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Difference between revisions of "Applications"

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== Application Support ==
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==Application Support==
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* Applications listed here refer to those list in the '''apps''' section of typing  ''[[General/Modules|module avail]]''..
 +
* Jump to [[Programming|Development]], [[Libraries|Libraries]], [[Libraries#Test Modules|Test Modules]].
 +
 
 +
 
 +
Click on the links below for support on the individual applications:
  
−
Click on the links below for support on the individual packages below:
 
  
 
{| class="wikitable"
 
{| class="wikitable"
−
| style="width:25%" | <Strong>Package</Strong>
+
| style="width:25%; background: #cccccc;" | <Strong>Package</Strong>
−
| style="width:75%" | <Strong>Description</Strong>
+
| style="width:75%; background: #cccccc;" | <Strong>Description</Strong>
 +
|-
 +
| [[applications/ABySS|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
 +
|-
 +
| [[applications/Anaconda|Anaconda]]
 +
| Anaconda is the leading open data science platform powered by Python. (See also [[Applications/Miniconda|Miniconda]]).
 
|-
 
|-
 
| [[applications/Ansys|Ansys]]
 
| [[applications/Ansys|Ansys]]
Line 13: Line 27:
 
| Avizo data visualisation and analysis tool
 
| Avizo data visualisation and analysis tool
 
|-
 
|-
−
| [[applications/Autotools|Autotools]]
+
| [[applications/BayesTraits|BayesTraits]]
−
| GNU Autotools, a suite of programming tools designed to assist in making source code packages
+
| 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.
 +
|-
 +
| [[applications/Blender|Blender]]
 +
|  Blender is a free and open-source 3D creation suite. It supports the entirety of the 3D pipeline—modelling, rigging, animation, simulation, rendering, compositing and motion tracking, and even video editing and game creation.
 
|-
 
|-
−
| [[applications/COMSOL|COMSOL]]
+
| [[applications/Bowtie1|Bowtie1]]
−
| COMSOL Multiphysics is a general-purpose software platform, based on advanced numerical methods, for modeling and simulating physics-based problems
+
| 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.
 +
|-
 +
| [[applications/Bowtie2|Bowtie2]]
 +
| Bowtie 2 is more suited to finding longer, gapped alignments in comparison with the original Bowtie1 method.
 +
|-
 +
| [[applications/Bridger|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. 
 +
|-
 +
| [[applications/Centrifuge|Centrifuge]]
 +
| Centrifuge is a novel microbial classification engine that enables rapid, accurate and sensitive labelling of reads and quantification of species on desktop computers. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem.
 +
|-
 +
| [[applications/Cmake|CMake]]
 +
| CMake is cross-platform free and open-source software for managing the build process of software using a compiler-independent method.
 
|-
 
|-
 
| [[applications/CP2K|CP2K]]
 
| [[applications/CP2K|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.
+
| 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.
 +
|-
 +
| [[applications/Cuda|CUDA]]
 +
| CUDA is NVIDIA’s parallel computing architecture that enables dramatic increases in computing performance by harnessing the power of the GPU nodes.
 +
|-
 +
| [[applications/Cufflinks|Cufflinks]]
 +
| Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
 
|-
 
|-
 
| [[applications/Delft3D|Delft3D]]
 
| [[applications/Delft3D|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.
+
| Delft3D is a world-leading 3D modelling suite to investigate hydrodynamics, sediment transport and morphology and water quality for fluvial, estuarine and coastal environments.
 
|-  
 
|-  
 
| [[applications/FDS-SMV|FDS-SMV]]
 
| [[applications/FDS-SMV|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.
+
| 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.
 +
|-
 +
| [[applications/FDTD|FDTD]]
 +
| 3D/2D Maxwell's solver for nanophotonic devices
 +
|-
 +
| [[Applications/ffmpeg|ffmpeg]]
 +
| FFmpeg is a very fast video and audio converter that can also grab from a live audio/video source.
 
|-  
 
|-  
 
| [[Applications/Flex|Flex]]
 
| [[Applications/Flex|Flex]]
−
| 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 that recognize lexical patterns in text.
 +
|-
 +
| [[Applications/Fiji|Fiji]]
 +
| Fiji Is Just ImageJ—a "batteries-included" distribution of ImageJ which includes many useful plugins contributed by the community.  
 
|-  
 
|-  
−
| [[applications/GCC|GCC]]
+
| [[applications/Gcc|gcc]]
−
| GCC (GNU Compiler Collection) is a collection of compilers consisting of C, C++, Fortran and more.
+
| gcc (GNU Compiler Collection) is a collection of compilers consisting of C, C++, Fortran and more.
 
