Updated documentation

docs/iBioSim.html

@@ -106,9 +106,9 @@
 <a href="#tth_sEc11"
 >11&nbsp; Time Series Data Format</a><br />
 <a href="#tth_sEc12"
->12&nbsp; Tutorial</a><br />
+>12&nbsp; Tutorials</a><br />
 <a href="#tth_sEc13"
->13&nbsp; Reporting Bugs and Feature Requests</a><br />
+>13&nbsp; Submitting Bugs and Feature Requests</a><br />
 
 
 <div class="p"><!----></div>
@@ -2121,15 +2121,31 @@ User preferences can be set by selecting the <tt>Preferences</tt> option under t
 <div class="p"><!----></div>
 </li>
 
+<li> Want to confirm file deletions.
+<div class="p"><!----></div>
+</li>
+
 <li> Use the libsbml or the <tt>iBioSim</tt> flatten procedure.
 <div class="p"><!----></div>
 </li>
 
-<li> Use the infix expression parser in mathematical expressions.
+<li> Use the libsbml or a webservice to validate models.
+<div class="p"><!----></div>
+</li>
+
+<li> Whether or not to report validation warnings.
+<div class="p"><!----></div>
+</li>
+
+<li> The command to open html or xhtml files in a browser.
+<div class="p"><!----></div>
+</li>
+
+<li> The command to open Graphviz files.
 <div class="p"><!----></div>
 </li>
 </ul>
-The Restore Defaults button on this tab and the others restores the default preferences.  In the Schematics preference tab, the user can decide the shape, color (fill, stroke, and font), and opacity for each schematic object.  The Synthesis Preferences allows the user to select a default URI authority for composite SBOL DNA components generated by iBioSim and a regular expression for validating the SO types of the subcomponents making up these generated components.  The Model Preferences tab allows users to select whether they wish to see warnings about undeclared units in SBML and whether they wish to check units at all.  Finally, it allows users to change the default model generation parameter values.  The Analysis Preferences tab allows users to change the default values used by the analysis tool.  The simulation command in particular can be useful to select an alternative simulator.  We've used it to select a script that executes the simulation on a compute server.  Finally, the Learn Preferences tab allows users to change the default values used by the learn tool.
+The Restore Defaults button on this tab and the others restores the default preferences.  In the Schematics preference tab, the user can decide the shape, color (fill, stroke, and font), and opacity for each schematic object.  The Model Preferences tab allows users to select whether they wish to see warnings about undeclared units in SBML and whether they wish to check units at all.  It also allows users to change the default model generation parameter values.  The Analysis Preferences tab allows users to change the default values used by the analysis tool.  The simulation command in particular can be useful to select an alternative simulator.  We've used it to select a script that executes the simulation on a compute server.  The SBOL Assembly Preferences tab allows the user to select a default URI authority for composite SBOL DNA components generated by iBioSim, a regular expression for validating the SO types of the subcomponents making up these generated components, whether to validate assembled constructs, and whether to give an incomplete construct warning.  Finally, the Learn Preferences tab allows users to change the default values used by the learn tool.
 
 <div class="p"><!----></div>
 
@@ -2297,22 +2313,24 @@ The time series data (tsd) format is composed of a parenthesized and comma-separ
 
 <div class="p"><!----></div>
  <h2><a name="tth_sEc12">
-12</a>&nbsp;&nbsp;Tutorial</h2>
+12</a>&nbsp;&nbsp;Tutorials</h2>
 
 <div class="p"><!----></div>
-A detailed 
-<a href="iBioSim_Tutorial.html">
+There is a detailed systems biology oriented 
+<a href="iBioSim_SysBio_Tutorial.html">
+tutorial 
+</a>
+that uses the phage &#955; decision circuit as an example.
+There is also a separate systems biology oriented
+<a href="iBioSim_SynBio_Tutorial.html">
 tutorial
 </a>
-and a separate
-<a href="iBioSim_Grid_Tutorial.html">
-grid tutorial
-</a>
-are available in the <tt>docs</tt> directory that comes with the distribution.
+that uses the genetic toggle switch as an example.
+These are located in the <tt>docs</tt> directory that comes with the distribution.
 
