File: ToDo.htm

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<html>
<head>
<title>To Do</title>
</head>
<body>
<h1>To Do</h1>

<ul>
  <li> Streamline the process of generating tables. Show one
  trajectory at a time.
  <li> Hide unused fields in the method editor.
  <li> Collect and analyze test problems.
  <li> Add copy and paste to the species, reaction and parameter lists.
  Also add ability to clear selected columns.
  <li> Plot reaction propensities.
  <li> Check export of compartments to SBML.
  <li> Add import/export capabilities for SBML shorthand.
  <li> The MS Windows backend for wxPython does not correctly fade
  disabled bitmap buttons. I have added explicit SetBitmapDisabled()
  calls to work around this issue. Remove these calls when this issue
  is resolved.
</ul>

<!-- Private ToDo
<ul>
  <li> Cache the model before duplication.
  <li> Refactor by moving code from ContentHandler, Mainframe, and State to
  the responsible classes.
  <li> Add undo edit to the grid editor.
  <li> I need to check if the species populations are negative. I can't just check that the propensities are non-negative. _computePropensities in OdeReaction.
  <li> Standardize the solver names.
  <li> Add an error tolerance to the inhomogeneous solvers. Then use numerical integration.
  <li> Why didn't the all reactions plot work for the Schlogl model?
  <li> Preserve the order of models and methods.
  <li> Task queue.
  <li> Fix names when exporting to Mathematica.
  <li> Sort by any field.
  <li> Index and large window for recorded species.
  <li> Search bar for species and reactions.
  <li> Select all species and reactions for Mathematica solver.
  <li> Try 53-bit discrete deviates with the direct methods.
  <li> Consider using kernel functions to obtain smooth PDF's for simulation
  output.
  <li> Perhaps I should scale the histogram values by the inverse bin width.
  This would give it unit area.
  <li> Support SBML export of non-mass-action kinetic laws.
  <li> Find out why Proctor fails with ODE.
  <li> Reduce validity checks in hybrid method.
  <li> Check for negative populations in ODE methods. Solve population == 0
  and reduce the time step.
  <li> Why doesn't Wilkinson's mm-stoch2 model work?
  <li> Get rid of read errors when killing simulations.
  <li> Save the preferences.
  <li> Write a mass-action propensities functor that stores the
  reactants in a StaticArrayOfArrays.
  <li> In Propensities: call a function that updates all affected
  propensities for a given reaction instead of computing the
  propensities individually. Use the reaction influence data
  structure. This will save overhead on function calls.
  <li> Tweak rebuilding frequencies for sorting methods.
  <li> Track errors for next reaction method.
  <li> Get rid of EssTerminationCondition.
  <li> Check out GUI2Exe.
  <li> Record the state of the discrete, uniform generator at the beginning
  of each trajectory. This would make each trajectory reproducible.
</ul>
-->

</body>
</html>