July 2019 Newsletter
Our July newsletter includes eight new titles and two new R packages. Two new workshops are available on the Harvard Longwood campus.
July also marks a milestone for BioGrids - 400 users. We look forward to working with you.
Many thanks to the participants at our July 25th workshop. If you would like to attend a future workshop or have a workshop provided in a small group setting for your laboratory please email help@biogrids.org.
As a reminder to all our new users, 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.
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 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.
Software Highlight: Nextflow
Nextflow is a reactive workflow framework and programming DSL that eases writing computational pipelines with complex data.
It is designed around the idea that the Linux platform is the lingua franca of data science. Linux provides many simple but powerful command-line and scripting tools that, when chained together, facilitate complex data manipulations.
Nextflow extends this approach, adding the ability to define complex program interactions and a high-level parallel computational environment based on the dataflow programming model.
A Nextflow script is defined by composing many different processes. Each process can be written in any scripting language that can be executed by the Linux platform (BASH, Perl, Ruby, Python, etc), to which is added the ability to coordinate and synchronize the processes execution by simply specifying their inputs and outputs.
Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages.
Its fluent DSL simplifies the implementation and the deployment of complex parallel and reactive workflows on clouds and clusters.
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
FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies.
Version: 6.0.1
Nextflow is a reactive workflow framework and programming DSL that eases writing computational pipelines with complex data.
Version: 19.04.1.5072
MRIQC extracts no-reference IQMs (image quality metrics) from structural (T1w and T2w) and functional MRI (magnetic resonance imaging) data.
Version: 0.15.0
Nilearn is a Python module for fast and easy statistical learning on neuroimaging data. It leverages the scikit-learn Python toolbox for multivariate statistics with applications such as predictive modeling, classification, decoding, or connectivity analysis.
Version : 0.5.2
ITK-SNAP is a software application used to segment structures in 3D medical images.
Version : 3.8.0
Connectome Workbench is an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project. The distribution includes wb_view, a GUI-based visualisation platform, and wb_command, a command-line program for performing a variety of algorithmic tasks using volume, surface, and grayordinate data.
Version: 1.3.2
AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity.
Version : 19.2.01
Slicer is a free and open-source platform for analyzing and understanding medical image data.
Version: 4.10.2
Software Training
Training sessions available to HMS trainees:
HMS Research Computing
Parallel Computing with MATLAB and Scaling to the O2 Cluster
08/13/2019 1-4p Countway 403
Please email: Alyssa Silverman <asilverm@mathworks.com>
The Harvard Chan Bioinformatics Core
Introduction to differential gene expression analysis - bulk RNA-seq (counts -> DE genes)
08/15 - 08/16 2 days
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.
|
