October 2021 Newsletter
Our October newsletter includes twenty one new and updated software titles. Samtools version 1.14 has been installed and is the new default.
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.
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, 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
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:1.14 | Linux 64 1.14 | OS X INTEL
CLIPper
A tool to detect CLIP-seq peaks.
Updated versions:2.0.1 | Linux 64 2.0.1 | OS X INTEL
R-pkgs-Biogrids
contains common and requested R packages for BIOGRIDS. This title is dependent on R.
Updated versions:r4.1-latest | OS X INTEL r4.1-20210924 | OS X INTEL r4.0.2-latest | OS X INTEL r4.0.2-20210924 | OS X INTEL r4.1-latest | Linux 64 r4.1-20210924 | Linux 64 r4.0.2-latest | Linux 64 r4.0.2-20210924 | Linux 64
TensorFlow
an open source software library for high performance numerical computation. Its flexible architecture allows easy deployment of computation across a variety of platforms (CPUs, GPUs, TPUs), and from desktops to clusters of servers to mobile and edge devices. Originally developed by researchers and engineers from the Google Brain team within Google’s AI organization, it comes with strong support for machine learning and deep learning, and the flexible numerical computation core is used across many other scientific domains.
Updated versions:2.0.0 | OS X INTEL 1.14.0 | OS X INTEL 2.0.0 | Linux 64 1.14.0 |
Linux 64
Python
a general-purpose, interpreted, object oriented, high-level dynamic programming language that emphasizes code readability. Its syntax allows programmers to express concepts in fewer lines of code than in C++ or Java, thus allowing programmers to work more quickly and integrate their systems more effectively.
Updated versions:3.6.5 | OS X INTEL 3.6.5 | Linux 64
SECAPR
Process sequence-capture FASTQ files into alignments for phylogenetic analyses. Integrates allele phasing.
Updated versions:2.2.3 | Linux 64 2.2.3 | OS X INTEL
chewBBACA
A complete suite for gene-by-gene schema creation and strain identification.
Updated versions:2.8.5 | OS X INTEL 2.8.5 | Linux 64
NanoSim
NanoSim is a fast and scalable read simulator for Nanopore sequencing data.
Updated versions:3.0.2 | OS X INTEL 3.0.2 | Linux 64
Megalodon
Nanopore modified base and sequence variant detection.
Updated versions:2.3.4 | OS X INTEL 2.3.4 | Linux 64
MOB-suite
MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies. The MOB-suite is designed to be a modular set of tools for the typing and reconstruction of plasmid sequences from WGS assemblies.
Updated versions:3.0.3 | OS X INTEL 3.0.3 | Linux 64
EggNOG-mapper
Fast genome-wide functional annotation through orthology assignment.
Updated versions:2.1.5 | OS X INTEL 2.1.5 | Linux 64
AMPtk
AMPtk: Amplicon tool kit for processing high throughput amplicon sequencing data.
Updated versions:1.5.3 | OS X INTEL 1.5.3 | Linux 64
Raven
a de novo genome assembler for long uncorrected reads.
Updated versions:1.6.1 | Linux 64 1.6.1 | OS X INTEL
ToulligQC
A post sequencing QC tool for Oxford Nanopore sequencers
Updated versions:2.1.1 | OS X INTEL 2.1.1 | Linux 64
FsnViz
Tool for plotting gene fusion events detected by various tools using Circos.
Updated versions:0.3.0 | OS X INTEL 0.3.0 | Linux 64
GMAP
Genomic mapping and alignment program for mRNA and EST sequences.
Updated versions:2021.08.25 | OS X INTEL 2021.08.25 | Linux 64
HiCUP
A tool for mapping and performing quality control on Hi-C data
Updated versions:0.8.2 | Linux 64 0.8.2 | OS X INTEL
nextclade
SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks
Updated versions:1.4.0 | OS X INTEL 1.4.0 | Linux 64
Nextalign
Viral genome sequence alignment tool
Updated versions:1.4.0 | Linux 64 1.4.0 | OS X INTEL
nanoq
Ultra-fast quality control and summary reports for nanopore reads
Updated versions:0.8.1 | OS X INTEL 0.8.1 | Linux 64
ngsplot
Quick mining and visualization of NGS data by integrating genomic databases
Updated versions:2.6.3 | OS X INTEL 2.6.3 | 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 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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