May 2020 Newsletter
Our May newsletter includes sixteen new and updated software titles as well as two new R packages.
We include a short tip on updating R and R packages in BioGrids.
Training schedules for online classes are now available.
Updated MacOS 10.15 Catalina Install Procedure
We have implemented a new workaround to install BioGrids and SBGrid on OSX 10.15 machines. The new method involves downloading a file followed by a single reboot. It is simpler than our previous method. See both methods here.
Remote Working Help
The BioGrids Wiki provides step by step instructions for installing BioGrids software on a local laptop or desktop machine. If you prefer a live demonstration, or run into trouble, please contact help@biogrids.org. We can set up a Zoom meeting to assist you.
Updating BioGrids R Packages
The BioGrids version of R (latest version 3.6.2) provides over 500 R packages. These are immediately available in R with no configuration required by the user.
We continually add new packages to the latest R version. How do you get these new packages if you already have BioGrids R installed? You receive new packages when you update R.
In the BioGrids CLI installer, packages with an available update are marked in blue:
To update the package use the "update" command to the CLI:
$ ./biogrids update r
In the BioGrids GUI installer, packages with an update available will show up under the 'Updates' tab on the left. Click Apply Changes to install these updates:
You will receive the splash screen indicating the action about to take place. Click on Apply to confirm:
That's it! The next time you start BioGrids R you will be using the updated version with the new packages available.
Cite BioGrids
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.
Register here to try out our software installer, which allows users to choose from over 290 bioinfomatics and life sciences 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 290 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
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 modelling, classification, decoding, or connectivity analysis.
Version: 0.6.2
Hail is an open-source, general-purpose, Python-based data analysis library with additional data types and methods for working with genomic data.
Version: 0.2
FastQC is a quality control tool for high throughput sequence data.
Version: 0.11.9
R packages for version 3.6.2 have been updated. To update packages for an existing R installation update R with the BioGrids CLI:
biogrids update r
or update with the BioGrids GUI Installer by clicking Apply Changes when updates are shown.
Version: 3.6.2
SPM software is a suite of MATLAB (MathWorks) functions and subroutines with some externally compiled C routines. SPM was written to organise and interpret our functional neuroimaging data.
Version: 12
AFNI (Analysis of Functional NeuroImages) 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 and 20.1.06
HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of sequencing analysis and sequence motif discovery tools.
Version: 4.9
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 visualization platform, and wb_command, a command-line program for performing a variety of algorithmic tasks using volume, surface, and grayordinate data.
Version: 1.4.2
BioGrids Installer - Installation Client for the BioGrids software collection.
Version: 2.0.44
EVcouplings is a tool to predict protein structure, function, and mutations using evolutionary sequence covariation.
Version: 0.0.5
Cyberduck is a libre server and cloud storage browser for Mac and Windows with support for FTP, SFTP, WebDAV, Amazon S3, OpenStack Swift, Backblaze B2, Microsoft Azure & OneDrive, Google Drive and Dropbox.
Version: 7.3.1
SRA Toolkit is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.
Version: 2.10.5
XNAT client tools comprise a number of command line tools to store and retrieve data from XNAT archives. - ArcGet: retrieves image data. - ArcRead: retrieves summary text documents describing imaging data. - ArcSim: retrieves a list of imaging sessions with similar IDs. - StoreXML: writes XML documents to the archive.
Version: 1.0
GATK (Genome Analysis Toolkit) is a software package developed to analyze high-throughput sequencing data capable of taking on projects of any size with a primary focus on variant discovery, genotyping, and data quality assurance.
Version: 4.1.7.0
Jupyter is a language-agnostic HTML notebook application for Project Jupyter. Jupyter has been updated with several more kernels, including Tensorflow and Nilearn.
Version: 4.4.0
AmberTools is a suite of programs that allows users to carry out molecular dynamics simulations, particularly on biomolecules. The suite can be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB) with either explicit water or generalized Born solvent models. The independently developed packages work well by themselves, and with Amber itself.
Version: 20
Software Training
Training sessions available to HMS trainees:
HMS Research Computing
As part of Harvard Medical School's response to COVID-19, HMS Research Computing is now working remotely.
All training classes will be held online until further notice, via Zoom meetings.
Classes are updated here. Enrollees will be sent additional details on how to use Zoom to attend class.
Demystifying deep learning: A practical approach in MATLAB
June 16, 1- 3pm, TMEC Rm. 128
The Harvard Chan Bioinformatics Core
Workshops for HSCI and on-quad HMS researchers:
Introduction to Differential Gene Expression Analysis
June (TBD) TBD Introduction to R
Countway Library of Medicine
Online Short-Seminar: Finding a Home for Your Data
June 1, 2020
2:00pm - 2:30pm
Online Workshop: Introduction to protocols.io and the art of writing protocols
Wednesday, June 3, 2020
12:00pm - 1:30pm
ONLINE Presentation Skills Workshop
Wednesday, June 3, 2020
5:30pm - 7:00pm
Online Short-Seminar: Building Blocks for Reproducibility
Tuesday, June 9, 2020
1:00pm - 1:30pm
Online Short-Seminar: Research Management with Open Science Framework
Wednesday, June 17, 2020
12:00pm - 12:30pm
ONLINE Presentation Skills Workshop
Wednesday, June 17, 2020
5:30pm - 7:00pm
Online Short-Seminar: Data Cleaning with OpenRefine
Thursday, June 25, 2020
2:00pm - 2:30pm
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 Harvard Medical School and Boston Children's Hospital and relies on a framework that was developed by SBGrid.
|
