April 2021 Newsletter
Our April newsletter includes twenty one new and updated software titles. Spring workshop and training registrations are open for both The Harvard Chan Bioinformatics Core and HMS Research Computing.
macOS 11 Big Sur support
We've been testing new application installations on macOS 11 Big Sur. The majority of applications appear to work normally on both x86_64 and Apple Silicon hardware, with a few exceptions. If you have a new Big Sur M1 mac, you should be able to install software with the BioGrids installation manager. Be sure to install XQuartz, and let us know if you encounter any problems
Installation Manager Beta Testing
Our new graphical Installation Manager for macOS and Linux is nearly ready to go and we are looking for some beta testers! Internal testing is going well and we would now like feedback from the community. Email help@biogrids.org and we'll get you set up.
As always, please let us know if you have any questions or problems upgrading - 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
While we recommend not upgrading to 10.15 on any Mac with BioGrids already installed, we have implemented 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 290 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 Installer
The BioGrids Installer is an easy to use application that makes installing and managing life sciences software simple and quick.
A command line version is also available for Macs and Linux. Download using the link button above and register here for activation.
The BioGrids team provides support, infrastructure and testing for scientific software packages. We currently provide 335 titles in five categories and over 1,500 R, python and perl packages and modules. The collection grows weekly. Learn more here: About BioGrids 
BioGrids QuickStart
If you are new to BioGrids and would like to quickly get started with the command line version, follow the instructions below:
1: Download the BioGrids Installer command line version
Linux CLI
curl -kLO https://biogrids.org/wiki/downloads/biogrids-1.0.695-Linux.tgz
tar zxf biogrids-1.0.694-Linux.tgz
cd biogrids-1.0.694-Linux
OSX CLI
curl -kLO https://biogrids.org/wiki/downloads/biogrids-1.0.695-Darwin.tgz
tar zxf biogrids-1.0.694-Darwin.tgz
cd biogrids-1.0.694-Darwin
2: Activate biogrids
./biogrids activate biogrid-production jvinent1 70rYFTDnmCr93VUklfbf1s3M4jdyC9bFVYHew==
Replace the site name, user name and activation key with your own credentials.
3: Install software with BioGrids
./biogrids install fastqc trimmomatic samtools star subread igv
When finished, verify applications are installed:
./biogrids installed
Software Updates
R-pkgs-Biogrids contains common and requested R packages for BIOGRIDS. This title is dependent on R.
Updated versions: r4.0.2-latest, r3.6.2-latest
LDSC is a command line tool for estimating heritability and genetic correlation from GWAS summary statistics. ldsc also computes LD Scores.
Updated versions: 1.0.1
PyTorch is an open source deep learning platform that provides a seamless path from research prototyping to production deployment.
Updated versions: 1.6.0, 1.7.0, 1.8.1
drop Detection of aberrant gene expression events in RNA sequencing data
Updated versions: 1.0.3
PEER is a collection of Bayesian approaches to infer hidden determinants and their effects from gene expression profiles using factor analysis methods.
Updated versions: 1.0
Python is 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: 3.8.8
CUDA contains redistributable software libraries to support CUDA applications for Linux.
Updated versions: 11.2
PyMOL Open Source is the open source version of the widely used molecular visualization package developed by Warren DeLano.
Updated versions: 2.4.0
telseq is a software that estimates telomere length from whole genome sequencing data (BAMs).
Updated versions: 0.0.2
assembly-stats gets assembly statistics from FASTA and FASTQ files.
Updated versions: 1.0.1
CRISPRitz is a software package containing 5 different tools dedicated to performing predictive analysis on CRISPR/Cas experiments.
Updated versions: 2.1.1
medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data.
Updated versions: 1.0.3
Hopla enables classic genomic single, duo, trio, etc., analysis, by studying a single (multisample) vcf-file, eventually generating interactive visualizations.
Updated versions: 0.2.1
csvtk is a set of tools for manipulation of CSV/TSV files. It is convenient for rapid data investigation and integration into analysis pipelines.
Updated versions: 0.23.0
STAR-Fusion is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set.
Updated versions: 1.10.0
Fast Data Transfer - FDT is an Application for Efficient Data Transfers which is capable of reading and writing at disk speed over wide area networks (with standard TCP). It is written in Java, runs an all major platforms and it is easy to use.
Updated versions: 0.25.1
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:1.12
MAPS (Model-based Analysis of PLAC-Seq data) pipeline is a a set of multiple scripts used to analyze PLAC-Seq and HiChIP data.
Updated versions: 03052021
NanoPlot is a plotting tool for long read sequencing data and alignments.
Updated versions: 1.35.5
TensorFlow is 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.
Updated versions:2.4.1
IGV (Integrative Genomics Viewer) a high-performance visualization tool for interactive exploration of large, integrated genomic datasets.
Updated versions: 2.9.4
ted versions:327 | OS X INTEL 327 | Linux 64 366 | Linux 64 366 | OS X INTEL
Software Training
Training sessions available to HMS trainees:
HMS Research Computing
New courses and registrations for Spring 2021 are now open.
See the HMS Research Computing Training Portal for the most current updates.
|
Date
|
Topic
|
|
|
May 5th
|
Distance Learning and Virtual Labs
|
Register |
The Harvard Chan Bioinformatics Core
Courses for Spring 2021 are now open. See the Workshop Updates page for updates.
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.
|
