Software Updates

FastQC

a quality control tool for high throughput sequence data.

AFNI

(Analysis of Functional NeuroImages) is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity.

R

a free software environment for statistical computing and graphics.

AmberTools

a suite of programs that allows users to carry out molecular dynamics simulations, particularly on biomolecules. The suite can be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB) with either explicit water or generalized Born solvent models. The independently developed packages work well by themselves, and with Amber itself.

SPM

Software Introduction SPM is made freely available to the [neuro]imaging community, to promote collaboration and a common analysis scheme across laboratories. The software represents the implementation of the theoretical concepts of Statistical Parametric Mapping in a complete analysis package.

The SPM software is a suite of MATLAB (MathWorks) functions and subroutines with some externally compiled C routines. SPM was written to organise and interpret our functional neuroimaging data.

AFNI

(Analysis of Functional NeuroImages) is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity.

HOMER

(Hypergeometric Optimization of Motif EnRichment) a suite of sequencing analysis and sequence motif discovery tools.

Connectome Workbench

is an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project. The distribution includes wb_view, a GUI-based visualization platform, and wb_command, a command-line program for performing a variety of algorithmic tasks using volume, surface, and grayordinate data.

AmberTools

a suite of programs that allows users to carry out molecular dynamics simulations, particularly on biomolecules. The suite can be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB) with either explicit water or generalized Born solvent models. The independently developed packages work well by themselves, and with Amber itself.

BioGrids Installer

Installation Client for the BioGrids software collection.

EVcouplings

a tool to predict protein structure, function, and mutations using evolutionary sequence covariation.

cyberduck

Cyberduck is a libre server and cloud storage browser for Mac and Windows with support for FTP, SFTP, WebDAV, Amazon S3, OpenStack Swift, Backblaze B2, Microsoft Azure & OneDrive, Google Drive and Dropbox.

SRA Toolkit

a collection of tools and libraries for using data in the INSDC Sequence Read Archives.

XNAT

XNAT client tools comprise a number of command line tools to store and retrieve data from XNAT archives. - ArcGet: retrieves image data. - ArcRead: retrieves summary text documents describing imaging data. - ArcSim: retrieves a list of imaging sessions with similar IDs. - StoreXML: writes XML documents to the archive.

GATK

(Genome Analysis Toolkit) a software package developed to analyze high-throughput sequencing data capable of taking on projects of any size with a primary focus on variant discovery, genotyping, and data quality assurance.

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.

Jupyter

a language-agnostic HTML notebook application for Project Jupyter.

AmberTools

a suite of programs that allows users to carry out molecular dynamics simulations, particularly on biomolecules. The suite can be used to carry out complete (non-periodic) molecular dynamics simulations (using NAB) with either explicit water or generalized Born solvent models. The independently developed packages work well by themselves, and with Amber itself.