 <div class="p"><!----></div>
  <h2><a name="tth_sEc13">
-13</a>&nbsp;&nbsp;Reporting Bugs and Feature Requests</h2>
+13</a>&nbsp;&nbsp;Submitting Bugs and Feature Requests</h2>
 
 <div class="p"><!----></div>
 When there is an un-handled exception, the window below allows the user to see more details about the exception.  These are likely not particularly useful to a user, but they are useful to us.  Therefore, the user can also submit this information as a bug report.  To make the bug report more useful, please provide an email address, a brief description of the bug, and a detailed description about how the bug occurred.  While all these fields are optional, the more information provided, the better.  A report can also be submitted from the Help menu.  In this case, the user can select whether the report is a BUG (an error or crash of the software), a CHANGE (something which can be improved), or a FEATURE (something new).  Finally, report can be submitted by sending an email to:<br />
@@ -2338,5 +2356,5 @@ mail will be filtered by our spam filters.
 T<sub><font size="-1">E</font></sub>X
 by <a href="http://hutchinson.belmont.ma.us/tth/">
 T<sub><font size="-1">T</font></sub>H</a>,
-version 3.81.<br />On  1 Jun 2014, 11:11.</small>
+version 3.81.<br />On 25 Jan 2015, 14:33.</small>
 </html>

docs/iBioSim.tex

@@ -1249,10 +1249,14 @@ User preferences can be set by selecting the {\tt Preferences} option under the
 \begin{itemize}
 \item Use a File Dialog for selecting files or the default Java File Chooser.  
 \item Use plus/minus for expanding and collapsing file trees.  
+\item Want to confirm file deletions.
 \item Use the libsbml or the {\tt iBioSim} flatten procedure.
-\item Use the infix expression parser in mathematical expressions.
+\item Use the libsbml or a webservice to validate models.
+\item Whether or not to report validation warnings.
+\item The command to open html or xhtml files in a browser.
+\item The command to open Graphviz files.
 \end{itemize}
-The Restore Defaults button on this tab and the others restores the default preferences.  In the Schematics preference tab, the user can decide the shape, color (fill, stroke, and font), and opacity for each schematic object.  The Synthesis Preferences allows the user to select a default URI authority for composite SBOL DNA components generated by iBioSim and a regular expression for validating the SO types of the subcomponents making up these generated components.  The Model Preferences tab allows users to select whether they wish to see warnings about undeclared units in SBML and whether they wish to check units at all.  Finally, it allows users to change the default model generation parameter values.  The Analysis Preferences tab allows users to change the default values used by the analysis tool.  The simulation command in particular can be useful to select an alternative simulator.  We've used it to select a script that executes the simulation on a compute server.  Finally, the Learn Preferences tab allows users to change the default values used by the learn tool.
+The Restore Defaults button on this tab and the others restores the default preferences.  In the Schematics preference tab, the user can decide the shape, color (fill, stroke, and font), and opacity for each schematic object.  The Model Preferences tab allows users to select whether they wish to see warnings about undeclared units in SBML and whether they wish to check units at all.  It also allows users to change the default model generation parameter values.  The Analysis Preferences tab allows users to change the default values used by the analysis tool.  The simulation command in particular can be useful to select an alternative simulator.  We've used it to select a script that executes the simulation on a compute server.  The SBOL Assembly Preferences tab allows the user to select a default URI authority for composite SBOL DNA components generated by iBioSim, a regular expression for validating the SO types of the subcomponents making up these generated components, whether to validate assembled constructs, and whether to give an incomplete construct warning.  Finally, the Learn Preferences tab allows users to change the default values used by the learn tool.
 
 \begin{center}
 \begin{tabular}{cc}
@@ -1349,20 +1353,22 @@ The time series data (tsd) format is composed of a parenthesized and comma-separ
 (("time","CI","CII"), (0,0,0), (100,0,19), (200,20,25), (300,19,18), (400,17,20), (500,17,46), \\
 (600,26,40), (700,43,43), (800,63,28), (900,72,34), (1000,72,28))
 
