September 2021 Newsletter
Our September newsletter includes thirty four new titles and two updated software titles. Fall registration is open for HMS Research Computing training. See the table of classes and link at the end of the newsletter.
As a reminder, 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.
macOS: Installation Manager 2.2.15
Linux: Installation Manager 2.2.15
You can also find a quick link to download MacOS and Linux versions at the top of our wiki page:
https://biogrids.org/wiki/Home
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, v2.2.15, is now available for Linux and MacOS computers:
macOS: Installation Manager 2.2.15
Linux: Installation Manager 2.2.15
BioGrids CLI Quick Start
Start 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
R
R is a free software environment for statistical computing and graphics.
Versions:4.1 | Linux 64 4.1 | OS X INTEL
MMseqs2
MMseqs2: ultra fast and sensitive sequence search and clustering suite
Versions:13.45111 | OS X INTEL 13.45111 | Linux 64
abeona
A simple transcriptome assembler based on kallisto and Cortex graphs.
Versions:0.45.0 | OS X INTEL 0.45.0 | Linux 64
proteinortho
Proteinortho is a tool to detect orthologous genes within different species.
Versions:6.0.31 | Linux 64 6.0.31 | OS X INTEL
rtg-tools
RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation
Versions:3.12.1 | OS X INTEL 3.12.1 | Linux 64
mlst
Scan contig files against PubMLST typing schemes
Versions:2.19.0 | OS X INTEL 2.19.0 | Linux 64
ABRicate
Mass screening of contigs for antibiotic resistance genes
Versions:1.0.1 | OS X INTEL 1.0.1 | Linux 64
WhatsHap
phase genomic variants using DNA sequencing reads (haplotype assembly)
Versions:1.1 | Linux 64 1.1 | OS X INTEL
ARIBA
ARIBA: Antibiotic Resistance Identification By Assembly
Versions:2.14.6 | OS X INTEL 2.14.6 | Linux 64
peddy
peddy compares familial-relationships and sexes as reported in a PED/FAM file with those inferred from a VCF.
Versions:0.4.8 | Linux 64 0.4.8 | OS X INTEL
IntaRNA
Efficient RNA-RNA interaction prediction incorporating seeding and accessibility of interacting sites
Versions:3.2.0 | OS X INTEL 3.2.0 | Linux 64
HMMER
is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).
Versions:3.3.2 | Linux 64 3.3.2 | OS X INTEL
Cactus
Cactus is a reference-free whole-genome multiple alignment program based upon notion of Cactus graphs
Versions:2019.03.01 | Linux 64
PHAST
PHAST is a freely available software package for comparative and evolutionary genomics.
Versions:1.5 | OS X INTEL 1.5 | Linux 64
fgbio
A set of tools to analyze genomic data with a focus on Next Generation Sequencing
Versions:1.3.0 | Linux 64 1.3.0 | OS X INTEL
Krona
Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.
Versions:2.8 | OS X INTEL 2.8 | Linux 64
umis
Tools for processing UMI RNA-tag data
Versions:1.0.7 | Linux 64 1.0.7 | OS X INTEL
cd-hit
Clusters and compares protein or nucleotide sequences
Versions:4.8.1 | Linux 64 4.8.1 | OS X INTEL
CIRCexplorer2
Circular RNA analysis toolkits
Versions:2.3.8 | OS X INTEL 2.3.8 | Linux 64
SEPP
SATe-enabled phylogenetic placement
Versions:4.5.1 | Linux 64 4.5.1 | OS X INTEL
prokka
Prokka is a software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.
Versions:1.14.6 | OS X INTEL 1.14.6 | Linux 64
TBProfiler
Profiling tool for Mycobacterium tuberculosis to detect drug resistance and lineage from WGS data
Versions:3.0.8 | Linux 64 3.0.8 | OS X INTEL
pygtftk
The gtftk suite providing facilities to manipulate genomic annotations in gtf format.
Versions:1.4.0 | Linux 64 1.4.0 | OS X INTEL
picard-slim
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Versions:2.26.2 | OS X INTEL 2.26.2 | Linux 64
HOMER
(Hypergeometric Optimization of Motif EnRichment) a suite of sequencing analysis and sequence motif discovery tools.
