Difference between revisions of "Applications"
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| Flex (Fast lexical analyser), Flex is a tool for generating scanners: programs which recognize lexical patterns in text. | | Flex (Fast lexical analyser), Flex is a tool for generating scanners: programs which recognize lexical patterns in text. | ||
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| − | | [[applications/ | + | | [[applications/Gcc|Gcc]] |
| − | | | + | | gcc (GNU Compiler Collection) is a collection of compilers consisting of C, C++, Fortran and more. |
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| [[applications/Gnuplot|GNUplot]] | | [[applications/Gnuplot|GNUplot]] | ||
Revision as of 09:42, 11 April 2017
Application Support
Click on the links below for support on the individual packages below:
| 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 |
| Boost | C++ Standard Library. Boost libraries are intended to be widely useful, and usable across a broad spectrum of applications. |
| 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. |
| 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. |
| 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. |
| Java | Java is a general-purpose computer programming language that is concurrent, class-based, object-oriented. |
| 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. |
| 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 |
| Libpng | The reference library for use in applications that read, create, and manipulate PNG (Portable Network Graphics) raster image files. |
| LS-DYNA | General-purpose finite element program capable of simulating complex real world problems. |
| 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. |
| 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. |
| 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. |
| 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 family of high-level, general-purpose, interpreted, dynamic programming languages. |
| Planatus | Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences of highly heterozygous diploids from massively parallel shotgun sequencing data. |
| 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. |
| 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. |
| 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-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. |
| Utilities | General utilities module including zip, wget and git utilities. |
| 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. |
| Zlib | zlib is a software library used for data compression. |
| Test-Modules | Access to modules currently in development |
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