-\section{Tutorial}
+\section{Tutorials}
 
 \noindent
-A detailed 
-%%tth:\begin{html}<a href="iBioSim_Tutorial.html">\end{html}
+There is a detailed systems biology oriented 
+%%tth:\begin{html}<a href="iBioSim_SysBio_Tutorial.html">\end{html}
+tutorial 
+%%tth:\begin{html}</a>\end{html}
+that uses the phage $\lambda$ decision circuit as an example.
+There is also a separate systems biology oriented
+%%tth:\begin{html}<a href="iBioSim_SynBio_Tutorial.html">\end{html}
 tutorial
 %%tth:\begin{html}</a>\end{html}
-and a separate
-%%tth:\begin{html}<a href="iBioSim_Grid_Tutorial.html">\end{html}
-grid tutorial
-%%tth:\begin{html}</a>\end{html}
-are available in the {\tt docs} directory that comes with the distribution.
+that uses the genetic toggle switch as an example.
+These are located in the {\tt docs} directory that comes with the distribution.
 
-\section{Reporting Bugs and Feature Requests}
+\section{Submitting Bugs and Feature Requests}
 
 \noindent
 When there is an un-handled exception, the window below allows the user to see more details about the exception.  These are likely not particularly useful to a user, but they are useful to us.  Therefore, the user can also submit this information as a bug report.  To make the bug report more useful, please provide an email address, a brief description of the bug, and a detailed description about how the bug occurred.  While all these fields are optional, the more information provided, the better.  A report can also be submitted from the Help menu.  In this case, the user can select whether the report is a BUG (an error or crash of the software), a CHANGE (something which can be improved), or a FEATURE (something new).  Finally, report can be submitted by sending an email to:\\ 

docs/iBioSim_Install.html

@@ -31,11 +31,13 @@
 <h1>Contents </h1><a href="#tth_sEc1"
 >1&nbsp; General Requirements</a><br />
 <a href="#tth_sEc2"
->2&nbsp; Installation on Windows</a><br />
+>2&nbsp; Java Installation</a><br />
 <a href="#tth_sEc3"
->3&nbsp; Installation on Linux</a><br />
+>3&nbsp; MacOS Installation</a><br />
 <a href="#tth_sEc4"
->4&nbsp; Installation on MacOS</a><br />
+>4&nbsp; Windows Installation</a><br />
+<a href="#tth_sEc5"
+>5&nbsp; Linux Installation</a><br />
 
 
 <div class="p"><!----></div>
@@ -48,11 +50,11 @@
 There are versions of <tt>iBioSim</tt> available for Windows, Linux, and
 MacOS.  You can download the appropriate installation file from:<br />
 <a href="http://www.async.ece.utah.edu/iBioSim/">
-<tt>http://www.async.ece.utah.edu/iBioSim</tt>
+<tt>http://www.async.ece.utah.edu/iBioSim</tt>.
 </a>
-<br /><tt>iBioSim</tt> requires that you have 
+<tt>iBioSim</tt> requires that you have 
 <a href="http://java.sun.com/javase/downloads/index.jsp">
-Java Runtime Environment 1.5
+Java Runtime Environment 1.6
 </a>
 or higher install on your system.  It is also useful to have 
 <a href="http://www.graphviz.org/">
@@ -60,11 +62,32 @@ Graphviz.
 </a>
 Also, you should associate files with a ".dot" extension with the 
 <tt>Graphviz</tt> tool, and files with the ".xhtml" extension to your
-web browswer.
+web browswer.  There is also a pure java version available that
+supports most though not all features of <tt>iBioSim</tt>.  This is a good option when having trouble with the other installations, since it is machine independent.
 
 <div class="p"><!----></div>
  <h2><a name="tth_sEc2">
-2</a>&nbsp;&nbsp;Installation on Windows</h2>
+2</a>&nbsp;&nbsp;Java Installation</h2>
+
+<div class="p"><!----></div>
+To install the pure Java version, you need to download <tt>iBioSim-2.8-Java.zip</tt> and unzip it in the directory you wish to install.  The <tt>iBioSim.jar</tt> file should be executable, but may require being invoked using the explicit command: <tt>java -jar iBioSim.jar</tt>.
+The <tt>iBioSim.mac64</tt> script makes it look better on Mac environment.
+
+<div class="p"><!----></div>
+ <h2><a name="tth_sEc3">
+3</a>&nbsp;&nbsp;MacOS Installation</h2>
+
+<div class="p"><!----></div>
+To install on MacOS, you need to download <tt>
+  iBioSim-&#9001;version&#9002;-MacOS.dmg</tt> file.  You should then
+open this file with <tt>DiskImageMounter.app</tt>.  This should open up
+this disk image in <tt>finder</tt>.  You should then copy the contents of
+this disk image to your Applications folder.  You should then be able
+to start <tt>iBioSim</tt> by double-clicking on this application. 
+
+<div class="p"><!----></div>
+ <h2><a name="tth_sEc4">
+4</a>&nbsp;&nbsp;Windows Installation</h2>
 
