Applications

Application Support

Click on the links below for support on the individual and library packages:

• Jump to Libraries or Test Modules

Package	Description
ABySS	Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler.
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
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.
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.
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 analyze 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 fantastic high-level, general-purpose, interpreted, dynamic programming languages with a large amount of libraries.
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.
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.
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.
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.
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.

Libraries

Library	Description
Boost	C++ Standard Library. Boost libraries are intended to be widely useful, and usable across a broad spectrum of applications.
Cfitsio	CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS.
Expat	Expat XML parser library in C
Fftw3	FFTW is a C subroutine library for computing the discrete Fourier transform (DFT).
Hdf5	HDF5 is a data model, library, and file format for storing and managing data.
Hypre	A library of high performance pre conditioners and solvers featuring multi-grid methods for the solution of large, sparse linear systems of equations on massively parallel computers.
Jemalloc	jemalloc is a general purpose malloc implementation that emphasizes fragmentation avoidance and scalable concurrency support.
Libgd	The module LibGD is an open source code library for the dynamic creation of images.
Libjpeg-turbo	The module Libjpeg-turbo is a JPEG image codec that uses SIMD instructions (MMX, SSE2, AVX2, NEON, AltiVec) to accelerate baseline JPEG compression and decompression
Parmetis	ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices.
Libpng	The reference library for use in applications that read, create, and manipulate PNG (Portable Network Graphics) raster image files.
Netcdf-c	NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
Openblas	OpenBLAS is an optimized BLAS library (based on GotoBLAS2 1.13 BSD version).
Osmesa	Mesa's off-screen interface is used for rendering into user-allocated memory without any sort of window system or operating system dependencies.
Qt	Qt is a cross-platform framework, that is usually used as a graphical toolkit, although it is also very helpful in creating CLI applications on Viper.
Sparsehash	Sparsehash Package (formerly Google Sparsehash)
Zlib	zlib is a software library used for data compression.

Test Modules

Library	Description
Test-Modules	Access to modules currently in development

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