Web interfaces as systems (#1690)

* Add web interfaces as systems

* Define availability in front matter

* Replace spaces with dashes in link anchor

* Remove repeated 'Available on'

* Revert "Define availability in front matter"

This reverts commit 0aa5ecb.

* Reorder systems

* List web interfaces separately

Additionally, some refactoring

* Available in Puhti and Mahti web interfaces

* Update page and make it a SectionPage for 'Interactive apps'

* More apps for web interfaces

* Fix outdated information

* Documentation on web interface tags

* Fixed heading

Newline to end of file

* Revert "Available in Puhti and Mahti web interfaces"

This reverts commit 0054436.

* Partially revert "More apps for web interfaces"

This partially reverts commit a82140e.

* Adjust punctuation and whitespace for consistency

* Added interactive applications

* Alphabetization

* Remove accidental whitespace

* Note to instructions about pull request not updating

---------

Co-authored-by: Ari-Matti Saren <ari-matti.saren@csc.fi>

Author: joonas-somero

CONTRIBUTING.md

@@ -56,6 +56,7 @@ must use pull requests.
         - Please add a link to the rahtiapp-preview page `https://csc-guide-preview.rahtiapp.fi/origin/<your-branch-name>/rest-of-url/`) in the Pull Request description to help reviewer.
     - You can also add a label to your PR. For example, if your edit is minor (e.g. fixed link or typo), you can add the label "trivial change" to expedite the reviewing process.
     - Pull requests which do not meet the requirements will not be accepted. Note that you can keep committing to a pull request after it has been submitted.
+        - If your commits aren't showing up on the pull request, i.e., the pull request isn't updating when making new commits, try switching the base branch ('Edit' button, top-right) from `master` to something else and then back again.
     - Write meaningful pull request messages, so it is easier for reviewers to do their job.
     - Communicate! Use "WIP" (= Work In Progress) in your pull request title, if you don't wish the branch to be merged to master (i.e. you want to continue working with it).
  - Once your PR has been accepted, remove the temporary branch (if not deleted by an admin at merge)

FAQ.md

@@ -23,6 +23,7 @@ The [contributing guide](CONTRIBUTING.md) outlines the basic steps of starting c
   - [How do I add definitions to the glossary / display definitions as tooltips?](#how-do-i-add-definitions-to-the-glossary--display-definitions-as-tooltips)
   - [How do I use the announcement bar?](#how-do-i-use-the-announcement-bar)
   - [How do I add a license tag to an application page?](#how-do-I-add-a-license-tag-to-an-application-page)
+  - [How do I tag an application as available under a web interface?](#how-do-i-tag-an-application-as-available-under-a-web-interface)
   - [How do I make footnotes?](#how-do-i-make-footnotes)
   - [How do I improve search results?](#how-do-i-improve-search-results)
 
@@ -296,6 +297,38 @@ where `<license>` is one of the predefined license categories: `Academic`, `Free
 
 The application will then be included on the Applications by license page automatically.
 
+## How do I tag an application as available under a web interface?
+
+As with [adding a license tag](#how-do-I-add-a-license-tag-to-an-application-page), an application
+can be tagged as available in a particular web interface. The application will then be listed under
+that web interface on the _Applications by availability_ page. The tags for web interfaces that an
+application is available on are added under the `system` key in the front matter.
+
+```yaml
+---
+system:
+  - www-<system1>
+  - www-<system2>
+---
+```
+
+where `<system1>` or `<system2>` is one of the systems where a web interface is available, for
+example (prefixed with `www-`) `mahti` or `puhti`.
+
+As a temporary workaround, to prevent an application getting listed under a system for merely
+mentioning the system, edit the [skip_system.txt](scripts/skip_system.txt) file.
+
+```text
+Workaround:
+
+...
+
+SKIP_<system1> application.md
+SKIP_<system2> application.md
+```
+
+where `<system1>` and `<system2>` are as above.
+
 ## How do I add footnotes?
 