 <div class="p"><!----></div>
 Download and execute <tt>iBioSim-&#9001;version&#9002;-Setup.exe</tt>.<br />
@@ -111,8 +134,8 @@ you remove <tt>iBioSim</tt> using this uninstall procedure before
 installing a new version.
 
 <div class="p"><!----></div>
- <h2><a name="tth_sEc3">
-3</a>&nbsp;&nbsp;Installation on Linux</h2>
+ <h2><a name="tth_sEc5">
+5</a>&nbsp;&nbsp;Linux Installation</h2>
 
 <div class="p"><!----></div>
 Since InstallJammmer is also used for the Linux install, the
@@ -192,23 +215,11 @@ Note that this is for bash shell, so you may need to change for your shell, if n
 </ul>
 You should see the usage lines for these programs.  If you do not, you may need custom builds, contact <tt>myers@ece.utah.edu</tt>.
 
-<div class="p"><!----></div>
- <h2><a name="tth_sEc4">
-4</a>&nbsp;&nbsp;Installation on MacOS</h2>
-
-<div class="p"><!----></div>
-To install on MacOS, you need to download <tt>
-  iBioSim-&#9001;version&#9002;-MacOS.dmg</tt> file.  You should then
-open this file with <tt>DiskImageMounter.app</tt>.  This should open up
-this disk image in <tt>finder</tt>.  You should then copy the contents of
-this disk image to your Applications folder.  You should then be able
-to start <tt>iBioSim</tt> by double-clicking on this application. 
-
 <div class="p"><!----></div>
 
 <br /><br /><hr /><small>File translated from
 T<sub><font size="-1">E</font></sub>X
 by <a href="http://hutchinson.belmont.ma.us/tth/">
 T<sub><font size="-1">T</font></sub>H</a>,
-version 3.81.<br />On 18 Jan 2013, 09:45.</small>
+version 3.81.<br />On 25 Jan 2015, 15:49.</small>
 </html>

docs/iBioSim_Install.tex

@@ -35,11 +35,11 @@
 There are versions of {\tt iBioSim} available for Windows, Linux, and
 MacOS.  You can download the appropriate installation file from:\\
 %%tth:\begin{html}<a href="http://www.async.ece.utah.edu/iBioSim/">\end{html}
-{\tt http://www.async.ece.utah.edu/iBioSim}
+{\tt http://www.async.ece.utah.edu/iBioSim}.
 %%tth:\begin{html}</a>\end{html}
-\\ {\tt iBioSim} requires that you have 
+{\tt iBioSim} requires that you have 
 %%tth:\begin{html}<a href="http://java.sun.com/javase/downloads/index.jsp">\end{html}
-Java Runtime Environment 1.5
+Java Runtime Environment 1.6
 %%tth:\begin{html}</a>\end{html}
 or higher install on your system.  It is also useful to have 
 %%tth:\begin{html}<a href="http://www.graphviz.org/">\end{html}
@@ -47,9 +47,26 @@ Graphviz.
 %%tth:\begin{html}</a>\end{html}
 Also, you should associate files with a ``.dot'' extension with the 
 {\tt Graphviz} tool, and files with the ``.xhtml'' extension to your
-web browswer.
+web browswer.  There is also a pure java version available that
+supports most though not all features of {\tt iBioSim}.  This is a good option when having trouble with the other installations, since it is machine independent.
 
