April 2023 Newsletter
Our April newsletter includes twenty one new and updated titles for Mac and Linux. New software titles can be requested by sending email to help@biogrids.org or filling out our Software Request Form.
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.
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 660 bioinformatics 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
OpenFold - a trainable, memory-efficient, and GPU-friendly PyTorch reproduction of DeepMind's AlphaFold 2.
Updated versions:1.0.1 | Linux 64
structure - inference of population structure using multilocus genotype data
Updated versions:2.3.4 | Linux 64 2.3.4 | OS X INTEL
Foldseek - enables fast and sensitive comparisons of large structure sets.
Updated versions:5-53465f0 | Linux 64
AmberTools - a suite of programs that allows users to carry out molecular dynamics simulations, particularly on biomolecules.
Updated versions:21 | Linux 64
DIAMOND - a high-throughput program for aligning a file of short DNA sequencing reads against a protein reference database such as NR, at 20,000 times the speed of BLASTX, with high sensitivity.
Updated versions:2.1.6 | Linux 64 2.1.6 | OS X INTEL
Segment Anything - (SAM) produces high quality object masks from input prompts such as points or boxes, and it can be used to generate masks for all objects in an image.
Updated versions:c3b8a88 | OS X INTEL c3b8a88 | Linux 64
strobealign - a read mapper that is typically significantly faster than other read mappers while achieving comparable or better accuracy, see the performance evaluation.
Updated versions:0.9.0 | Linux 64 0.9.0 | OS X INTEL
VERSE - a versatile and efficient RNA-Seq read counting tool
Updated versions:0.1.5 | Linux 64 0.1.5 | OS X INTEL
BCFtools - a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF.
Updated versions:1.17 | Linux 64 1.17 | OS X INTEL
regtools - a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context.
Updated versions:1.0.0 | Linux 64 1.0.0 | OS X INTEL
deSALT - De Bruijn graph-based Spliced Aligner for Long Transcriptome reads
Updated versions:1.5.6 | Linux 64 1.5.6 | OS X INTEL
Salmon - a tool for quantifying the expression of transcripts using RNA-seq data.
Updated versions:1.10.1 | Linux 64 1.10.1 | OS X INTEL
pangolin - (Phylogenetic Assignment of Named Global Outbreak LINeages) software package for assigning SARS-CoV-2 genome sequences to global lineages.
Updated versions:4.2 | Linux 64 4.2 | OS X INTEL
StringTie - a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.
Updated versions:2.2.1 | Linux 64 2.2.1 | OS X INTEL
pbipa - IPA HiFi Genome Assembler
Updated versions:1.8.0 | Linux 64
lordec - a hybrid error correction program for long, PacBio reads
Updated versions:0.9 | OS X INTEL 0.9 | Linux 64
Canu - a fork of the Celera Assembler designed for high-noise single-molecule sequencing.
Updated versions:2.2 | Linux 64 2.2 | OS X INTEL
hera - a bioinformatics tool that helps analyze RNA-seq data, providing base-to-base alignment BAM files, transcript abundance estimation, and fusion gene detection.
Updated versions:1.1 | Linux 64 1.1 | OS X INTEL
Ryuto - Network-Flow based Transcriptome Reconstruction
Updated versions:1.6.3 | OS X INTEL 1.6.3 | Linux 64
MultiQC - aggregates results from bioinformatics analyses across many samples into a single report.
Updated versions:1.14 | Linux 64 1.14 | OS X INTEL
PCAone - Principal Component Analysis All in One
Updated versions:0.3.2 | Linux 64 0.3.2 | OS X INTEL
Software Training
Center for Computational Biomedicine
The Center for Computational Biomedicine (CCB) Fall newsletter contains training and collaboration opportunities.
HMS Research Computing
HMS Research Computing 2023 Spring User Training is now open.
| Class |
Date |
Time |
| Intro to O2 Portal |
May 3, 2023 |
10am to 11pm |
Where Should I Put My Data?
Understanding Data Storage at HMS |
May 10, 2023 |
10am to 11am |
| Intermediate O2 |
May 17, 2023 |
10am to 12pm |
| Intro to Python |
May 24, 2023 |
10am to 12pm |
RCBio: Easy and Quick HPC Pipeline
Builder and Runner |
May 31, 2023 |
10am to 11am |
| Intro to Git and GitHub |
Jun. 7, 2023 |
10am to 11am |
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.
|
|
|
|
|
