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Multimedia player that supports a variety of different video codecs and formats.

Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks.

As a library, it presents a single abstract data model to the calling application for all supported formats.

Wall's Practical Extraction and Report Language.

Fix an infinite loop in the flac packetizer.

Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.

ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations.

It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.

DICOM format to the NIfTI format.

GPUs, Parallel Processing, and Job Arrays.

It also comes with a variety of useful commandline utilities for data translation and processing.

Fix reads of uninitialized pointers in the MKV demuxer.

Qhull implements the Quickhull algorithm for computing the convex hull.

Support for interactive data visualization and use of GUI toolkits.

ACCRE Commands for Job Monitoring.

It is independent of (but designed to be complementary to) the existing PLINK package.

Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance.

Martinos Center for Biomedical Imaging.

Basic Tutorial: One Million Digits of Pi.

Like BASH, it has job control and uses the readline library for input.

HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.

Flexible, embeddable interpreters to load into your own projects.

The Aspera CLI is for users and organizations who want to automate their transfer workflows.

Engine2018b (Py2)2018b (Py3)The MATLAB Engine API for Python provides a package for Python to call MATLAB as a computational engine.

Singularity: Running Containers on ACCRE.

Setting Up Fairshare Usage.

Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis.

It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.

Fortran library for fast updates of QR and Cholesky decompositions.

BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage.

MUSCLE can align hundreds of sequences in seconds.

Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis.

Building Software on the ACCRE Cluster.

Pysam also includes an interface for tabix.

CLR that is binary compatible with Microsoft.

OpenGATE collaboration and dedicated to the numerical simulations in medical imaging.

Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions.

Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.

Fix an integer overflow in the avi demuxer.

List of modules available on regular compute nodes.

Last updated May 1, 2019.

Amber17 (Py2)Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction.

WYSIWYG 2D plotting tool for X Windows System and Motif.

Fix a floating point exception in the MKV demuxer.

MIT style Open Source license by the Open Source Geospatial Foundation.

It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation.

Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies.

It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics.

List of modules available on ACCRE.

We can read and write Freesurfer geometry, and read Freesurfer morphometry and annotation files.

Open a Helpdesk Ticket.

The source code is available for those wanting to do their own ports.

There is some very limited support for DICOM.

This page contains a list of modules available on Lmod, including modules available on the GPU accelerated nodes.

Easy to use, high performance tools for parallel computing.

It is used to build the majority of Google's software.

Circos ideal for exploring relationships between objects or positions.

Versatile media player which can cover various types of container format such as VCD, DVD, AVI, WMV among others.

Apache Hadoop software library is a framework that allows for the distributed processing of large data sets across clusters of computers using simple programming models.

ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way.

The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance.

FMRI, MRI and DTI brain imaging data.

It plays all your digital music and video.

Ruby on the ACCRE Cluster.

It includes tools to complement SPM and FSL.

SLURM: Scheduling and Managing Jobs.

Fortran77 subroutines designed to solve large scale eigenvalue problems.

Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science.

Native format is NIFTI but includes a conversion program (see dcm2nii) for converting DICOM images.

BerkeleyGW Package is a set of computer codes that calculates the quasiparticle properties and the optical responses of a large variety of materials from bulk periodic crystals to nanostructures such as slabs, wires and molecules.

It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in visual interfaces for other technical domains.

It was designed with reliability in mind.

MATLAB on the ACCRE Cluster.

Request A Cluster Account.

The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator.

Simulation Tool for Electrical, Mechanical, Fluid Flow, and Chemical Applications.

Just Another Gibbs Sampler.

Recent VLC Media Player news.

MIT to model electromagnetic systems.

DNA sequences for interspersed repeats and low complexity DNA sequences.

ANTs is useful for managing, interpreting and visualizing multidimensional data.

This list is updated at the start of each month.

Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors.

It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages).

Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.

It is fully parallelized and can run with as low as just a few kilobytes of memory.

OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products.