Modules - Revision history

Pysdlb at 10:07, 27 November 2025

2025-11-27T10:07:45Z

Pysdlb at 09:55, 27 November 2025

2025-11-27T09:55:09Z

Pysdlb at 09:50, 27 November 2025

2025-11-27T09:50:24Z

Pysdlb at 09:42, 21 November 2023

2023-11-21T09:42:26Z

Pysdlb at 09:29, 21 November 2023

2023-11-21T09:29:35Z

Pysdlb: /* Applications */

2023-09-26T15:11:43Z

‎Applications

Pysdlb at 10:16, 17 August 2023

2023-08-17T10:16:19Z

Pysdlb: /* Applications */

2023-05-04T08:25:03Z

‎Applications

Chris.collins at 08:27, 20 April 2023

2023-04-20T08:27:29Z

Pysdlb at 16:18, 1 March 2023

2023-03-01T16:18:17Z

@@ Line 158: / Line 158: @@
 |-
 |[[applications/Perl|Perl]]
-| Perl is a flexible high-level, general-purpose, interpreted, dynamic programming language with a large number of libraries.
+| Perl is a general-purpose, interpreted, dynamic programming language with a large number of libraries.
 |-
 |[[applications/Prinseq-lite|Prinseq-lite]]
@@ Line 164: / Line 164: @@
 |-
 |[[applications/Python|Python]]
-| Python is a family of high-level, general-purpose, interpreted, dynamic programming languages and includes IPython.
+| Python is an interpreted, dynamic programming language with a massive set of libraries covering just about every area.
 |-
 |[[applications/Qiime2|Qiime2]]
@@ Line 206: / Line 206: @@
 |-
 | [[applications/Transrate|Transrate]]
-| Transrate is software for de-novo transcriptome assembly quality analysis
+| Transrate is software for de novo transcriptome assembly quality analysis
 |-
 | [[applications/Trinityrnaseq|Trinityrnaseq]]
@@ Line 265: / Line 265: @@
 |-
 | [[programming/OpenACC|OpenACC]]
-|  OpenACC is an implementation of multithreading, a method of parallelizing whereby a master thread (a series of instructions executed consecutively) forks a specified number of slave threads and the system divides a task among them. This is similar to OpenMP but has had CPU/GPU support from the beginning. There is language support from C/C++ and Fortran.
+|  OpenACC is an implementation of multithreading, a method of parallelising whereby a master thread (a series of instructions executed consecutively) forks a specified number of slave threads and the system divides a task among them. This is similar to OpenMP but has had CPU/GPU support from the beginning. There is language support from C/C++ and Fortran.
 |-
 | [[applications/Openblas|Openblas]]
-| OpenBLAS is an optimized BLAS library (based on ''GotoBLAS2'' 1.13 BSD version).
+| OpenBLAS is an optimised BLAS library (based on ''GotoBLAS2'' 1.13 BSD version).
 |-
 | [[programming/OpenCL|OpenCL]]

@@ Line 291: / Line 291: @@
 ==Test Modules==
-The test-modules module does not provide access to a specific application; instead, it provides access to a further set of modules that are in a development state.
+The test-modules module does not provide access to a specific application; instead, it provides access to a set of additional modules in development.
 These modules should not be relied on to be stable modules and are subject to change as software installations are tuned.
-If you request an application to be installed, we may ask you to test the module while it is in the test modules area before we make it widely available as a standard module.
+If you request an application to be installed, we may ask you to test the module in the test modules area before we make it widely available as a standard module.
 <pre style="background-color:#000000; color: white; font-family: monospace, sans-serif;">

