File: UserSpecies.htm

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<html>
<head>
<title>Species Editor</title>
</head>
<body>
<h1>Species Editor</h1>

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

<p>
The species editor allows you to view and edit the species. The
identifier (ID) field is required. In order to be compatible with
<a href="http://sbml.org/">SBML</a>, there are a couple of restrictions.
The identifier is a string that starts with an underscore or a letter
and is composed entirely of underscores, letters and digits. Spaces
and special characters like $ are not allowed.  &quot;s1&quot;,
&quot;species158&quot;, &quot;unstableDimer&quot;, and
&quot;_pi_314&quot; are all valid identifiers. (Don't enter the
quotes.) &quot;2x4&quot;, &quot;species 158&quot;, &quot;s-158&quot;
are invalid. Finally, the identifiers must be unique.  The name field
is optional. It is an arbitrary string that describes the species, for
example &quot;unstable dimer&quot;.  &quot;Coolest #*@$ species
ever!!!&quot; is also a valid name, but show a little restraint - this
is science. The compartment field is optional. It does not affect the
simulation output. By default the name and compartment fields are hidden.
Click <img src="system-search.png">&nbsp; in the tool bar to show
or hide these columns.
</p>

<p>
The initial amount field is required. It is the initial
population of the species and must evaluate to a non-negative integer.
You may enter a number or any Python expression involving the parameters.
The following are examples of valid initial amounts.
<ul>
  <li> <tt>100</tt>
  <li> <tt>1e10</tt>
  <li> <tt>2**10</tt>
  <li> <tt>pow(X0, 3)</tt>
  <li> <tt>ceil(pi * R**2)</tt>
</ul>
Here we assume that <tt>X0</tt> and <tt>R</tt> have been defined as
parameters. <tt>pow</tt> and <tt>ceil</tt> are math functions.
<tt>pi</tt> is a mathematical constant.
</p> 
<p>
There is a tool bar for editing the species. You can select rows by clicking
on the row label along the left side of the table. The following operations
are available:
<ul>
  <li> <img src="add.png">&nbsp; Add a species to the table. If you
  select a row, the new species will be inserted above that row.
  <li> <img src="cancel.png">&nbsp; Delete the selected rows.
  <li> <img src="up.png">&nbsp; Left click to move the selected
  row up. Right click to move the selected row to the top. This has no
  effect if no rows or multiple rows are selected.
  <li> <img src="down.png">&nbsp; Left click to move the selected
  row down. Right click to move the selected row to the bottom. 
  <li> <img src="sort.png">&nbsp; Left click to sort by identifier
  in ascending order. Right click to sort in descending order.
  <li> <img src="scale.png">&nbsp; Automatically size the cells in
  the table to fit their contents.
  <li> <img src="system-search.png">&nbsp; Show/hide the optional
  fields.
</ul>
If the species table is not valid, you will get an error message when you
try to launch a simulation.
</p>

<p>
<b>A Note About Identifiers and Compartments.</b><br>
Note that in designing a scheme to describe species and compartments
one could use either species identifiers that have compartment scope
or global scope. We follow the <a href="http://sbml.org/">SBML</a>
convention that the identifiers have global scope and therefore must
be unique.  Consider a trivial problem with two species <em>X</em> and
<em>Y</em> and two compartments <em>A</em> and <em>B</em>. If species
identifiers had compartment scope then one could describe the species
as below.
</p>

<!--CONTINUE: Tables are not currently rendered correctly.
<table border="1">
  <tr><th>ID<th>Compartment
  <tr><td>X<td>A
  <tr><td>Y<td>A
  <tr><td>X<td>B
  <tr><td>Y<td>B
</table>
-->
<pre><b>
ID  Compartment</b>
---------------
X   A
Y   A
X   B
Y   B
</pre>

<p>
This notation is handy because we can easily see that although the
populations of <em>X</em> in <em>A</em> and <em>B</em> are distinct,
they are populations of the same type of species. The disadvantage of
this notation is that writing reactions is verbose. One cannot simply
write &quot;<em>X &rarr; Y</em>&quot;, because it does not specify
whether the reaction occurs in <em>A</em>, or <em>B</em>, or
both. Furthermore a notation such as &quot;<em>X &rarr; Y</em> in
<em>A</em>&quot; is not sufficient because it cannot describe
transport between compartments. Thus, one is stuck with a notation
such as &quot;<em>X</em> in <em>A</em> &rarr; <em>Y</em> in
<em>A</em>.&quot; In Cain, the species identifiers must be unique:
</p>

<!--CONTINUE: Tables are not currently rendered correctly.
<table border="1">
  <tr><th>ID<th>Compartment
  <tr><td>X_A<td>A
  <tr><td>Y_A<td>A
  <tr><td>X_B<td>B
  <tr><td>Y_B<td>B
</table>
-->
<pre><b>
ID    Compartment</b>
-----------------
X_A   A
Y_A   A
X_B   B
Y_B   B
</pre>

<p>
Thus the compartment field is optional; it is not used to describe the
reactions and does not affect simulation results. It's only use is in
visually categorizing the species. If you leave the compartment field
blank, then internally each species is placed in the same unnamed compartment.
If you export such a model in SBML format, the compartment will be given an
identifier such as &quot;Unnamed&quot;.
</p>

</body>
</html>