Our January newsletter includes eleven new and updated titles for Mac and Linux. 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
RSEM (RNA-Seq by Expectation-Maximization) a software package for estimating gene and isoform expression levels from RNA-Seq data.
Versions:1.3.3 | OS X INTEL 1.3.3 | Linux 64
Bowtie2 an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
Versions:2.4.4 | Linux 64 2.4.4 | OS X INTEL
bpp implements a versatile high-performance version of the BPP software
Versions:4.4.1 | Linux 64 4.4.1 | OS X INTEL
ExaBayes is a software package for Bayesian tree inference.
Versions:1.5.1 | OS X INTEL 1.5.1 | Linux 64
treePL is a phylogenetic penalized likelihood program.
Versions:1.0 | OS X INTEL 1.0 | Linux 64
IQ-TREE efficient and versatile phylogenomic software by maximum likelihood.
Versions:2.1.3 | Linux 64 2.1.3 | OS X INTEL
Picard a set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats.
Versions:2.18.14 | OS X INTEL 2.18.14 | Linux 64
PASTA is an implementation of the PASTA (Practical Alignment using Saté and TrAnsitivity) algorithm.
Versions:1.7.8 | Linux 64 1.7.8 | OS X INTEL
IGV (Integrative Genomics Viewer) a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.
Versions:2.11.9 | Linux 64 2.11.9 | OS X INTEL
beast is a cross-platform program for Bayesian analysis of molecular sequences using MCMC.
GATE is a Monte-Carlo simulation toolkit for medical physics applications
Versions: Linux 64: 9.0