@@ Line 1: / Line 1: @@
 [[FurtherTopics/FurtherTopics #Modules| Back to Further Topics]]
 ==Applications==
-The following is a list of core applications installed on Viper, with links to further information on using those applications on Viper. If you are looking for an application that requires a special license visit: [[Applications/Special Licenses| Applications requiring special licenses]].
+The following is a list of core applications installed on Viper, with links to further information on using those applications on Viper. If you are looking for an application that requires a special license, visit: [[Applications/Special Licenses| Applications requiring special licenses]].
-If you are looking for how to use a module use the [[Quickstart/Using Modules| Quickstart]].
+If you are looking for how to use a module, use the [[Quickstart/Using Modules| Quickstart]].
 An up-to-date list of all modules available on Viper can be found at [https://hpc.hull.ac.uk/upload/module.html Module List]
@@ Line 44: / Line 44: @@
 |-
 | [[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.
+| 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, optimised 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.
+| CMake is cross-platform, free and open-source software for managing the build process of software using a compiler-independent method.
 |-
 | [[applications/Crop|Crop]]
@@ Line 65: / Line 65: @@
 |-
 | [[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 visualisation program used to display the output of FDS and CFAST simulations.
 |-
 | [[Applications/ffmpeg|ffmpeg]]
@@ Line 71: / Line 71: @@
 |-
 | Flex
-| Flex (Fast lexical analyser), Flex is a tool for generating scanners: programs that recognize lexical patterns in text.
+| Flex (Fast lexical analyser), Flex is a tool for generating scanners: programs that recognise lexical patterns in text.
 |-
 | [[Applications/Fiji|Fiji]]
@@ Line 113: / Line 113: @@
 |-
 | [[Applications/modflow|Modflow]]
-|  Program and framework developed to provide a platform for supporting multiple models and multiple types of models within the same simulation.
+|  Program and framework were developed to provide a platform for supporting multiple models and multiple types of models within the same simulation.
 |-
 | [[applications/Mpich|Mpich]]
@@ Line 274: / Line 274: @@
 |-
 | [[programming/OpenMP|OpenMP]]
-|  OpenMP is an implementation of multithreading, a method of parallelizing whereby a master thread (a series of instructions executed consecutively) forks a specified number of slave threads and the system divides a task among them. There is language support from C/C++ and Fortran.
+|  OpenMP is an implementation of multithreading, a method of parallelising whereby a master thread (a series of instructions executed consecutively) forks a specified number of slave threads and the system divides a task among them. There is language support from C/C++ and Fortran.
 |-
 | [[applications/OpenMPI|OpenMPI]]
@@ Line 280: / Line 280: @@
 |-
 | [[applications/Parmetis|Parmetis]]
-|  ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, and meshes, and for computing fill-reducing orderings of sparse matrices.
+|  ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs and meshes, and for computing fill-reducing orderings of sparse matrices.
 |-
 |[[applications/Qt|Qt]]
@@ Line 291: / Line 291: @@
 ==Test Modules==
-The test-modules module does not provide access to a specific application, instead, it provides access to a further set of modules that are in a development state.
+The test-modules module does not provide access to a specific application; instead, it provides access to a further set of modules that are in a development state.
 These modules should not be relied on to be stable modules and are subject to change as software installations are tuned.

@@ Line 68: / Line 68: @@
 |-
 | [[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 be grabbed from a live audio/video source.
 |-
 | Flex

@@ Line 223: / Line 223: @@
 ==Libraries==
-Library software listed here refers to those listed in the libs section of typing module avail.
+Library software listed here refers to those listed in the libs section of the typing module avail.
 {| class="wikitable mw-collapsible"
 | style="width:25%; background: #f5a091;" | <Strong>Library</Strong>
@@ Line 295: / Line 295: @@
 These modules should not be relied on to be stable modules and are subject to change as software installations are tuned.
-If you request an application to be installed, we may ask you to test the module while it is in the test-modules area before we make it widely available as a standard module.
+If you request an application to be installed, we may ask you to test the module while it is in the test modules area before we make it widely available as a standard module.
 <pre style="background-color:#000000; color: white; font-family: monospace, sans-serif;">

@@ Line 195: / Line 195: @@
 |  [[applications/STAR|STAR]]
 |  Ultrafast universal RNA-seq aligner.
 |-
 | [[applications/Tophat|Tophat]]

@@ Line 119: / Line 119: @@
 |-
 | [[applications/Miniconda|Miniconda]]
-| Miniconda is a lite version of anaconda used for creating virtual environments.
+| Miniconda is a lite version of Anaconda used for creating virtual environments.
 |-
 | [[applications/Minimap2|Minimap2]]
@@ Line 137: / Line 137: @@
 |-
 | [[applications/Netcdf-c|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.
+|  NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support creating, accessing, and sharing array-oriented scientific data.
 |-
 | [[applications/Nwchem|Nwchem]]
@@ Line 143: / Line 143: @@
 |-
 | [[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.
+| The OBITools package is a set of programs specifically designed for analysing NGS data in a DNA meta-barcoding context, considering taxonomic information.
 |-
 | [[applications/Openfoam|Openfoam]]
@@ Line 277: / Line 277: @@
 |-
 | [[applications/Parmetis|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.
+|  ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, and meshes, and for computing fill-reducing orderings of sparse matrices.
 |-
 |[[applications/Qt|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.
+| Qt is a cross-platform framework, usually used as a graphical toolkit, although it is also very helpful in creating CLI applications on Viper.
 |-
 | [[applications/Zlib|Zlib]]

@@ Line 109: / Line 109: @@
 | [[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]]