Versions:4.11 | Linux 64 4.11 | OS X INTEL
cyvcf2
cyvcf2 is a cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files.
Versions:0.30.11 | Linux 64 0.30.11 | OS X INTEL
phyluce
phyluce (phy-loo-chee) is a software package that is useful for analyzing both data collected from UCE loci and also data collection from other types of loci for phylogenomic studies at the species, population, and individual levels.
Versions:1.7.1 | OS X INTEL 1.7.1 | Linux 64
MUMmer4
MUMmer is a system for rapidly aligning large DNA sequences to one another.
Versions:4.0.0rc1 | Linux 64 4.0.0rc1 | OS X INTEL
andi
estimates the evolutionary distance between closely related genomes. These distances can be used to rapidly infer phylogenies for big sets of genomes. Because andi does not compute full alignments, it is so efficient that it scales even up to thousands of bacterial genomes.
Versions:0.13 | Linux 64 0.13 | OS X INTEL
bracken
Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
Versions:2.6.1 | OS X INTEL 2.6.1 | Linux 64
kraken2
Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.
Versions:2.1.2 | Linux 64 2.1.2 | OS X INTEL
CrossMap
CrossMap is a program for genome coordinates conversion between different genome assemblies.
Versions:0.5.2 | OS X INTEL 0.5.2 | Linux 64
Trinotate
Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms
Versions:3.2.2 | OS X INTEL 3.2.2 | Linux 64
cellranger-arc
The set of analysis pipelines in this suite perform sample demultiplexing, barcode processing, identification of open chromatin regions, and simultaneous counting of transcripts and peak accessibility in single cells.
Versions:2.0.0 | Linux 64
bam-readcount
bam-readcount generates metrics at single nucleotide positions.
Versions:0.8 | OS X INTEL 0.8 | Linux 64
circos
Circos is a software package for visualizing data and information. It visualizes data in a circular layout
Versions:0.69.8 | Linux 64 0.69.8 | OS X INTEL
STREAM
STREAM Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data.
Versions:1.0 | OS X INTEL 1.0 | Linux 64
swarm
A robust and fast clustering method for amplicon-based studies.
Versions:3.1.0 | OS X INTEL 3.1.0 | Linux 64
MultiQC
aggregates results from bioinformatics analyses across many samples into a single report.
Versions:1.11 | Linux 64 1.11 | OS X INTEL
Racon
Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.
Versions:1.4.20 | Linux 64 1.4.20 | OS X INTEL
Barrnap
Barrnap predicts the location of ribosomal RNA genes in genomes. (bacteria, archaea, metazoan mitochondria and eukaryotes.)
Versions:0.9 | OS X INTEL 0.9 | Linux 64
MEGAHIT
MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
Versions:1.2.9 | OS X INTEL 1.2.9 | Linux 64
Software Training
Training sessions available to HMS trainees:
HMS Research Computing
Please see the HMS Research Computing Training Portal for the most current updates.
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Class
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Date
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Time
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Intro to O2
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Sept. 15, 2021
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3-5pm
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Intro to Matlab
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Sept. 22, 2021
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3-5pm
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RCBio: easy and quick HPC
pipeline builder & runner
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Sept. 29, 2021
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3-5pm
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Intro to Parallel Computing
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Oct. 6, 2021
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3-5pm
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Intro to Python
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Oct. 13, 2021
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3-5pm
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Intro to O2
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Oct. 20, 2021
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3-5pm
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Intro to R/Bioconductor
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Oct. 27, 2021
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3-5pm
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Intro to Git/Github
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Nov. 3, 2021
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3-5pm
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Intro to Python
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Nov. 10, 2021
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3-5pm
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Intermediate O2
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Nov. 17, 2021
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3-5pm
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Intro to R/Bioconductor
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Dec. 1, 2021
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3-5pm
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Introduction to Globus Data
Transfer and Data Collaboration
on O2
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Dec. 8, 2021
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3-5pm
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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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