February 2022 Newsletter
Our February newsletter includes twelve new and updated titles for Mac and Linux. This month we have added AlphaFold 2.1.2 to BioGrids.
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
C3POa (Concatemeric Consensus Caller with Partial Order alignments) is a computational pipeline for calling consensi on R2C2 nanopore data.
Versions: 5431d3b | Linux 64 5431d3b | OS X INTEL 2.3.0 | Linux 64 2.3.0 | OS X INTEL
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.
Versions: 1.15 | Linux 64 1.15 | OS X INTEL
CEFCIG (Computational Epigenetic Framework for Cell Identity Gene Discovery)
Versions: 5431d3b | OS X INTEL 5431d3b | Linux 64
GATK (Genome Analysis Toolkit) 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.
Versions: 4.2.5.0 | Linux 64 4.2.5.0 | OS X INTEL
AlphaFold an implementation of the inference pipeline of AlphaFold v2.0 using a completely new model that was entered in CASP14.
Versions: 2.1.2 | Linux 64
HDF5 is a data model, library, and file format for storing and managing data.
Versions:1.8.15 | OS X INTEL 1.12.1 | OS X INTEL 1.12.1 | Linux 64
xPore is a Python package for identification and quantification of differential RNA modifications from direct RNA sequencing
Versions: 2.1 | OS X INTEL 2.1 | Linux 64
Cytoscape a software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data.
Versions: 3.9.1 | Linux 64 3.9.1 | OS X INTEL
FlashPCA performs fast principal component analysis (PCA) of single nucleotide polymorphism (SNP) data, similar to smartpca from EIGENSOFT (http://www.hsph.harvard.edu/alkes-price/software/) and shellfish (https://github.com/dandavison/shellfish). FlashPCA is based on the https://github.com/yixuan/spectra/ library.
Versions: 2.0 | Linux 64 2.0 | OS X INTEL
HiCPro
An optimized and flexible pipeline for Hi-C data processing
Versions: 3.1.0 | Linux 64 3.1.0 | OS X INTEL
SEACR Sparse Enrichment Analysis for CUT&RUN
Versions: 1.3 | Linux 64 1.3 | OS X INTEL
SUPPA2 Fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions.
Versions: 2.3 | Linux 64 2.3 | OS X INTEL
Software Training
HMS RC Spring 2022 registration is now open.
| Class |
Date |
Time |
| Intro to Python |
March 2 2022 |
3-5pm |
| Intro to Parallel Computing |
March 9 2022 |
3-5pm |
| Intermediate O2 |
March 16 2022 |
3-5pm |
| Intro to Matlab |
March 23 2022 |
3-5pm |
| Optimizing O2 Jobs |
March 30 2022 |
3-4pm |
| 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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