|-  
 
|-  
 
| [[applications/Gnuplot|GNUplot]]
 
| [[applications/Gnuplot|GNUplot]]
−
| Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms.
+
| Gnuplot is a portable command-line-driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms.
 
|-  
 
|-  
 +
| [[applications/Grace|Grace]]
 +
| Grace is a WYSIWYG 2D plotting tool for the X Window System and M*tif. Grace is a descendant of ACE/gr, also known as Xmgr.
 +
|-
 +
| [[applications/guppy|Guppy]]
 +
| Local accelerated basecalling for Nanopore data.
 +
|-
 +
|[[applications/Java|Java]]
 +
| Java is a general-purpose computer programming language that is concurrent, class-based, and object-oriented.
 +
|-
 +
|[[applications/Hpl|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 the freely available implementation of the High-Performance Computing Linpack Benchmark.
 +
|-
 +
|[[applications/HyPhy|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.
 +
|-
 
|[[applications/IDL|IDL]]
 
|[[applications/IDL|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.
 
|  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.
 
|-
 
|-
−
|[[applications/Libgd|Libgd]]
+
|[[applications/Intel|Intel Parallel Studio]]
−
|  The module LibGD is an open source code library for the dynamic creation of images.
+
|  Intel Parallel Studio is a software development product that facilitates native code development on Viper in C, C++ and Fortran for parallel computing.  
 
|-
 
|-
−
|[[applications/Libjpeg-turbo|Libjpeg-turbo]]
+
|[[applications/iqtree|IQtree]]
−
|  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
+
|  stochastic algorithm to reconstruct phylogenetic trees using maximum likelihood.
 
|-
 
|-
−
|[[applications/Libpng|Libpng]]
+
| [[applications/Likwid|Libwid]]
−
|  The reference library for use in applications that read, create, and manipulate PNG (Portable Network Graphics) raster image files.  
+
|  Likwid is a simple to install and use tool suite of command-line applications for performance-oriented programmers.
 
|-
 
|-
 
|[[applications/LS-DYNA|LS-DYNA]]
 
|[[applications/LS-DYNA|LS-DYNA]]
−
|  General-purpose finite element program capable of simulating complex real world problems.
+
|  General-purpose finite element program capable of simulating complex real-world problems.
 +
|-
 +
| [[Applications/Mafft|Mafft]]
 +
|  MAFFT is a multiple sequence alignment program for Unix-like operating systems.  It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences).
 +
|-
 +
| [[Applications/Maker|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 create genome databases.
 +
|-
 +
| Mathematica
 +
|  Symbolic mathematical computation program.
 
|-
 
|-
 
| [[Applications/Matlab|Matlab]]
 
| [[Applications/Matlab|Matlab]]
 
|  Numerical Computing Environment.
 
|  Numerical Computing Environment.
 
|-
 
|-
 +
| [[Applications/Mercurial|Mercurial]]
 +
|  Mercurial is truly distributed, giving each developer a local copy of the entire development history. This way it works independently of network access or a central server. Committing, branching and merging are fast and cheap.
 +
|-
 +
| [[applications/Mpich|Mpich]]
 +
| MPICH is a high-performance and widely portable implementation of the Message Passing Interface (MPI) standard.
 +
|-
 +
| [[applications/Miniconda|Miniconda]]
 +
| Miniconda is a lite version of anaconda used for creating virtual environments.
 +
|-
 +
| [[applications/Minimap2|Minimap2]]
 +
| Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database.
 +
|-
 +
| [[applications/MIKE|MIKE]]
 +
| MIKE coastal modelling tool (restricted license)
 +
|-
 
| [[Applications/Mono|Mono]]
 
| [[Applications/Mono|Mono]]
 
|  .NET Framework-compatible set of tools including, among others, a C# compiler and a Common Language Runtime.
 
|  .NET Framework-compatible set of tools including, among others, a C# compiler and a Common Language Runtime.
Line 61: Line 144:
 
| MrBayes: Bayesian Inference of Phylogeny  
 
| MrBayes: Bayesian Inference of Phylogeny  
 
|-
 
|-
−
| [[applications/ngspice|NgSpice]]
+
| [[applications/Mvapich2|Mvapich2]]
−
| Ngspice is a mixed-level/mixed-signal circuit simulator. Its code is based on three open source software packages: Spice3f5, Cider1b1 and Xspice.
+
| MVAPICH2 is a BSD-licensed implementation of the MPI standard with support for Intel Omni-Path is a high performance.
 
