Applications - Revision history

Pysdlb at 16:26, 10 November 2022

2022-11-10T16:26:42Z

Pysdlb at 12:25, 3 November 2022

2022-11-03T12:25:04Z

Pysdlb at 09:23, 23 August 2022

2022-08-23T09:23:05Z

Pysdlb at 15:41, 10 May 2021

2021-05-10T15:41:39Z

Pysdlb at 07:48, 12 August 2020

2020-08-12T07:48:34Z

Pysdlb at 09:18, 6 August 2020

2020-08-06T09:18:09Z

Pysdlb at 14:30, 27 June 2019

2019-06-27T14:30:20Z

Pysdlb at 14:29, 27 June 2019

2019-06-27T14:29:33Z

Pysdlb at 16:05, 17 June 2019

2019-06-17T16:05:39Z

Pysdlb at 15:50, 17 June 2019

2019-06-17T15:50:28Z

@@ Line 176: / Line 176: @@
 |[[applications/Perl|Perl]]
 | Perl is a flexible high-level, general-purpose, interpreted, dynamic programming language with a large number of libraries.
 |-
 |[[applications/Prinseq-lite|Prinseq-lite]]

@@ Line 31: / Line 31: @@
 |-
 | [[applications/Blender|Blender]]
-|  Blender is the free and open-source 3D creation suite. It supports the entirety of the 3D pipeline—modelling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation.
+|  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/Bowtie1|Bowtie1]]
@@ Line 67: / Line 67: @@
 |-
 | [[Applications/ffmpeg|ffmpeg]]
-| ffmpeg is a very fast video and audio converter that can also grab from a live audio/video source.
+| FFmpeg is a very fast video and audio converter that can also grab from a live audio/video source.
 |-
 | [[Applications/Flex|Flex]]
@@ Line 79: / Line 79: @@
 |-
 | [[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]]
@@ Line 88: / Line 88: @@
 |-
 |[[applications/Java|Java]]
-| Java is a general-purpose computer programming language that is concurrent, class-based, object-oriented.
+| Java is a general-purpose computer programming language that is concurrent, class-based, and object-oriented.
 |-
 |[[applications/Hpl|HPL]]
@@ Line 118: / Line 115: @@
 |-
 | [[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 to create genome databases.
+|  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
@@ Line 130: / Line 127: @@
 |-
 | [[applications/Mpich|Mpich]]
-| MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard.
+| MPICH is a high-performance and widely portable implementation of the Message Passing Interface (MPI) standard.
 |-
 | [[applications/Miniconda|Miniconda]]
@@ Line 169: / Line 166: @@
 |-
 |[[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]]
@@ Line 178: / Line 175: @@
 |-
 |[[applications/Perl|Perl]]
-| Perl is a flexible high-level, general-purpose, interpreted, dynamic programming languages with a large number of libraries.
+| Perl is a flexible high-level, general-purpose, interpreted, dynamic programming language with a large number of libraries.
 |-
 |[[applications/Pgi|PGI]]
-| PGI Community Edition is a no-cost license to a recent release of the PGI Fortran, C and C++ compilers and tools for multi-core CPUs and NVIDIA GPUs, including all OpenACC, OpenMP and CUDA Fortran .
+| PGI Community Edition is a no-cost license to a recent release of the PGI Fortran, C and C++ compilers and tools for multi-core CPUs and NVIDIA GPUs, including all OpenACC, OpenMP and CUDA Fortran.
 |-
 |[[applications/Prinseq-lite|Prinseq-lite]]
@@ Line 190: / Line 187: @@
 |-
 |[[applications/Qiime2|Qiime2]]
-| QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open-source, and community developed.
+| QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open-source, and community-developed.
 |-
 |[[applications/QuantumPackage2|Quantum Package Shell]]
@@ Line 196: / Line 193: @@
 |-
 |[[applications/R|R]]
-| R is an open source programming language and software environment for statistical computing and graphics.
+| R is an open-source programming language and software environment for statistical computing and graphics.
 |-
 |[[applications/RaXML|RaXML]]
@@ Line 205: / Line 202: @@
 |-
 |[[applications/RStudio|RStudio]]
-| RStudio provides popular open source and enterprise-ready professional software for the R statistical computing environment.
+| RStudio provides popular open-source and enterprise-ready professional software for the R statistical computing environment.
 |-
 | [[applications/Samtools|Samtools]]

@@ Line 41: / Line 41: @@
 | [[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/Cmake|CMake]]