 Usage of the footnotes feature is described
@@ -314,4 +347,4 @@ search:
 ...
 ```
 Start with low values.  
-More information [here](https://squidfunk.github.io/mkdocs-material/setup/setting-up-site-search/#rank-up)
+More information [here](https://squidfunk.github.io/mkdocs-material/setup/setting-up-site-search/#rank-up)

docs/apps/accelerated-visualization.md

@@ -0,0 +1,29 @@
+---
+tags:
+  - Free
+system:
+  - www-puhti
+---
+
+# Accelerated visualization
+
+A selection of GPU accelerated visualization applications.
+
+
+## License
+
+Free
+
+
+## Available
+
+Accelerated visualization is available as an interactive application via the Puhti web interface.
+
+
+## More information
+
+More information on Accelerated visualization, interactive applications, and the web interfaces can be found under the [Computing section](../computing/index.md):
+
+  - [Accelerated visualization](../computing/webinterface/accelerated-visualization.md)
+  - [Interactive applications](../computing/webinterface/apps.md)
+  - [Web interfaces](../computing/webinterface/index.md)

docs/apps/by_discipline.md

@@ -3,26 +3,27 @@
 !!! Note
     In addition to technical support, CSC also provides expert consulting in questions related to sciences and methods. For more details, see our [science-specific support pages at research.csc.fi](https://research.csc.fi/sciences) or directly [contact our Service Desk](../support/contact.md).
 
+
 ## Biosciences
 
 * [BAMtools](bamtools.md) Tools for working with BAM formatted files
-* [BayeScan](bayescan.md) Tool for identifying candidate loci under natural selection based on allele frequencies in populations.
+* [BayeScan](bayescan.md) Tool for identifying candidate loci under natural selection based on allele frequencies in populations
 * [Bioconda](bioconda.md) Package manger for installing bioinformatics software
 * [BioPerl](bioperl.md) Perl environment with bioperl extension
 * [BioPython](biopython.md) Python environment with biopython and other bioinformatics related Python libraries
 * [BLAST](blast.md) Sequence similarity search tool for nucleotides and proteins
-* [Bowtie2](bowtie2.md) Short read aligner 
+* [Bowtie2](bowtie2.md) Short read aligner
 * [BRAKER](braker.md) Automatic genome annotator for eucaryots
 * [BWA](bwa.md) Short read aligner
 * [CD-hit](cd-hit.md) Sequence clustering and redundancy removal tool
 * [Chipster](https://chipster.csc.fi/) Easy-to-use analysis platform for RNA-seq, single cell RNA-seq and other NGS data
 * [Chipster_genomes](chipster_genomes.md) Tool to download aligner indexes used by Chipster to Puhti
 * [Cutadapt](cutadapt.md) Trimming high-throughput sequencing reads
 * [Diamond](diamond.md ) Sequence similarity search tool for proteins and nucloeotides
-* [Discovery Studio](discovery-studio.md) Protein modeling environment.
+* [Discovery Studio](discovery-studio.md) Protein modeling environment
 * [Edirect](edirect.md) Entrez direct - command line tool to search and retrieve data from NCBI
 * [EMBOSS](emboss.md) Toolkit for classical sequence analysis
-* [Exonerate](exonerate.md) A generic tool for pairwise sequence comparison.
+* [Exonerate](exonerate.md) A generic tool for pairwise sequence comparison
 * [FastQC](fastqc.md) Quality control tool for high throughput sequence data
 * [Freebayes](freebayes.md) Genetic variant detector
 * [GOLD](gold.md) Protein Ligand Docking Software
@@ -43,7 +44,7 @@
 * [Megahit](megahit.md) Metagenomics assembly
 * [MetaPhlAn](metaphlan.md) Profiling the composition of microbial communities with metagenomic data
 * [Minimap2](minimap2.md) Short read aligner
-* [Mothur](mothur.md) Package for microbial community analysis of amplicon sequencing data 
+* [Mothur](mothur.md) Package for microbial community analysis of amplicon sequencing data
 * [MrBayes](mrbayes.md) Program for inferring phylogenies using Bayesian methods
 * [Pannzer](pannzer.md) Automatic protein annotation tool
 * [Picard](picard.md) Tools for working with SAM,BAM,CRAM and VCF files
@@ -62,15 +63,16 @@
 * [Trinity](trinity.md) Traskriptome assembly tool
 * [Velvet](velvet.md) Genome assembler
 * [VirusDetect](virusdetect.md) Virus identification with sRNA data
-* [VMD](vmd.md) Molecular visualization program 
+* [VMD](vmd.md) Molecular visualization program
 * [wtdbg2](wtdbg2.md) Fast assembler for long-read data
 * [XHMM](xhmm.md) Copy number variation calling from targeted sequencing data
 
+
 ## Chemistry
 
 * [Amber](amber.md) Molecular dynamics suite