-\section{Installation on Windows}
+\section{Java Installation}
+
+\noindent
+To install the pure Java version, you need to download {\tt iBioSim-2.8-Java.zip} and unzip it in the directory you wish to install.  The {\tt iBioSim.jar} file should be executable, but may require being invoked using the explicit command: {\tt java -jar iBioSim.jar}.
+The {\tt iBioSim.mac64} script makes it look better on Mac environment.
+
+\section{MacOS Installation}
+
+\noindent
+To install on MacOS, you need to download {\tt
+  iBioSim-$\langle$version$\rangle$-MacOS.dmg} file.  You should then
+open this file with {\tt DiskImageMounter.app}.  This should open up
+this disk image in {\tt finder}.  You should then copy the contents of
+this disk image to your Applications folder.  You should then be able
+to start {\tt iBioSim} by double-clicking on this application. 
+
+\section{Windows Installation}
 
 \noindent
 Download and execute {\tt iBioSim-$\langle$version$\rangle$-Setup.exe}.\\
@@ -63,8 +80,6 @@ Press {\tt Next} to continue.
 
 \includegraphics[height=95mm]{screenshots/setup}
 
-\clearpage
-
 Next, it ask you for an installation location.  Please make sure to
 select a path that does not have any spaces or special symbols as
 these cause problems with {\tt iBioSim}.
@@ -75,8 +90,6 @@ You are now ready to install.  Press {\tt Next} to continue.
 
 \includegraphics[height=95mm]{screenshots/confirm}
 
-\clearpage
-
 You are all done.  Press {\tt Finish}.  If selected, {\tt iBioSim}
 will launch immediately.  Otherwise, you can start it using your
 desktop shortcut or from your start menu.
@@ -89,7 +102,7 @@ remove {\tt iBioSim} from your system.  It is highly recommended that
 you remove {\tt iBioSim} using this uninstall procedure before
 installing a new version.
 
-\section{Installation on Linux}
+\section{Linux Installation}
 
 \noindent
 Since InstallJammmer is also used for the Linux install, the
@@ -105,8 +118,6 @@ preferred installation language.  Make your selection and press {\tt OK}.
 
 \includegraphics[height=40mm]{screenshots/language}
 
-\clearpage
-
 The next screen tells you that you what version you are installing.
 Press {\tt Next} to continue.
 
@@ -118,8 +129,6 @@ these cause problems with {\tt iBioSim}.
 
 \includegraphics[height=95mm]{screenshots/location}
 
-\clearpage
-
 You are now ready to install.  Press {\tt Next} to continue.
 
 \includegraphics[height=95mm]{screenshots/confirm}
@@ -149,16 +158,4 @@ Note that this is for bash shell, so you may need to change for your shell, if n
 \end{itemize}
 You should see the usage lines for these programs.  If you do not, you may need custom builds, contact {\tt myers@ece.utah.edu}.
 
-\clearpage
-
-\section{Installation on MacOS}
-
-\noindent
-To install on MacOS, you need to download {\tt
-  iBioSim-$\langle$version$\rangle$-MacOS.dmg} file.  You should then
-open this file with {\tt DiskImageMounter.app}.  This should open up
-this disk image in {\tt finder}.  You should then copy the contents of
-this disk image to your Applications folder.  You should then be able
-to start {\tt iBioSim} by double-clicking on this application. 
-
 \end{document}

docs/iBioSim_SynBio_Tutorial.html

@@ -14,9 +14,9 @@
  
 
 
-<title> iBioSim Version 2.7 \ Tutorial</title>
+<title> iBioSim Version 2.8 \ Synthetic Biology Tutorial</title>
  
-<h1 align="center">iBioSim Version 2.7 <br />Tutorial </h1>
+<h1 align="center">iBioSim Version 2.8 <br />Synthetic Biology Tutorial </h1>
 
 <div class="p"><!----></div>
 
@@ -193,7 +193,7 @@ Let us know see how to create a new model using the Model Editor.  First, select
 </center>
 
