File: UserSimulation.htm

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<html>
<head>
<title>Simulation Output</title>
</head>
<body>
<h1>Simulation Output</h1>

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

<p>
Information about the simulation output is displayed in the upper,
right corner.
The outputs are grouped according to the model and method used to generate
them. After selecting an item, the following operations are available in
the toolbar:
<ul>
  <li> <img src="cancel.png">&nbsp; Delete the output.
  
  <li> <img src="up.png">&nbsp; Move the selection up in the list.
  
  <li> <img src="down.png">&nbsp; Move the selection down in the
  list.
  
  <li> <img src="plot.png">&nbsp; Open the plot configuration window
  which allows one to choose the output and kind of plot to generate.
  
  <li> <img src="gnuplot.png">&nbsp; Export the selected output as
  a <a href="http://www.gnuplot.info/">gnuplot</a> data file and
  script. Note that working with the plot configuration window is
  likely more convenient, but some may prefer to work with gnuplot.
  This option will create the files <tt>x.dat</tt> and
  <tt>x.gnu</tt> for a specified base name <tt>x</tt>. You can use
  gnuplot to generate graphs 
  with the shell command &quot;gnuplot x.gnu&quot;. For trajectory output
  this will create
  the files <tt>x-Populations.jpg</tt> and <tt>x-Reactions.jpg</tt>
  that plot the populations and reaction counts, respectively. It will
  also create plots for each species and each reaction.
  For histogram output it will generate graphs of each histogram.
  <!--CONTINUE Move these options from the preferences to a dialog
  that is show when one click the gnuplot button.-->
  Note that you can set some plotting options through the preferences button
  <img src="preferences-system.png">&nbsp; in the main tool bar.

  <li> <img src="x-office-spreadsheet.png">&nbsp; Display the
  species populations or reaction counts in a table.

  <li> <img src="HistogramDistance.png">&nbsp; Calculate the
  distance between histograms. This button opens a frame that allows you to
  select individual histograms or sets of histograms.

  <li> <img src="pValue.png">&nbsp; Test the hypothesis that two species
  populations have the same mean. This button opens the p-value
  analysis window. One may select species (in the same or different
  simulation outputs) and statistically test the null hypothesis
  that the means are equal. See the
  <a href="DsmtsBirthDeath.htm">Birth-Death</a> section in the
  <a href="Dsmts.htm">DSMTS</a> chapter for an example.

  <li> <img src="filesave.png">&nbsp; Open the data export
  configuration window. One may export data as
  comma-separated values
  (<a href="http://en.wikipedia.org/wiki/Comma-separated_values">CSV</a>)
  or as a text file.
  These can be imported into spreadsheet programs like
  <a href="http://www.openoffice.org/product/calc.html">Calc</a>,
  <a href="http://www.apple.com/iwork/numbers/">Numbers</a>, or
  <a href="http://office.microsoft.com/excel/">Excel</a>.
</ul>
</p>

</body>
</html>