October 2022 Newsletter
Our October newsletter includes five new and updated titles for Mac and Linux. 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 2.6.17
Linux: Installation Manager 2.6.17
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
Google Cloud SDK
tools and libraries for interacting with Google Cloud products and services.
Updated versions:406.0.0 | Linux 64 406.0.0 | OS X INTEL
R-pkgs-Biogrids contains common and requested R packages for BIOGRIDS. This title is dependent on R.
Updated versions:r4.2.0-latest | Linux 64 r4.2.0-20221019 | Linux 64 r4.1-20221013 | Linux 64
R a free software environment for statistical computing and graphics.
Updated versions:4.2.0 | Linux 64
pairtools
CLI tools to process mapped Hi-C data
Updated versions:0.3.0 | Linux 64 0.3.0 | OS X INTEL
pairix
2D indexing on bgzipped text files of paired genomic coordinates
Updated versions:0.3.7 | OS X INTEL 0.3.7 | Linux 64
Software Training
Center for Computational Biomedicine
The Center for Computational Biomedicine (CCB) Fall newsletter contains training and collaboration opportunities.
HMS Research Computing
User Training Fall 2022 registration is now open.
| Class |
Date |
Time |
| Intro to Git/GitHub |
11/2/2022 |
10am-11am |
| RCBio: Easy and Quick HPC Pipeline Builder and Runner |
11/2/2022 |
11am-12pm |
| Intro to Python |
11/9/2022 |
10am-12pm |
| Intro to O2 |
11/16/2022 |
10am-12pm |
| |
11/23/2022 |
no class |
| Intro to O2 Portal (new workshop) |
11/30/2022 |
10am-12pm |
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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