March 2022 Newsletter
Our March newsletter includes ten new and updated titles for Mac and Linux. A new version of AlphaFold, 2.2.0, has been added.
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
End Of Life for Version 1 BioGrids Installer
BioGrids installation managers in the 1.X series will no longer work. The last released version was 1.0.695. Attempting installation with this older version will fail and will appear to be a network connection issue. Please upgrade to the new installation manager.
You do not need to reinstall titles or reactivate. Simply download the new Installation Manager and begin using.
Download MacOS and Linux versions from our wiki downloads page:
https://biogrids.org/wiki/downloads.md
We welcome any and all feedback from the community at help@biogrids.org.
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
vembrane simultaneously filters variants based on any INFO field, CHROM, POS, REF, ALT, QUAL, and the annotation field ANN.
Updated versions:0.7.1 | Linux 64 0.7.1 | OS X INTEL
DROP (Detection of RNA Outlier Pipeline) pipeline to find aberrant gene expression events in RNA sequencing data.
Updated versions:1.0.5 | OS X INTEL 1.0.4 | OS X INTEL 1.0.3 | OS X INTEL 1.1.3 | OS X INTEL 1.1.3 | Linux 64
Emacs an extensible, customizable, free/libre text editor.
Updated versions:27.2 | Linux 64 27.2 | OS X INTEL
RSEM (RNA-Seq by Expectation-Maximization) a software package for estimating gene and isoform expression levels from RNA-Seq data.
Updated versions:1.3.3 | OS X INTEL 1.3.3 | Linux 64
bioawk an extension to Brian Kernighan's awk, with added support for several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q, and TAB-delimited formats with column names along with new built-in functions and a command line option to use TAB as the input/output delimiter. When the new functionality is not used, bioawk should behave exactly like the original BWK awk.
Updated versions:1.0 | Linux 64
AlphaFold implementation of the inference pipeline of AlphaFold v2.0 using a completely new model that was entered in CASP14.
Updated versions:2.2.0 | Linux 64
Horovod distributed training framework for TensorFlow, Keras, PyTorch, and Apache MXNet.
Updated versions:0.23.0 | Linux 64 0.22.1 | Linux 64
TensorFlow an open source software library for high performance numerical computation. Its flexible architecture allows easy deployment of computation across a variety of platforms (CPUs, GPUs, TPUs), and from desktops to clusters of servers to mobile and edge devices. Originally developed by researchers and engineers from the Google Brain team within Google’s AI organization, it comes with strong support for machine learning and deep learning, and the flexible numerical computation core is used across many other scientific domains.
Updated versions:2.0.0 | OS X INTEL 2.0.0 | Linux 64
Foldseek enables fast and sensitive comparisons of large structure sets.
Updated versions:1.3c64211 | Linux 64 1.3c64211 | OS X INTEL
bamtools a fast, flexible C++ API & toolkit for reading, writing, and manipulating BAM files.
Updated versions:2.5.2 | OS X INTEL
Software Training
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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