 * [AMS](ams.md) Modelling suite providing engines like ADF, BAND, DFTB and MOPAC
-* [AMS-GUI](ams-gui.md) AMS integrated GUI 
+* [AMS-GUI](ams-gui.md) AMS integrated GUI
 * [CP2k](cp2k.md) DFT, quantum chemistry, QM/MM, AIMD etc. in particular for periodic systems
 * [CSD](csd.md) Cambridge Crystallographic Database - organic and metallo-organic crystal structures and tools
 * [Gaussian](gaussian.md) Versatile computational chemistry package
@@ -83,14 +85,15 @@
 * [MOLDEN](molden.md) Processing program for molecular and electronic structure calculations
 * [MOLPRO](molpro.md) Package for accurate ab initio quantum chemistry calculations
 * [NAMD](namd.md) Highly scalable classical molecular dynamics
-* [NWChem](nwchem.md) A computational chemistry software package designed to perform well on parallel HPC systems.
+* [NWChem](nwchem.md) A computational chemistry software package designed to perform well on parallel HPC systems
 * [Open Babel](openbabel.md) Program to interconvert file formats currently used in molecular modeling
 * [ORCA](orca.md) General purpose quantum chemistry package
 * [Plumed](plumed.md) Library and tools for enhanced sampling methods
 * [TmoleX](tmolex.md) GUI for setting up and analyzing TURBOMOLE jobs
 * [Turbomole](turbomole.md) Efficient program package for electronic structure calculations
 * [VASP](vasp.md) Ab initio DFT electronic structures
-* [VMD](vmd.md) Molecular visualization program 
+* [VMD](vmd.md) Molecular visualization program
+
 
 ## Computational Engineering
 
@@ -102,15 +105,17 @@
 * [PALM](palm.md) Meteorological model system for atmospheric and oceanic boundary-layer flows
 * [Star-CCM+](starccm+.md) Computational Fluid Dynamics software by Siemens Digital Industries Software
 
+
 ## Data Analytics and Machine Learning
 
+* [JAX](jax.md) Autograd and XLA, brought together for high-performance machine learning
 * [Python Data](python-data.md) Collection of Python libraries for data analytics and machine learning
-* [JAX](jax.md) Autograd and XLA, brought together for high-performance machine learning 
 * [PyTorch](pytorch.md) Machine learning framework for Python
 * [RAPIDS](rapids.md) Suite of libraries for data analytics and machine learning on GPUs
-* [Spark](spark.md) High-performance distributed computing framework 
+* [Spark](spark.md) High-performance distributed computing framework
 * [TensorFlow](tensorflow.md) Deep learning library for Python
 
+
 ## Geosciences
 
 * [Ames Stereo Pipeline](ames-stereo.md) for processing stereo images
@@ -131,39 +136,50 @@
 * [Sen2Cor](sen2cor.md) for atmospheric-, terrain and cirrus correction of the Sentinel-2 products
 * [Sen2mosaic](sen2mosaic.md) for download, preprocessing and mosaicing of Sentinel-2 products
 * [SNAP](snap.md) for remote sensing applications
-* [WhiteboxTools](whiteboxtools.md) an advanced geospatial data analysis platform 
-* [Zonation](zonation.md) Spatial conservation prioritization framework 
+* [WhiteboxTools](whiteboxtools.md) an advanced geospatial data analysis platform
+* [Zonation](zonation.md) Spatial conservation prioritization framework
+
 
 ## Language Research and Other Digital Humanities and Social Sciences
 
 * [eBay's tsv-tools](http://urn.fi/urn:nbn:fi:lb-202006081) Utilities for manipulating large tabular data files
-* [finnish-parse](http://urn.fi/urn:nbn:fi:lb-2017030801) Dependency Parser for Finnish
 * [Finnish Tagtools](http://urn.fi/urn:nbn:fi:lb-201908161) Finnish Tagtools
+* [finnish-parse](http://urn.fi/urn:nbn:fi:lb-2017030801) Dependency Parser for Finnish
 * [HFST](http://urn.fi/urn:nbn:fi:lb-20140730183) Helsinki Finite-State Transducer Technology
 * [HFST-fi](http://urn.fi/urn:nbn:fi:lb-201509034) Helsinki Finite-State Technology for Finnish
 * [HFST-sv](http://urn.fi/urn:nbn:fi:lb-201509035) Helsinki Finite-State Technology for Swedish
 * [Kaldi](http://urn.fi/urn:nbn:fi:lb-2019121020) Kaldi Speech Recognition Toolkit
 * [UDPipe](http://urn.fi/urn:nbn:fi:lb-201902131) UDPipe Kielipankki version
 
+
 ## Mathematics and Statistics
 
 * [IDL](idl.md) Programming Language, Numeric Analysis, Manipulation and Visualization of Scientific Data
 * [Julia](julia.md)  High-level, high-performance dynamic programming language for numerical computing
 * [MATLAB](matlab.md) High-level technical computing language
-* [Octave](octave.md) High-level interpreted language for numerical computations.
-* [Python](python.md) programming language and its modules at CSC.
