The full range of possible items for scoping the 2 year open cmiss redevelopment plan
<br>
Initially we need to detail all possibilities so that we can work out
dependencies, requirements and priorities. This should be done along with specific deliverable outcomes from the PI group (see [outcomes] for an initial listing of possible outcomes).
The planned scope and [development program] is now being created separately.
<br>

<h2>Computation</h2>

<h3>Techniques</h3>
<ul>
  <li>Finite element</li>
  <li>Finite difference</li>
  <li>Finite volume</li>
  <li>Boundary element</li><li>Method of Characteristics: Lagrange-Galerkin<br>
  </li>

  <li>ODE integration</li>
  <li>Adaptivity in time and space</li>
  <li>Optimization with/without linear/nonlinear constraints</li>
  <li>Software independent specification of simulation specific mathematical equations (!CellML)</li>
  <li>GPU utilisation</li>
  <li>Field operators (computed fields/computed variables)</li>
  <li>Reactions between possibly different equations in adjacent (or far field or coexisting) domains</li>
</ul>

<h3>Applications</h3>
<ul>
  <li>Finite deformation elasticity</li>
  <li>Linear elasticity</li>
  <li>Heat Equation</li>
  <li>Monodomain electrical activation</li>
  <li>Bidomain electrical activation</li>
  <li>3D CFD</li>
  <li>1D CFD</li><li>1D advection-diffusion with source<br>
  </li>

  <li>Coupled electromechanics</li>
  <li>Inverse electrocardiography</li>
  <li>Forward electrocardiography</li>
  <li>Signal analysis - !APDs, QT intervals, etc.</li>
</ul>

<h2>Meshing</h2>
<ul>
  <li>Volume fitting</li>
  <li>Surface fitting</li>
  <li>Face fitting</li>
  <li>Host mesh fitting</li>
  <li>Automatic mesh generation/refinement/validation/checking</li>
  <li>Image-based fitting</li>
  <li>Algorithmic mesh construction</li><li>Standard meshes (sphere, cube, heart, lung)<br>
  </li>

</ul>

<h2>Visualisation</h2>
<ul>
  <li>Volume rendering</li>
  <li>Iso-surfaces, contours</li>
  <li>Streamlines</li>
  <li>Time series data</li><li>Real time visualisation of computations<br>
  </li>

</ul>

<h2>Framework</h2>
<ul>
  <li>Data structures</li>
  <li>Module communication/API protocol</li>
  <li>File formats</li>
  <li>Data storage and access</li>
  <li>High performance computation -- shared and distributed memory</li>
  <li>Source code management (including tracking changes in code that is under development but untested)</li>
  <li>Modular code design</li>
  <li>Code testing and validation (unit tests)</li>
  <li>Bug tracking</li>
  <li>Computational platforms: AIX, Linux, win32, OSX</li><li>Computational steering</li>
  <li>!CellML API and implementation</li>
  <li>!FieldML API and implementation<br>
  </li>

</ul>

<h2>Image processing</h2>
<ul>
  <li>3D image processing</li>
  <li>Image filtering and enhancement</li>
  <li>Noise reduction (wavelets, curvelets, ...)</li>
  <li>Colour space modification, lookup table mapping, 3D volume rendering</li>
  <li>Edge detection</li>
  <li>Segmentation and thresholding</li>
  <li>Kernel convolution</li>
  <li>Deconvolution</li>
  <li>Cross-correlation and alignment</li>
  <li>Object definition, measurement and statistical analysis</li>
  <li>Digitising and mesh/model creation</li>
  <li>Vessel centreline extraction</li>
  <li>3D reconstruction, montaging</li>
  <li>Multi-modal image registration</li>
  <li>Model-based image processing</li>
</ul>

<h2>Interfaces</h2>
<ul><li>Web-based interfaces</li>
  <li>GUI Toolkits: win32, gtk, XUL, QT, Mac, X11, Motif, wxWindows, Java</li>
  <li>Scripting languages: python, ruby, perl, matlab, mathematica, octave, maxima</li>
  <li>Programming languages used internally: C, C++, f77, f90/95/..., java(CellML tools)<br>
</li><li>Supported programming languages: C, Objective C, C++, f77, f90/95/..., C#, java, .net</li>

</ul>

<h2>Documentation and website</h2>
<ul>
  <li>Programmer documentation, tools and website</li>
  <li>API documentation</li>
  <li>User documentation</li>
  <li>User tutorials</li>
  <li>User website</li>
  <li>User examples</li>
  <li>Programmer examples</li>
</ul>