@@ Line 31: / Line 31: @@
 |-
 | [[applications/Blender|Blender]]
-|  Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline—modelling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation.
+|  Blender is the free and open-source 3D creation suite. It supports the entirety of the 3D pipeline—modelling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation.
 |-
 | [[applications/Bowtie1|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.
+| 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]]
@@ Line 46: / Line 46: @@
 |-
 | [[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]]
@@ Line 55: / Line 55: @@
 |-
 | [[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]]
@@ Line 67: / Line 67: @@
 |-
 | [[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]]
@@ Line 91: / Line 91: @@
 |-
 |[[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 freely available implementation of the High Performance Computing Linpack Benchmark.
+| 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]]
@@ Line 106: / Line 106: @@
 |-
 | [[applications/Likwid|Libwid]]
-|  Likwid is a simple to install and use toolsuite of command line applications for performance oriented programmers.
+|  Likwid is a simple to install and use tool suite of command-line applications for performance-oriented programmers.
 |-
 |[[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).
+|  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]]
@@ Line 124: / Line 124: @@
 |-
 | [[Applications/Mercurial|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.
+|  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]]
@@ Line 145: / Line 145: @@
 |-
 | [[applications/Mvapich2|Mvapich2]]
-| MVAPICH2 is a BSD-licensed implementation of the MPI standard  with support for Intel Omni-Path is a high performance.
+| 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]]
@@ Line 154: / Line 154: @@
 |-
 | [[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]]
@@ Line 166: / Line 166: @@
 |-
 |[[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 specific emphasis on 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.
+| 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]]
@@ Line 175: / Line 175: @@
 |-
 |[[applications/Perl|Perl]]
-| Perl is a flexible high-level, general-purpose, interpreted, dynamic programming languages with a large amount of libraries.
+| Perl is a flexible high-level, general-purpose, interpreted, dynamic programming languages with a large number of libraries.
 |-
 |[[applications/Pgi|PGI]]
-| PGI Community Edition is a no-cost license to a recent release of the PGI Fortran, C and C++ compilers and tools for multi core CPUs and NVIDIA GPUs, including all OpenACC, OpenMP and CUDA Fortran .
+| PGI Community Edition is a no-cost license to a recent release of the PGI Fortran, C and C++ compilers and tools for multi-core CPUs and NVIDIA GPUs, including all OpenACC, OpenMP and CUDA Fortran .
 |-
 |[[applications/Prinseq-lite|Prinseq-lite]]
-| PRINSEQ can be used to filter, reformat, or trim genomic and meta-genomic sequence data.
+| PRINSEQ can be used to filter, reformat, or trim genomic and metagenomic sequence data.
 |-
 |[[applications/Python|Python]]
@@ Line 187: / Line 187: @@
 |-
 |[[applications/Qiime2|Qiime2]]
-| QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.
+| QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open-source, and community developed.
 |-
 |[[applications/QuantumPackage2|Quantum Package Shell]]
@@ Line 196: / Line 196: @@
 |-
 |[[applications/RaXML|RaXML]]
-| RaXML is an open source tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.
+| RaXML is an open-source tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies.
 |-
 |[[applications/Readline|Readline]]
@@ Line 214: / Line 214: @@
 |-
 | [[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]]
@@ Line 244: / Line 244: @@
 |-
 |  [[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.
+|  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.
 |-
 |}

@@ Line 41: / Line 41: @@
 | [[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/Cmake|CMake]]

@@ Line 66: / Line 66: @@
 | 3D/2D Maxwell's solver for nanophotonic devices
 |-
-| [[Applications/ffmpeg|Ffmpeg]]
+| [[Applications/ffmpeg|ffmpeg]]
 | ffmpeg is a very fast video and audio converter that can also grab from a live audio/video source.
 |-
@@ Line 75: / Line 75: @@
 | 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.
 |-

@@ Line 19: / Line 19: @@
 |-
 | [[applications/Anaconda|Anaconda]]
-| Anaconda is the leading open data science platform powered by Python.
+| Anaconda is the leading open data science platform powered by Python. (See also [[Applications/Miniconda|Miniconda]]).
 |-
 | [[applications/Ansys|Ansys]]

@@ Line 132: / Line 132: @@
 | MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard.
 |-
 | [[applications/Minimap2|Minimap2]]
 | Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database.

@@ Line 143: / Line 143: @@
 | [[Applications/MrBayes|MrBayes]]
 | MrBayes: Bayesian Inference of Phylogeny
 |-
 | [[applications/Mvapich2|Mvapich2]]
@@ Line 182: / Line 179: @@
 |[[applications/Pgi|PGI]]
 | PGI Community Edition is a no-cost license to a recent release of the PGI Fortran, C and C++ compilers and tools for multi core CPUs and NVIDIA GPUs, including all OpenACC, OpenMP and CUDA Fortran .
 |-
 |[[applications/Prinseq-lite|Prinseq-lite]]
@@ Line 206: / Line 200: @@
 |[[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]]
@@ Line 215: / Line 206: @@
 | [[applications/Samtools|Samtools]]
 |  Tools (written in C using htslib) for manipulating next-generation sequencing data
 |-
 | [[applications/Savu|Savu]]

@@ Line 156: / Line 156: @@
 | 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]]
 | NWChem provides computational chemistry tools  and particularly large scientific computational chemistry problems.
@@ Line 181: / Line 175: @@
 |-
 |[[applications/Paraview|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.
+| 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]]
@@ Line 187: / Line 181: @@
 |-
 |[[applications/Pgi|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 .
+| PGI Community Edition is a no-cost license to a recent release of the PGI Fortran, C and C++ compilers and tools for multi core CPUs and NVIDIA GPUs, including all OpenACC, OpenMP and CUDA Fortran .
 |-
 |[[applications/Planatus|Planatus]]
@@ Line 193: / Line 187: @@
 |-
 |[[applications/Prinseq-lite|Prinseq-lite]]
-| PRINSEQ can be used to filter, reformat, or trim genomic and metagenomic sequence data.
+| PRINSEQ can be used to filter, reformat, or trim genomic and meta-genomic sequence data.
 |-
 |[[applications/Python|Python]]
@@ Line 230: / Line 224: @@
 | [[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]]
@@ Line 250: / Line 241: @@
 |-
 | [[applications/transabyss|Transabyss]]
-| Software pipeline for analyzing ABySS-assembled transcriptome contigs
+| Software pipeline for analysing ABySS-assembled transcriptome contigs
 |-
 | [[applications/Transrate|Transrate]]
@@ Line 262: / Line 253: @@
 |-
 |  [[applications/Voxfe|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.
+| 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]]