | OS X INTEL 3088992 | Linux 64
Jupyter notebook is a language-agnostic HTML notebook application for Project Jupyter. Versions: 4.4.0 | Linux 64 4.4.0 | OS X INTEL
Nextflow is a reactive workflow framework and a programming DSL for computational pipelines. Versions: 0.32.0.4897 | OS X INTEL 0.32.0.4897 | Linux 64
Picard is a set of Java command line tools for manipulating high-throughput sequencing (HTS) data. Versions: 2.18.14 | Linux 64 2.18.14 | OS X INTEL
plmc infers undirected graphical models to describe coevolution and covariation in families of biological sequences. Versions: 20171002 | OS X INTEL 20171002 | Linux 64
Pysam is a python module that makes it easy to read and manipulate genomic data sets. Versions: 0.15.0 | Linux 64 0.15.0 | OS X INTEL
PyTorch is an open source deep learning platform that provides a seamless path from research prototyping to production deployment. Versions: 0.4.1 | Linux 64
QUAST evaluates genome assemblies by computing various metrics. QUAST builds convenient plots for different metrics; cumulative contigs length, all kinds of N-metrics, genes and operons covered and GC content. Versions: 5.0.0 | Linux 64 5.0.0 | OS X INTEL
Sambamba is a high performance highly parallel robust and fast tool for working with SAM and BAM files. Versions: 0.6.8 | OS X INTEL 0.6.8 | Linux 64
samblaster is a fast and flexible program for marking duplicates in read-id grouped1 paired-end SAM files. Versions: 0.1.24 | OS X INTEL 0.1.24 | Linux 64
seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. Versions: 1.3 | OS X INTEL 1.3 | Linux 64
Snakemake is a workflow management system is a tool to create reproducible and scalable data analyses. Versions: 5.3.0 | OS X INTEL 5.3.0 | Linux 64
UCSC Tools contain utilities designed to work with UCSC Genome Browser data and databases. Versions: 372 | OS X INTEL 372 | Linux 64
VSEARCH is an alternative to the USEARCH tool developed by Robert C. Edgar (2010). Versions: 2.9.0 | OS X INTEL 2.9.0 | Linux 64
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 and activate using the link button below.
The BioGrids team provides support, infrastructure and testing for scientific software packages. We currently provide 160 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 Training
Training sessions available to HMS trainees:
Learn how to save time by using EndNote bibliographic software.
1:00pm - 1:50pm Wednesday, November 7, 2018 Kresge 200 (Harvard Chan School of Public Health), Harvard Longwood Campus
Countway Practical Presentation Skills
This weekly study group is for students & postdocs who would like to practice their oral presentation skills.
5:00pm - 6:30pm Wednesday, November 7, 2018 Countway Floor L2: 025, Harvard Longwood Campus
Zotero: An Alternative to EndNote Zotero is a free bibliographic management tool, which provides users with a powerful alternative to EndNote or Refworks.
1:00pm - 1:50pm Wednesday, November 14, 2018 Kresge 200 (Harvard Chan School of Public Health), Harvard Longwood Campus
Countway Practical Presentation Skills
This weekly study group is for students & postdocs who would like to practice their oral presentation skills.
5:00pm - 6:30pm Wednesday, November 14, 2018 Countway Floor L2: 025, Harvard Longwood Campus
This class is part of the Research Data Management Seminar Series Good documentation is a critical part of managing research data well, now and into the future.
1:00pm - 2:00pm Friday, November 16, 2018 Harvard Longwood Campus
The NGS technologies have the potential to dramatically accelerate biomedical research by enabling comprehensive analysis of genomes and transcriptomes to become inexpensive, routine, and widespread tools.
10:00am - 1:00pm Wednesday, November 28, 2018 Countway Floor L2: 025, Harvard Longwood Campus
Countway Practical Presentation Skills
This weekly study group is for students & postdocs who would like to practice their oral presentation skills.
11:00am - 1:00pm Wednesday, December 5, 2018 Countway Floor 5: Ballard Room, Harvard Longwood Campus
Countway Practical Presentation Skills
This weekly study group is for students & postdocs who would like to practice their oral presentation skills.
5:00pm - 6:30pm Wednesday, December 19, 2018 Countway Floor L2: 025, Harvard Longwood Campus
The Harvard Chan Bioinformatics Core
Introduction to RNA-seq Analysis Using High-Performance Computing and R October 31st - November 2nd and Nov 14th - 16th, 2018
------------------------------------------------------------
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 (mailto:help@biogrids.org)
BioGrids is supported by the HMS TnT fund and based upon SBGrid.org