+* [Octave](octave.md) High-level interpreted language for numerical computations
+* [Python](python.md) programming language and its modules at CSC
 * [r-env](r-env.md) R, RStudio Server, SAGA and TensorFlow
 * [RStudio](rstudio.md) Integrated development environment for R
 * [SageMath](sagemath.md) Free open-source mathematics software system
 
+
 ## Physics
 
 * [VASP](vasp.md) Ab initio DFT electronic structures
 
+
 ## Miscellaneous
 
-* [DDT](ddt.md) Parallel debugger 
-* [MySQL](../data/kaivos/overview.md) MySQL database client. 
+* [Accelerated visualization](accelerated-visualization.md) A selection of GPU accelerated visualization applications
+* [DDT](ddt.md) Parallel debugger
+* [Desktop](desktop.md) Remote desktop environment
+* [HyperQueue](hyperqueue.md) Scheduler for sub-node tasks
+* [Julia-Jupyter](julia-jupyter.md) Interactive computational environment with Julia
+* [Jupyter](jupyter.md) Interactive computational environment with Python
+* [Jupyter for courses](jupyter-for-courses.md) A version of the Jupyter app for course environments
+* [MySQL](../data/kaivos/overview.md) MySQL database client.
 * [ParaView](paraview.md) Free open-source visualization application
+* [TensorBoard](tensorboard.md) The visualization toolkit for TensorFlow
 * [VisIt](visit.md) Free open-source visualization application
-* [HyperQueue](hyperqueue.md) Scheduler for sub-node tasks 
+* [Visual Studio Code](vscode.md) Source code editor

docs/apps/by_system.md

@@ -11,3 +11,7 @@ These headings are needed by the tests:
 ## Puhti
 
 ## LUMI
+
+## Mahti web interface
+
+## Puhti web interface

docs/apps/desktop.md

@@ -0,0 +1,33 @@
+---
+tags:
+  - Free
+system:
+  - www-mahti
+  - www-puhti
+---
+
+# Desktop
+
+Access a remote Xfce desktop environment on a supercomputer.
+
+
+## License
+
+Free
+
+
+## Available
+
+Desktop is available as an interactive application via the web interface for
+
+  - Mahti
+  - Puhti
+
+
+## More information
+
+More information on Desktop, interactive applications, and the web interfaces can be found under the [Computing section](../computing/index.md):
+
+  - [Desktop](../computing/webinterface/desktop.md)
+  - [Interactive applications](../computing/webinterface/apps.md)
+  - [Web interfaces](../computing/webinterface/index.md)

docs/apps/julia-jupyter.md

@@ -0,0 +1,33 @@
+---
+tags:
+  - Free
+system:
+  - www-mahti
+  - www-puhti
+---
+
+# Julia-Jupyter
+
+A version of the [Jupyter app](jupyter.md) for Julia programming language.
+
+
+## License
+
+Free
+
+
+## Available
+
+Julia-Jupyter is available as an interactive application via the web interface for
+
+  - Mahti
+  - Puhti
+
+
+## More information
+
+More information on Julia-Jupyter, interactive applications, and the web interfaces can be found under the [Computing section](../computing/index.md):
+
+  - [Julia-Jupyter](../computing/webinterface/julia-on-jupyter.md)
+  - [Interactive applications](../computing/webinterface/apps.md)
+  - [Web interfaces](../computing/webinterface/index.md)

docs/apps/jupyter-for-courses.md

@@ -0,0 +1,33 @@
+---
+tags:
+  - Free
+system:
+  - www-mahti
+  - www-puhti
+---
+
+# Jupyter for courses
+
+A version of the [Jupyter app](jupyter.md) for setting up custom course environments.
+
+
+## License
+
+Free
+
+
+## Available
+
+Jupyter for courses is available as an interactive application via the web interface for
+
+  - Mahti
+  - Puhti
+
+
+## More information
+
+More information on Jupyter for courses, interactive applications, and the web interfaces for courses can be found under the [Computing section](../computing/index.md):
+
+  - [Jupyter for courses](../computing/webinterface/jupyter-for-courses.md)
+  - [Interactive applications](../computing/webinterface/apps.md)
+  - [Web interfaces](../computing/webinterface/index.md)

docs/apps/jupyter.md

@@ -0,0 +1,33 @@
+---
+tags:
+  - Free
+system:
+  - www-mahti
+  - www-puhti
+---
+
+# Jupyter
+
+Web-based interactive computational environment for Python programming language.
+
+
+## License
+
+Free
+
+
+## Available
+
+Jupyter is available as an interactive application via the web interface for
+
+  - Mahti
+  - Puhti
+
+
+## More information
+
+More information on Jupyter, interactive applications, and the web interfaces can be found under the [Computing section](../computing/index.md):
+
+  - [Jupyter](../computing/webinterface/jupyter.md)
+  - [Interactive applications](../computing/webinterface/apps.md)
+  - [Web interfaces](../computing/webinterface/index.md)