features.yml

page_title: Features

features:
  - id: gui
    title: Graphical User Interface
    description: >
      Creating, editing and simulating a spatial model is all done using a user friendly Graphical User Interface.
      See the <a href="https://spatial-model-editor.readthedocs.io/en/stable/quickstart/get-started.html">Getting Started</a> section
      in the documentation to learn more.
    images:
      - screenshots/geometry0.png
      - screenshots/geometry1.png
      - screenshots/geometry2.png
      - screenshots/species0.png
      - screenshots/species1.png
      - screenshots/species2.png
      - screenshots/reactions.png
      - screenshots/simulation.png
    image_width: 8

  - id: dune
    title: DuneCopasi FEM Solver
    description: >
      The <a href="https://dune-copasi.netlify.app">dune-copasi</a> solver is used to simulate models.
      This solves the PDE on a tetrahedral mesh using finite element discretization methods.
      See the <a href="https://spatial-model-editor.readthedocs.io/en/stable/reference/dune.html">simulator documentation</a>
      for more information on the available options when using it in the GUI.
      For more technical information about the DuneCopasi solver itself,
      see the <a href="https://dune-copasi.netlify.app">dune-copasi</a> website.
    images:
      - dune/dune-copasi.svg
    image_width: 5

  - id: mesh
    title: Automatic mesh generation
    description: >
      Starting from a segmented image of the compartments in the model,
      the boundaries are automatically identified and simplified,
      and from them a triangular mesh approximation to the geometry is constructed.
      For more details see the <a href="https://spatial-model-editor.readthedocs.io/en/stable/reference/mesh.html">mesh documentation</a>.
    images:
      - mesh/mesh_original_image.png
      - mesh/mesh_pixel_contours.png
      - mesh/mesh_split_edge_contours.png
      - mesh/mesh_simplify_lines.png
      - mesh/mesh_triangulate_0.png
      - mesh/mesh_triangulate_1.png
      - mesh/mesh_triangulate_2.png
      - mesh/mesh_triangulate_3.png
    image_width: 6

  - id: pixel
    title: Pixel FTCS Solver
    description: >
      The <a href="https://spatial-model-editor.readthedocs.io/en/stable/reference/pixel.html">Pixel</a>
      solver is an alternative solver which uses the <a href="https://en.wikipedia.org/wiki/FTCS_scheme">FTCS</a>
      method to solve the PDE using the pixels of the geometry image as the grid.
      It features automatic timestep control, just-in-time compilation, and multi-threading support.
    images:
      - pixel/convergence.png
      - pixel/embedded.png
      - pixel/runtime.png
      - pixel/pixel_options.png
    image_width: 8

  - id: opt
    title: Parameter fitting
    description: >
      The parameters of your model can be automatically optimized using a variety of optimization algorithms to make the simulated model concentrations match experimental images of species concentrations.
      See the <a href="https://spatial-model-editor.readthedocs.io/en/stable/reference/parameter-fitting.html">Parameter fitting</a> section
      in the documentation to learn more.
    images:
      - opt/opt.png
      - opt/opt_setup.png
      - opt/opt_target.png
      - opt/opt_target_concentration.png
      - opt/opt_param.png
    image_width: 7

  - id: ode-import
    title: Automatic reaction rescaling
    description: >
      Guided
      <a href="https://spatial-model-editor.readthedocs.io/en/stable/quickstart/rescale-reactions.html">workflow</a>
      to import a non-spatial model from
      <a href="http://sbml.org/Basic_Introduction_to_SBML">SBML xml</a>
      or
      <a href="http://copasi.org/Support/Technical_Documentation/File_Format/">Copasi cps</a>
      format, which automatically rescales the reaction rates to construct a valid spatial PDE model
      that initially reproduces the behaviour of the non-spatial ODE model.
    images:
      - ode/ode1.png
      - ode/ode2.png
      - ode/ode3.png
    image_width: 6

  - id: sme
    title: Python interface
    description: >
      The Python interface, <a href="https://pypi.org/project/sme">sme</a>, allows scripted editing and simulation of a model.
      See the <a href="https://spatial-model-editor.readthedocs.io/en/stable/sme/notebooks.html#example-notebooks">Example Notebooks</a>
      or the <a href="https://spatial-model-editor.readthedocs.io/en/stable/sme/api.html">API reference</a> for more information.
    images:
      - sme/sme1.png
      - sme/sme2.png
      - sme/sme3.png
      - sme/sme4.png
    image_width: 6

  - id: sme-contrib
    title: Python extras
    description: >
      Additional functionality such as plotting, animations and parameter fitting is provided by
      <a href="https://pypi.org/project/sme-contrib">sme-contrib</a>.
      See the <a href="https://sme-contrib.readthedocs.io/en/latest/">documentation</a> for more information
      and example notebooks.
    images:
      - sme-contrib/sme-contrib1.png
      - sme-contrib/sme-contrib2.png
    image_width: 7

  - id: sbml
    title: SBML Spatial
    description: >
      Spatial models are imported and exported in
      <a href="http://sbml.org/Documents/Specifications">SBML Level 3</a> format with the
      <a href="http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/spatial">spatial</a>
      package, using the <a href="http://sbml.org/Software/libSBML">libSBML</a> library.
      All Level 3 math is supported, and is parsed, differentiated and compiled using the
      <a href="https://github.com/symengine/symengine">SymEngine</a> symbolic manipulation library.
    images:
      - libsbml.svg
    image_width: 3