|-  
 
|-  
 +
| [[Applications/Ncbi-blast|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.
 +
|-
 +
| [[Applications/Ncurses|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.
 +
|-
 
| [[applications/Nwchem|Nwchem]]
 
| [[applications/Nwchem|Nwchem]]
−
| NWChem provides computational chemistry tools and particularly large scientific computational chemistry problems.
+
| NWChem provides computational chemistry tools and particularly large scientific computational chemistry problems.
 +
|-
 +
| [[applications/Obitools|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.
 +
|-
 +
| [[applications/Openfoam|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.
 +
|-
 +
| [[applications/OpenMPI|OpenMPI]]
 +
| Open MPI is a Message Passing Interface (MPI) library used for communicating between HPC nodes.
 
|-  
 
|-  
 
|[[applications/Orca|Orca]]
 
|[[applications/Orca|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.
+
| ORCA is a flexible, efficient and easy-to-use general-purpose tool for quantum chemistry with a specific emphasis on the spectroscopic properties of open-shell molecules.
 +
|-
 +
|[[applications/Packmol|Packmol]]
 +
| PACKMOL creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The packing guarantees that short-range repulsive interactions do not disrupt the simulations.
 +
|-
 +
|[[applications/Paraview|Paraview]]
 +
| ParaView is an open-source, multi-platform data analysis and visualisation application. ParaView users can quickly build visualisations to analyse their data using qualitative and quantitative techniques.
 +
|-
 +
|[[applications/Perl|Perl]]
 +
| Perl is a flexible high-level, general-purpose, interpreted, dynamic programming language with a large number of libraries.
 
|-  
 
|-  
−
|[[applications/Perl|Perl]]
+
|[[applications/Prinseq-lite|Prinseq-lite]]
−
| Perl is a family of high-level, general-purpose, interpreted, dynamic programming languages.
+
| PRINSEQ can be used to filter, reformat, or trim genomic and metagenomic sequence data.
 +
|-
 +
|[[applications/Python|Python]]
 +
| Python is a family of high-level, general-purpose, interpreted, dynamic programming languages and includes IPython.
 +
|-
 +
|[[applications/Qiime2|Qiime2]]
 +
| QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open-source, and community-developed.
 +
|-
 +
|[[applications/QuantumPackage2|Quantum Package Shell]]
 +
| Quantum Package is an open-source programming environment for quantum chemistry specially designed for wave function methods. Its main goal is the development of determinant-driven selected configuration interaction (sCI) methods and multi-reference second-order perturbation theory (PT2).
 
|-  
 
|-  
−
| [[applications/SAS|SAS]]
+
|[[applications/R|R]]
−
|  Statistical Analysis System.
+
| R is an open-source programming language and software environment for statistical computing and graphics.
 +
|-
 +
|[[applications/RaXML|RaXML]]
 +
| RaXML is an open-source tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.
 +
|-
 +
|[[applications/Readline|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.
 +
|-
 +
|[[applications/RStudio|RStudio]]
 +
| RStudio provides popular open-source and enterprise-ready professional software for the R statistical computing environment.
 +
|-
 +
| [[applications/Samtools|Samtools]]
 +
|  Tools (written in C using htslib) for manipulating next-generation sequencing data
 +
|-
 +
| [[applications/Savu|Savu]]
 +
|  Python package to assist with the processing and reconstruction of parallel-beam tomography data.
 +
|-
 +
| [[applications/Scalapack|Scalapack]]
 +
|  The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers
 
|-
 
|-
 
| [[applications/ssw|SSW]]
 
| [[applications/ssw|SSW]]
−
|  Integrated software libraries, data bases, and system utilities which provide a common programming and data analysis environment for Solar Physics
+
|  Integrated software libraries, databases, and system utilities which provide common programming and data analysis environment for Solar Physics
 +
|-
 +
|  [[applications/STAR|STAR]]
 +
|  Ultrafast universal RNA-seq aligner.
 
|-
 
|-
 
|  [[applications/Star-ccm+|Star-ccm+]]
 
|  [[applications/Star-ccm+|Star-ccm+]]
Line 85: Line 222:
 
| Stata is a commercial statistical package, which provides a complete solution for data analysis, data management, and graphics.
 
| Stata is a commercial statistical package, which provides a complete solution for data analysis, data management, and graphics.
 
|-  
 
|-  
 +
| [[applications/Tophat|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.
 +
|-
 +
| [[applications/transabyss|Transabyss]]
 +
| Software pipeline for analysing ABySS-assembled transcriptome contigs
 +
|-
 +
| [[applications/Transrate|Transrate]]
 +
| Transrate is software for de-novo transcriptome assembly quality analysis
 +
|-
 +
| [[applications/Trinityrnaseq|Trinityrnaseq]]
 +
| Trinity assembles transcript sequences from Illumina RNA-Seq data.
 +
|-
 
|  [[applications/Utilities|Utilities]]
 
|  [[applications/Utilities|Utilities]]
 
|  General utilities module including zip, wget and git utilities.
 
