January 2022 Newsletter
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 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
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.
Versions: 1.10.4
GATE is a Monte-Carlo simulation toolkit for medical physics applications
Versions: Linux 64: 9.0
Software Training
HMS RC Spring 2022 registration is now open.
| Class |
Date |
Time |
| Intro to O2 |
February 16, 2022 |
3-5pm |
| Intro to R/Bioconductor |
February 23, 2022 |
3-5pm |
| 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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