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 email@example.com or filling out our webform:
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:
We welcome any and all feedback from the community at firstname.lastname@example.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 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
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: 220.127.116.11 | Linux 64 18.104.22.168 | 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
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