|  General utilities module including zip, wget and git utilities.
 
|-
 
|-
−
|  [[applications/test-modules|Test-Modules]]
+
|  [[applications/Voxfe|Voxfe]]
−
|  Access to modules currently in development
+
| VOX-FE is voxel-based FE software with a sophisticated graphical user interface that allows the complex loading regimes that are inevitably present in bio-mechanical analyses to be readily applied to the model geometry, and the resultant 3D stress and strain patterns to be visualised easily.
 +
|-
 +
|  [[applications/Yt|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.
 +
|-
 +
|}
 +
 
 +
{|
 +
|style="width:5%; border-width: 0" | [[File:icon_up.png]]
 +
|style="width:95%; border-width: 0" |  [[#Application Support|Top]]
 
|-
 
|-
 
|}
 
|}
 +
 +
 +
 +
* [[Main_Page|Home]]
 +
* [[Applications|Application support]]
 +
* [[Libraries|Library support]]
 +
* [[Programming|Development support]]
 +
* [[General|General]]

Latest revision as of 16:26, 10 November 2022

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. (See also Miniconda).
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.
Blender Blender is a free and open-source 3D creation suite. It supports the entirety of the 3D pipeline—modelling, rigging, animation, simulation, rendering, compositing and motion tracking, and even video editing and game creation.
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.
Centrifuge Centrifuge is a novel microbial classification engine that enables rapid, accurate and sensitive labelling of reads and quantification of species on desktop computers. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem.
CMake CMake is cross-platform free and open-source software for managing the build process of software using a compiler-independent method.
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.
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 modelling 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.
FDTD 3D/2D Maxwell's solver for nanophotonic devices
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 that recognize lexical patterns in text.
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.
Grace Grace is a WYSIWYG 2D plotting tool for the X Window System and M*tif. Grace is a descendant of ACE/gr, also known as Xmgr.
Guppy Local accelerated basecalling for Nanopore data.
Java Java is a general-purpose computer programming language that is concurrent, class-based, and 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 the 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.
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.
IQtree stochastic algorithm to reconstruct phylogenetic trees using maximum likelihood.
Libwid Likwid is a simple to install and use tool suite of command-line applications for performance-oriented programmers.
LS-DYNA General-purpose finite element program capable of simulating complex real-world problems.
Mafft MAFFT is a multiple sequence alignment program for Unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences).
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 create genome databases.
Mathematica Symbolic mathematical computation program.
Matlab Numerical Computing Environment.
Mercurial Mercurial is truly distributed, giving each developer a local copy of the entire development history. This way it works independently 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.
Miniconda Miniconda is a lite version of anaconda used for creating virtual environments.
Minimap2 Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database.
MIKE MIKE coastal modelling tool (restricted license)
Mono .NET Framework-compatible set of tools including, among others, a C# compiler and a Common Language Runtime.
MrBayes MrBayes: Bayesian Inference of Phylogeny
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.
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 a specific emphasis on the spectroscopic properties of open-shell molecules.
Packmol PACKMOL creates an initial point for molecular dynamics simulations by packing molecules in defined regions of space. The packing guarantees that short-range repulsive interactions do not disrupt the simulations.
Paraview ParaView is an open-source, multi-platform data analysis and visualisation application. ParaView users can quickly build visualisations to analyse their data using qualitative and quantitative techniques.
Perl Perl is a flexible high-level, general-purpose, interpreted, dynamic programming language with a large number of libraries.
Prinseq-lite PRINSEQ can be used to filter, reformat, or trim genomic and metagenomic sequence data.
Python Python is a family of high-level, general-purpose, interpreted, dynamic programming languages and includes IPython.
Qiime2 QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open-source, and community-developed.
Quantum Package Shell Quantum Package is an open-source programming environment for quantum chemistry specially designed for wave function methods. Its main goal is the development of determinant-driven selected configuration interaction (sCI) methods and multi-reference second-order perturbation theory (PT2).
R R is an open-source programming language and software environment for statistical computing and graphics.
RaXML RaXML is an open-source tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.
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.
RStudio RStudio provides popular open-source and enterprise-ready professional software for the R statistical computing environment.
Samtools Tools (written in C using htslib) for manipulating next-generation sequencing data
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
SSW Integrated software libraries, databases, and system utilities which provide 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 analysing 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 bio-mechanical analyses to be readily applied to the model geometry, and the resultant 3D stress and strain patterns to be visualised 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.
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