June 2019 Newsletter
Our June newsletter includes three new titles, fourteen new R packages and three updates. Six new workshops and classes are available on the Harvard Longwood campus. Thanks to all who attended our May workshops.
As a reminder, BioGrids is now available to all Harvard affiliates on a trial basis for the 2019 calendar year.
Register here 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: firstname.lastname@example.org.
Software Highlight - IGV
The Integrative Genomics Viewer (IGV) 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.
IGV is well supported by the Broad Institute. It has excellent documentation, including a YouTube channel
of IGV tutorials.
For users new to bioinformatics or NGS data sets, the IGV provides a variety of built in data, including human and mouse genomes, and a variety of sequencing datasets, including RNASeq data from the ENCODE project. This enables one to explore fully mapped NGS data sets without having to move large files around or upload your own data.
IGV (and its dependent Java application) can be easily installed through the BioGrids GUI or the BioGrids CLI.
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 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
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
curl -kLO https://biogrids.org/wiki/downloads/biogrids-1.0.694-Linux.tgz
tar zxf biogrids-1.0.694-Linux.tgz
curl -kLO https://biogrids.org/wiki/downloads/biogrids-1.0.694-Darwin.tgz
tar zxf biogrids-1.0.694-Darwin.tgz
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:
ANTs extracts information from complex datasets that include imaging. ANTs is considered a state-of-the-art medical image registration and segmentation toolkit. ANTsR is an emerging tool supporting standardized multimodality image analysis.
Cytoscape a software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.
MRIcron is a cross-platform NIfTI format image viewer. It can load multiple layers of images, generate volume renderings and draw volumes of interest. It also provides dcm2nii for converting DICOM images to NIfTI format and NPM for statistics.
pigz stands for parallel implementation of gzip, and is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data.
R New additional packages available by default in R.
ade4, alakazam, AneuFinderData, AnnotationDbi, DNAcopy, doParallel, ecp, ggdendro, kedd, ReorderCluster, scrm, seqinr, shazam, tigger
SAMtools (Sequence Alignment/Map) a generic format for storing large nucleotide sequence alignments that provides various utilities for manipulating alignments, including sorting, merging, indexing and generating alignments in a per-position format.
tmux is a terminal multiplexer: it enables a number of terminals to be created, accessed, and controlled from a single screen. tmux may be detached from a screen and continue running in the background, then later reattached.
Training sessions available to HMS trainees:
HMS Research Computing
From Pixels to Features to Models: Image Processing, Computer Vision, and Machine- and Deep Learning with Images in MATLAB
07/16/2019 1-3p TMEC209
Please email: Alyssa Silverman <email@example.com>
Intro to Python
07/17/2019 3-5p TMEC306 Register
Intro to O2
07/31/2019 3-5p TMEC306 Register
The Harvard Chan Bioinformatics Core
Introduction to R (Registration is closed)
July 1st & 2nd 1.5 days
Introduction to single-cell RNA-seq
July 17th & 18th 2 days
Introduction to R
July 29th & 30th 1.5 days
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: firstname.lastname@example.org
BioGirds is supported by Harvard Medical School and Boston Children's Hospital and relies on a framework that was developed by SGBGrid.