 <div class="p"><!----></div>
-To add a chemical species, select the Add Species icon <img src="../gui/icons/modelview/add_species_selected.png" alt="../gui/icons/modelview/add_species_selected.png" /> and click on the schematic canvas.  This will drop a new species with default ID and other values.  You may change these defaults by clicking on the selection icon 
+To add a chemical species, select the Add Species icon <img src="../gui/icons/modelview/add_species_selected.png" alt="../gui/icons/modelview/add_species_selected.png" /> and click on the schematic canvas  (note that this can also be done using the Edit menu or the hotkeys shown in this menu).  This will drop a new species with default ID and other values.  You may change these defaults by clicking on the selection icon 
 <img src="../gui/icons/modelview/select_mode_selected.png" alt="../gui/icons/modelview/select_mode_selected.png" />, and
 double-clicking on the species to open the Species Editor.  In this case, let us change the ID to LacI and change the Port type to <em>input</em>.  We will leave all the other values at their default values.  The port type of input indicates that this species will be used as an input for the LacI inverter.   
 Note that while in the select mode, you can also select an object in the schematic and move it by moving the mouse while holding the left mouse button.  Pressing the right mouse button while an object is selected brings up a menu that allows you to delete an object from the schematic.  Repeat the steps above to add TetR and GFP species.  Give these species port type of <em>output</em>. 
@@ -229,7 +229,7 @@ The pLac promoter is repressed by the LacI species.  To create this relationship
 </center>
 
 <div class="p"><!----></div>
-As mentioned earlier, the pLac promoter initiates the production of the TetR and GFP species.  Highlight the pLac promoter and, while holding the mouse button, stretch the production arc to the TetR species.  Repeat these steps to create a production arc between the pLac promoter and GFP species.  Note that the icons selected for this are not important because all arcs from promoters to species are always production arcs.  
+As mentioned earlier, the pLac promoter initiates the production of the TetR and GFP species.  Highlight the pLac promoter and, while holding the mouse button, stretch the production arc to the TetR species.  Repeat these steps to create a production arc between the pLac promoter and GFP species.  Note that any regulation icon can be selected for this because all arcs from promoters to species are always production arcs.  
 
 <div class="p"><!----></div>
 
@@ -497,7 +497,7 @@ The schematic in a grid model is a bit different.  It includes a grid in which e
 </center>
 
 <div class="p"><!----></div>
-Next, right-click on the Population model and create an analysis view.  Select Abstraction, Monte Carlo, and the SSA-Direct simulator.  Set the time limit to 10000 with a print interval of 100, and perform the simulation.  Now, go to the schematic tab and press the Choose Simulation button to select run-1.tsd.  Click on one of the genetic toggle switch models to bring up the Edit Species editor.  Select the GFP species and a green color gradient, and apply to all components with this model.  Now, play back the simulation to see the toggle switches turn on and off.
+Next, right-click on the Population model and create an analysis view.  Select Abstraction, Monte Carlo, and the SSA-Direct simulator.  Set the time limit to 10000 with a print interval of 100, change the number of runs to 1, and perform the simulation.  Now, go to the schematic tab and press the Choose Simulation button to select run-1.tsd.  Click on one of the genetic toggle switch models to bring up the Edit Species editor.  Select the GFP species and a green color gradient, and apply to all components with this model.  Now, play back the simulation to see the toggle switches turn on and off.
 
 <div class="p"><!----></div>
 
@@ -522,5 +522,5 @@ Next, right-click on the Population model and create an analysis view.  Select A
 T<sub><font size="-1">E</font></sub>X
 by <a href="http://hutchinson.belmont.ma.us/tth/">
 T<sub><font size="-1">T</font></sub>H</a>,
-version 3.81.<br />On 10 Sep 2014, 21:33.</small>
+version 3.81.<br />On 25 Jan 2015, 14:23.</small>
 </html>

docs/iBioSim_SynBio_Tutorial.tex

@@ -7,7 +7,7 @@
 
 \usepackage{indentfirst,graphics,alltt,epsfig,color}
 
-\title{iBioSim Version 2.7 \\ Tutorial}
+\title{iBioSim Version 2.8 \\ Synthetic Biology Tutorial}
 
 \author{Chris J. Myers}
 
@@ -128,7 +128,7 @@ Let us know see how to create a new model using the Model Editor.  First, select
 \includegraphics[width=160mm]{screenshots/schematicGT}
 \end{center}
 
