April 2022 Newsletter
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 help@biogrids.org or filling out our webform:
https://biogrids.org/help/?tab=software
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.
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.
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 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: help@biogrids.org.
BioGrids Quickstart
The latest version of the BioGrids Installation Manager is available for Linux and MacOS computers:
macOS: Installation Manager 2.5.12
Linux: Installation Manager 2.5.12
Start the BioGrids environment:
source /programs/biogrids.shrc
List available titles (Linux):
cat /programs/x86_64-linux/biogrids_x86_64-linux
List available titles (Mac):
cat /programs/i386-mac/biogrids_i386-mac
Get version and override info:
biogrids-info -l star
Get list of executables for a title:
biogrids-list star
Need more help? Send mail to: help@biogrids.org
Software Updates
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
Software Training
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.
Schedule
- 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
Zoom Registration Links
HMS RC Spring 2022 registration is now open.
| Class |
Date |
Time |
| Intro to O2 |
April 6 2022 |
3-5pm |
| Intro to Python |
April 13 2022 |
3-5pm |
| Intro to R/Bioconductor |
April 20 2022 |
3-5pm |
| Intro to Git/Github |
April 27 2022 |
3-4pm |
| BioGrids Academic Software Platform: No Installation Required |
May 4 2022 |
3-4pm |
| Intro to RCBio |
May 11 2022 |
3-5pm |
| Intro to Python |
May 18 2022 |
3-5pm |
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.
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