File: UserModel.htd

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<html>
<head>
<title>Models List</title>
</head>
<body>
<h1>Models List</h1>

<p>
The simplest exercise in using stochastic simulation software is to
generate trajectories for a given model using a given simulation
method. Beyond this, one may want to compare different models, or
different simulation methods. For example, one might investigate how
changing a rate parameter affects the output. Or one might compare how
an approximate method like <a href="SimulationTau.htm">tau-leaping</a>
with an exact method such as the <a href="SimulationDirect.htm">direct
method</a>. To accomodate these use cases, Cain maintains lists of
the models and methods that have been defined during a session. These
lists are shown in the first two panels of the application window.
</p>

<p align="center">
<img src="ModelList.png">
</p>

<p>
The models list panel, shown above, lists the models by their identifiers.
You must select a model before editing it or launching a simulation;
do this by clicking on its identifier in the list.
The species, reactions, etc. for the model will be shown in the model
editor, which is comprised of the panels in the bottom two rows
of the application window.
A model identifier can be any string, but must be
unique. You can edit the names by clicking twice (not double clicking,
but clicking twice in succesion) on a list item. When
a simulation is run, the identifiers for the model and the method
are listed in the output panel in the upper right corner of the
application window. Thus you can identify the model and method used
to generate each output (which could be time series data or histograms).
</p>

<p>
Note that you cannot edit or a delete a model that has dependent
output. Otherwise the stored model would no longer correspond to that
used to generate the simulation results. If you want to delete a
model, you must delete any dependent simulation output first. If you
want to modify a model that has dependent output, clone the model to
obtain a copy with a distinct identifier.  You may, however, change
the model or the method names at any time; the simulation output will
be updated to reflect the change.
</p>

<p>
The following actions are available from the models list toolbar:
<ul>
  <li><img src="add.png">&nbsp;
  Add a new model.
  <li><img src="editcopy.png">&nbsp;
  Add a clone of the selected model.
  <li><img src="chess-board.png">&nbsp;
  Add a duplicated version of the selected model. This duplicates the species
  and reactions to form a larger system, which is useful for testing the
  scalability of methods. You can choose the multiplicity (how many times to
  duplicate) and whether to multiply the propensity functions by unit
  random numbers.
  <li><img src="cancel.png">&nbsp;
  Delete the selected model.
  <li><img src="up.png">&nbsp;
  Move the selected model up in the list.
  <li><img src="down.png">&nbsp;
  Move the selected model down in the list.
</ul>
</p>

</body>
</html>