Our April newsletter includes six new and updated titles for Mac and Linux.
New versions of software titles become the default version in BioGrids. For example, samtools version 1.15.1 was added this month and is now the default. It is a best practice to explicitly set the version of titles being used rather than depend on the default. This leads to more reproducible results.
Registration is now open for Spring 2022 HMS RC training classes. Please see the table and link at the end of this newsletter.
New software titles can be requested by sending email to firstname.lastname@example.org or filling out our webform:
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 email@example.com. We can set up a Zoom meeting to assist you.
MacOS 10.15 Catalina
Due to new security measures in OSX, installation under MacOS 10.15 requires an additional step. We have detailed a workaround to install BioGrids and SBGrid on new machines. Two approaches are available.
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.)"
Register here to try out our software installer, which allows users to choose from over 530 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: firstname.lastname@example.org.
The latest version of the BioGrids Installation Manager is available for Linux and MacOS computers:
Start the BioGrids environment:
List available titles (Linux):
List available titles (Mac):
Get version and override info:
biogrids-info -l star
Get list of executables for a title:
Need more help? Send mail to: email@example.com
Nextflow a reactive workflow framework and programming DSL that ease writing computational pipelines with complex data.
Updated versions:21.04.3.5560 | Linux 64 21.04.3.5560 | OS X INTEL 22.04.0.5697 | Linux 64
seaview is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny.
Updated versions:5.0.4 | OS X INTEL 5.0.4 | Linux 64
hdbscan (Hierarchical Density-Based Spatial Clustering of Applications with Noise) performs DBSCAN over varying epsilon values and integrates the result to find a clustering that gives the best stability over epsilon.
Updated versions:0.8.28 | OS X INTEL 0.8.28 | Linux 64
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.
Updated versions:1.15.1 | Linux 64 1.15.1 | OS X INTEL
calib clusters paired-end reads using their barcodes and sequences.
Updated versions:0.3.4 | Linux 64 0.3.4 | OS X INTEL
Chromap is an ultrafast method for aligning and preprocessing high throughput chromatin profiles.
Updated versions:0.2.1 | OS X INTEL 0.2.1 | Linux 64
HMS Research Computing is running a series of short, free information sessions - an overview of RC followed by weekly sessions on particular services and resources. The Research Computing team provides solutions to researchers in diverse life science areas with all levels of technological expertise. So please join us for one or more lunchtime sessions on Wednesdays, April 13 to May 25. Visit our IT News Article for more information.
Research Computing Services and Resources | April 13th | 12PM-1PM
Optimizing O2 Jobs | April 20th | 12:30PM-1PM
Data Transfers with Globus | April 27th | 12:30PM-1PM
Why use RStudio on O2? | May 4th | 12:30PM-1PM
RCBio: HPC Pipeline Builder and Runner | May 11th | 12:30PM-1PM
Research Data Management: Tips and Tools | May 18th | 12:30PM-1PM
Electronic Data Capture with REDCap | May 25th | 12:30PM-1PM