Applications

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Application Support


Click on the links below for support on the individual applications:


Package Description
ABySS Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler.
Albacore Albacore is a software project that provides an entry point to the Oxford Nanopore basecalling algorithms
Anaconda Anaconda is the leading open data science platform powered by Python.
Ansys ANSYS Fluent software includes broad physical modelling capabilities to model flow, turbulence, heat transfer, and reactions for industrial applications.
Avizo Avizo data visualisation and analysis tool
BayesTraits BayesTraits is a computer package for performing analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available.
Beast BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC.
Bison Bison, is a parser generator that is part of the GNU Project.
Bowtie1 The aligner is typically used with short reads and a large reference genome, or for whole genome analysis. Bowtie is promoted as an ultrafast, memory-efficient short aligner for short DNA sequences.
Bowtie2 Bowtie 2 is more suited to finding longer, gapped alignments in comparison with the original Bowtie1 method.
Bridger Bridger is an efficient de novo trascriptome assembler for RNA-Seq data. It can assemble all transcripts from short reads (single or paired) without using a reference.
Cegma CEGMA (Core Eukaryotic Genes Mapping Approach) is a pipeline for building a set of high reliable set of gene annotations in virtually any eukaryotic genome.
CMake CMake is cross-platform free and open-source software for managing the build process of software using a compiler-independent method.
COMSOL COMSOL Multiphysics is a general-purpose software platform, based on advanced numerical methods, for modeling and simulating physics-based problems
CP2K CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems.
Crop CROP is an unsupervised nucleic acid sequence clustering algorithm.
CUDA CUDA is NVIDIA’s parallel computing architecture that enables dramatic increases in computing performance by harnessing the power of the GPU nodes.
Cufflinks Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
Delft3D Delft3D is a world leading 3D modeling suite to investigate hydrodynamics, sediment transport and morphology and water quality for fluvial, estuarine and coastal environments.
Discovardenovo DISCOVAR de novo can generate de novo assemblies for both large and small genomes.
FDS-SMV Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires. Smokeview (SMV) is a visualization program used to display the output of FDS and CFAST simulations.
Ffmpeg ffmpeg is a very fast video and audio converter that can also grab from a live audio/video source.
Flex Flex (Fast lexical analyser), Flex is a tool for generating scanners: programs which recognize lexical patterns in text.
FreeIPMI FreeIPMI provides in-band and out-of-band IPMI software based on the IPMI v1.5/2.0 specification.
Fiji Fiji Is Just ImageJ—a "batteries-included" distribution of ImageJ which includes many useful plugins contributed by the community.
Gcc gcc (GNU Compiler Collection) is a collection of compilers consisting of C, C++, Fortran and more.
GNUplot Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms.
Hwloc hwloc provides command line tools and a C API to obtain the hierarchical map of key computing elements
Java Java is a general-purpose computer programming language that is concurrent, class-based, object-oriented.
HPL HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers as well as freely available implementation of the High Performance Computing Linpack Benchmark.
HyPhy HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package for the analysis of genetic sequences (in particular the inference of natural selection) using techniques in phylogenetics, molecular evolution, and machine learning.
IDL IDL, short for Interactive Data Language, is a programming language used for data analysis. It is popular in particular areas of science, such as astronomy, atmospheric physics and medical imaging.
Insighttoolkit ITK is an open-source software toolkit for performing registration and segmentation.
Intel Parallel Studio Intel Parallel Studio is a software development product that facilitates native code development on Viper in C, C++ and Fortran for parallel computing.
Libwid Likwid is a simple to install and use toolsuite of command line applications for performance oriented programmers.
LS-DYNA General-purpose finite element program capable of simulating complex real world problems.
Maker MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases.
Matlab Numerical Computing Environment.
Mercurial Mercurial is truly distributed, giving each developer a local copy of the entire development history. This way it works independent of network access or a central server. Committing, branching and merging are fast and cheap.
Mpich MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard.