-To add a chemical species, select the Add Species icon \includegraphics{../gui/icons/modelview/add_species_selected} and click on the schematic canvas.  This will drop a new species with default ID and other values.  You may change these defaults by clicking on the selection icon 
+To add a chemical species, select the Add Species icon \includegraphics{../gui/icons/modelview/add_species_selected} and click on the schematic canvas  (note that this can also be done using the Edit menu or the hotkeys shown in this menu).  This will drop a new species with default ID and other values.  You may change these defaults by clicking on the selection icon 
 \includegraphics{../gui/icons/modelview/select_mode_selected}, and
 double-clicking on the species to open the Species Editor.  In this case, let us change the ID to LacI and change the Port type to \emph{input}.  We will leave all the other values at their default values.  The port type of input indicates that this species will be used as an input for the LacI inverter.   
 Note that while in the select mode, you can also select an object in the schematic and move it by moving the mouse while holding the left mouse button.  Pressing the right mouse button while an object is selected brings up a menu that allows you to delete an object from the schematic.  Repeat the steps above to add TetR and GFP species.  Give these species port type of \emph{output}. 
@@ -163,7 +163,7 @@ The pLac promoter is repressed by the LacI species.  To create this relationship
 \includegraphics[width=160mm]{screenshots/repressionGT} 
 \end{center}
 
-As mentioned earlier, the pLac promoter initiates the production of the TetR and GFP species.  Highlight the pLac promoter and, while holding the mouse button, stretch the production arc to the TetR species.  Repeat these steps to create a production arc between the pLac promoter and GFP species.  Note that the icons selected for this are not important because all arcs from promoters to species are always production arcs.  
+As mentioned earlier, the pLac promoter initiates the production of the TetR and GFP species.  Highlight the pLac promoter and, while holding the mouse button, stretch the production arc to the TetR species.  Repeat these steps to create a production arc between the pLac promoter and GFP species.  Note that any regulation icon can be selected for this because all arcs from promoters to species are always production arcs.  
 
 \begin{center}
 \includegraphics[width=160mm]{screenshots/productionGT}
@@ -350,7 +350,7 @@ The schematic in a grid model is a bit different.  It includes a grid in which e
 \includegraphics[width=160mm]{screenshots/gridModelGT}
 \end{center}
 
-Next, right-click on the Population model and create an analysis view.  Select Abstraction, Monte Carlo, and the SSA-Direct simulator.  Set the time limit to 10000 with a print interval of 100, and perform the simulation.  Now, go to the schematic tab and press the Choose Simulation button to select run-1.tsd.  Click on one of the genetic toggle switch models to bring up the Edit Species editor.  Select the GFP species and a green color gradient, and apply to all components with this model.  Now, play back the simulation to see the toggle switches turn on and off.
+Next, right-click on the Population model and create an analysis view.  Select Abstraction, Monte Carlo, and the SSA-Direct simulator.  Set the time limit to 10000 with a print interval of 100, change the number of runs to 1, and perform the simulation.  Now, go to the schematic tab and press the Choose Simulation button to select run-1.tsd.  Click on one of the genetic toggle switch models to bring up the Edit Species editor.  Select the GFP species and a green color gradient, and apply to all components with this model.  Now, play back the simulation to see the toggle switches turn on and off.
 
 \begin{center}
 \includegraphics[width=160mm]{screenshots/gridSimGT}

docs/iBioSim_SysBio_Tutorial.html

@@ -14,9 +14,9 @@
  
 
 
-<title> iBioSim Version 2.5 \ Tutorial</title>
+<title> iBioSim Version 2.8 \ Systems Biology Tutorial</title>
  
-<h1 align="center">iBioSim Version 2.5 <br />Tutorial </h1>
+<h1 align="center">iBioSim Version 2.8 <br />Systems Biology Tutorial </h1>
 
 <div class="p"><!----></div>
 
@@ -611,5 +611,5 @@ is available in the <tt>docs</tt> directory that comes with the distribution.
 T<sub><font size="-1">E</font></sub>X
 by <a href="http://hutchinson.belmont.ma.us/tth/">
 T<sub><font size="-1">T</font></sub>H</a>,
-version 3.81.<br />On  6 Sep 2014, 09:48.</small>
+version 3.81.<br />On 25 Jan 2015, 14:23.</small>
 </html>

docs/iBioSim_SysBio_Tutorial.tex

@@ -7,7 +7,7 @@
 
 \usepackage{indentfirst,graphics,alltt,epsfig,color}
 
-\title{iBioSim Version 2.5 \\ Tutorial}
+\title{iBioSim Version 2.8 \\ Systems Biology Tutorial}
 
 \author{Chris J. Myers}