November 2019 Newsletter
Our November newsletter includes eleven new and updated titles. Four new workshops are available on the Harvard Longwood campus. Please be sure to read our note on Max OSX 10.15 below.
BioGrids is not compatible with MacOS 10.15
BioGrids is not compatible with MacOS 10.15 Catalina. Apple enforces strict filesystem controls that will break existing BioGrids installations.
While we recommend not upgrading to 10.15 on any Mac with BioGrids already installed,
we have also implemented a workaround to install BioGrids and SBGrid on new machines.
Apple has also dropped support for 32-bit binaries. We are compiling a list of 32-bit software applications that will not be available in MacOS 10.15.
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.
BioGrids is 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 over 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.
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 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 
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
MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <200 sequences), FFT-NS-2 (fast; for alignment of <30,000 sequences).
Version: 7.453
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.
Versions: 2.7.2
OpenMS is an open-source software C++ library for LC-MS data management and analyses. It offers an infrastructure for rapid development of mass spectrometry related software.
Version: 2.4.0
juicer is a one-click pipeline for processing terabase scale Hi-C datasets. Using Juicer, you can:
Go from raw fastq files to Hi-C maps binned at many resolutions Automatically annotate loops and contact domains with the Juicer tools Run the pipeline in the cloud, on LSF, Univa, or SLURM, or on a single CPU
Juicer creates hic files from raw (unaligned) reads derived from a Hi-C experiment.
Version: 1.5.6
Phantompeakqualtools computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.
Version: 1.2.1.1
FFmpeg is a complete, cross-platform solution to record, convert and stream audio and video.
Version: 4.2.1
deepTools addresses the challenge of handling the large amounts of data that are now routinely generated from DNA sequencing centers. deepTools contains useful modules to process the mapped reads data for multiple quality checks, creating normalized coverage files in standard bedGraph and bigWig file formats, that allow comparison between different files (for example, treatment and control). Finally, using such normalized and standardized files, deepTools can create many publication-ready visualizations to identify enrichments and for functional annotations of the genome.
Version: 3.3.1
HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.
Version: 0.9.1
MACS2 (Model Based Analysis of ChIP-Seq data) is a novel algorithm for identifying transcript factor binding sites.
Version: 2.2.4
FASTA is a DNA and protein sequence alignment software package that searches for matching sequence patterns or words, called k-tuples.
Version: 14-aug-2019
PyMC3 is a Python package for Bayesian statistical modeling and Probabilistic Machine Learning focusing on advanced Markov chain Monte Carlo (MCMC) and variational inference (VI) algorithms. Its flexibility and extensibility make it applicable to a large suite of problems.
Version: 3.7
Software Training
Training sessions available to HMS trainees:
HMS Research Computing
Intro to O2 12/04/2019 3:15-5p Countway 403 32
The Harvard Chan Bioinformatics Core
Introduction to single-cell RNA-seq Dec. 2nd & 3rd 2 days
Setting up for Success: Introduction to Version Control (Git) Dec. 13th 1 PM HSPH Kresge G2
Countway Library of Medicine
Analysis of MicroRNA Expression and Function by a Variety of Techniques
This session will be useful for any researcher who wants to investigate miRNA's in detail. Topics covered include basic techniques for miRNA isolation, expression profiling and validation, as well as their functional analysis in mammalian cells.
Dec. 18, 2019 10:00am - 12:00pm 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
BioGirds 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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