August 2022 Newsletter
Our August newsletter includes twenty new and updated titles for Mac and Linux. These include SAMtools 1.16 and RStdudio 2022.02.3.
New software titles can be requested by sending email to help@biogrids.org or filling out our webform:
https://biogrids.org/help/?tab=software
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 2.6.17
Linux: Installation Manager 2.6.17
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
AlphaFold is an implementation of the inference pipeline of AlphaFold v2.0 using a completely new model that was entered in CASP14.
Updated versions:2.2.3 | Linux 64
BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.
Updated versions:2.4.41 | Linux 64 2.4.41 | OS X INTEL
RStudio is an integrated development environment (IDE) for R that includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.
Updated versions:2022.02.3 | Linux 64 2022.02.3 | OS X INTEL
merlin uses sparse trees to represent gene flow in pedigrees and is a fast pedigree analysis package.
Updated versions:1.1.2 | Linux 64 1.1.2 | OS X INTEL
FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies.
Updated versions:7.3.2 | OS X INTEL 7.3.2 | Linux 64
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.
Updated versions:1.16 | Linux 64 1.16 | OS X INTEL
Spyder is a powerful scientific environment written in Python, for Python, and designed by and for scientists, engineers and data analysts.
Updated versions:5.3.2 | Linux 64
tidk Identify and find telomeres, or telomeric repeats in a genome.
Updated versions:0.2.1 | Linux 64 0.2.1 | OS X INTEL
alevin-fry is a tool for the efficient processing of single-cell data based on RAD files produced by alevin.
Updated versions:0.7.0 | Linux 64 0.7.0 | OS X INTEL
terminus enables the discovery of data-driven, robust transcript groups from RNA-seq data.
Updated versions:0.1.0 | Linux 64 0.1.0 | OS X INTEL
Longshot a variant calling tool for diploid genomes using long error prone reads such as Pacific Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT).
Updated versions:0.4.5 | Linux 64
mudskipper is a tool for converting genomic BAM/SAM files to transcriptomic BAM/RAD files.
Updated versions:0.1.0 | OS X INTEL 0.1.0 | Linux 64
seqcomplexity calculates Per-Read and Total Sequence Complexity from FastQ file.
Updated versions:0.1.2 | OS X INTEL 0.1.2 | Linux 64
vapor is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis.
Updated versions:1.0.2 | OS X INTEL 1.0.2 | Linux 64
flexbar preprocesses high-throughput sequencing data efficiently.
Updated versions:3.5.0 | Linux 64 3.5.0 | OS X INTEL
10xbamtofastq is a tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis.
Updated versions:1.4.1 | OS X INTEL 1.4.1 | Linux 64
LiftoffTools is a toolkit to compare genes lifted between genome assemblies.
Updated versions:0.4.3 | Linux 64 0.4.3 | OS X INTEL
vembrane allows to simultaneously filter variants based on any INFO field, CHROM, POS, REF, ALT, QUAL, and the annotation field ANN.
Updated versions:0.11.0 | Linux 64 0.11.0 | OS X INTEL
popscle is a suite of population scale analysis tools for single-cell genomics data.
Updated versions:0.1beta | Linux 64 0.1beta | OS X INTEL
pLannotate is web server for automatically annotating engineered plasmids.
Updated versions:1.2.0 | Linux 64
Software Training
HMS Research Computing User Training Fall 2022 registration is now open.
| Class |
Date |
Time |
| Intro to O2 |
9/7/2022 |
10am-12pm |
| |
9/14/2022 |
no class |
| Intro to O2 Portal (new workshop) |
9/21/2022 |
10am-12pm |
| Optimizing O2 Jobs |
9/28/2022 |
10am-11am |
| Intro to MATLAB |
10/5/2022 |
10am-12pm |
| Intro to Parallel Computing |
10/12/2022 |
10am-12pm |
| Intro to Python |
10/19/2022 |
10am-12pm |
| Intermediate O2 |
10/26/2022 |
10am-12pm |
| Intro to Git/GitHub |
11/2/2022 |
10am-11am |
| RCBio: Easy and Quick HPC Pipeline Builder and Runner |
11/2/2022 |
11am-12pm |
| Intro to Python |
11/9/2022 |
10am-12pm |
| Intro to O2 |
11/16/2022 |
10am-12pm |
| |
11/23/2022 |
no class |
| Intro to O2 Portal (new workshop) |
11/30/2022 |
10am-12pm |
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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