Mono .NET Framework-compatible set of tools including, among others, a C# compiler and a Common Language Runtime.
MrBayes MrBayes: Bayesian Inference of Phylogeny
Munge It is an authentication service that creates and validates user credentials.
Mvapich2 MVAPICH2 is a BSD-licensed implementation of the MPI standard with support for Intel Omni-Path is a high performance.
Ncbi blast It finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.
Ncurses ncurses (new curses) is a programming library providing an application programming interface (API) that allows the programmer to write text-based user interfaces in a terminal-independent manner.
Netloc Netloc software package provides network topology discovery tools, and an abstract representation of those networks topologies for a range of network types and configurations.
NgSpice Ngspice is a mixed-level/mixed-signal circuit simulator. Its code is based on three open source software packages: Spice3f5, Cider1b1 and Xspice.
Nwchem NWChem provides computational chemistry tools and particularly large scientific computational chemistry problems.
Open64 Open64 is a discontinued, free, open source, optimizing compiler for the Itanium and x86-64 microprocessor architectures.
Openuh Openuh is an open version of the openACC compiler suite.
Obitools The OBITools package is a set of programs specifically designed for analysing NGS data in a DNA meta-barcoding context, taking into account taxonomic information.
Openfoam OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to acoustics, solid mechanics and electromagnetics.
OpenMPI Open MPI is a Message Passing Interface (MPI) library used for communicating between HPC nodes.
Orca ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules.
Paraview ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyse their data using qualitative and quantitative techniques.
Petsc PETSc is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modelled by partial differential equations. It supports MPI, and GPUs through CUDA or OpenCL, as well as hybrid MPI-GPU parallelism.
Perl Perl is a flexible high-level, general-purpose, interpreted, dynamic programming languages with a large amount of libraries.
PGI PGI Community Edition is a no-cost license to a recent release of the PGI Fortran, C and C++ compilers and tools for multicore CPUs and NVIDIA GPUs, including all OpenACC, OpenMP and CUDA Fortran .
Planatus Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing data.
Python Python is a family of high-level, general-purpose, interpreted, dynamic programming languages and includes IPython.
R R is an open source programming language and software environment for statistical computing and graphics.
Readline GNU Readline is a software library that provides line-editing and history capabilities for interactive programs with a command-line interface, such as Bash.
Rsem RSEM is an RNA-Seq transcript quantification program.
Samtools Tools (written in C using htslib) for manipulating next-generation sequencing data
SAS Statistical Analysis System.
Savu Python package to assist with the processing and reconstruction of parallel-beam tomography data.
Scalapack The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers
Siesta SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.
SSW Integrated software libraries, data bases, and system utilities which provide a common programming and data analysis environment for Solar Physics
STAR Ultrafast universal RNA-seq aligner.
Star-ccm+ Computational Fluid Package.
Stata Stata is a commercial statistical package, which provides a complete solution for data analysis, data management, and graphics.
Tophat It is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyses the mapping results to identify splice junctions between exons.
Transabyss Software pipeline for analyzing ABySS-assembled transcriptome contigs
Transrate Transrate is software for de-novo transcriptome assembly quality analysis
Trinityrnaseq Trinity assembles transcript sequences from Illumina RNA-Seq data.
Utilities General utilities module including zip, wget and git utilities.
Voxfe VOX-FE is voxel-based FE software with a sophisticated graphical user interface that allows the complex loading regimes that are inevitably present in biomechanical analyses to be readily applied to the model geometry, and the resultant 3D stress and strain patterns to be visualized easily.
Xyce An open source, SPICE-compatible, high-performance analog circuit simulator, capable of solving extremely large circuit problems by supporting large-scale parallel computing platforms.
Wgs Celera Assembler is a de novo whole-genome shotgun (WGS) DNA sequence assembler.
Yt yt supports structured, variable-resolution meshes, unstructured meshes, and discrete or sampled data such as particles. Focused on driving physically-meaningful inquiry, yt has been applied in domains such as astrophysics, seismology, nuclear engineering, molecular dynamics, and oceanography.
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