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@ -14,9 +14,9 @@
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<title> LEMA: User's Manual</title>
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<title> ATACS User's Manual</title>
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<h1 align="center">LEMA: User's Manual </h1>
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<h1 align="center">ATACS User's Manual </h1>
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<div class="p"><!----></div>
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@ -24,11 +24,103 @@
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<div class="p"><!----></div>
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<h3 align="center">Created: February 20th, 2009<br />
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Last Revised: February 20th, 2009
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</h3>
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<div class="p"><!----></div>
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<div class="p"><!----></div>
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<h1>Contents </h1><a href="#tth_sEc1"
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>1 Introduction</a><br />
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<a href="#tth_sEc2"
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>2 Project Management</a><br />
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<a href="#tth_sEc2.1"
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>2.1 Creating and Opening Projects</a><br />
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<a href="#tth_sEc2.2"
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>2.2 Creating Models and Graphs</a><br />
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<a href="#tth_sEc2.3"
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>2.3 Importing Models</a><br />
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<a href="#tth_sEc2.4"
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>2.4 Editing Project Objects</a><br />
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<a href="#tth_sEc2.5"
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>2.5 Viewing Project Objects</a><br />
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<a href="#tth_sEc2.6"
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>2.6 Creating Tool Views</a><br />
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<a href="#tth_sEc3"
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>3 SBML Editor</a><br />
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<a href="#tth_sEc3.1"
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>3.1 SBML Math Formulas</a><br />
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<a href="#tth_sEc3.2"
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>3.2 Main Elements</a><br />
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<a href="#tth_sEc3.2.1"
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>3.2.1 Compartments</a><br />
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<a href="#tth_sEc3.2.2"
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>3.2.2 Species</a><br />
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<a href="#tth_sEc3.2.3"
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>3.2.3 Reactions</a><br />
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<a href="#tth_sEc3.2.4"
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>3.2.4 Global Parameters</a><br />
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<a href="#tth_sEc3.3"
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>3.3 Definitions/Types</a><br />
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<a href="#tth_sEc3.3.1"
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>3.3.1 Function Definitions</a><br />
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<a href="#tth_sEc3.3.2"
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>3.3.2 Unit Definitions</a><br />
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<a href="#tth_sEc3.3.3"
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>3.3.3 Compartment Types</a><br />
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<a href="#tth_sEc3.3.4"
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>3.3.4 Species Types</a><br />
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<a href="#tth_sEc3.4"
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>3.4 Initial Assignments/Rules/Constraints/Events</a><br />
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<a href="#tth_sEc3.4.1"
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>3.4.1 Initial Assignments</a><br />
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<a href="#tth_sEc3.4.2"
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>3.4.2 Rules</a><br />
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<a href="#tth_sEc3.4.3"
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>3.4.3 Constraints</a><br />
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<a href="#tth_sEc3.4.4"
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>3.4.4 Events</a><br />
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<a href="#tth_sEc4"
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>4 GCM Editor</a><br />
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<a href="#tth_sEc4.1"
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>4.1 Promoters</a><br />
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<a href="#tth_sEc4.2"
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>4.2 GCM Species</a><br />
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<a href="#tth_sEc4.3"
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>4.3 Influences</a><br />
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<a href="#tth_sEc4.4"
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>4.4 GCM Parameters</a><br />
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<a href="#tth_sEc5"
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>5 Analysis View</a><br />
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<a href="#tth_sEc5.1"
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>5.1 Simulation Options</a><br />
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<a href="#tth_sEc5.2"
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>5.2 Abstraction Options</a><br />
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<a href="#tth_sEc5.3"
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>5.3 Parameter Editor</a><br />
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<a href="#tth_sEc6"
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>6 Learn View</a><br />
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<a href="#tth_sEc6.1"
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>6.1 Data Manager</a><br />
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<a href="#tth_sEc6.2"
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>6.2 Learn Tool</a><br />
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<a href="#tth_sEc7"
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>7 TSD Graph Editor</a><br />
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<a href="#tth_sEc8"
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>8 Probability Graph Editor</a><br />
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<a href="#tth_sEc9"
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>9 Preferences</a><br />
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<a href="#tth_sEc10"
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>10 Genetic Circuit Model Format</a><br />
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<a href="#tth_sEc11"
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>11 Time Series Data Format</a><br />
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<a href="#tth_sEc12"
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>12 List of Hot Keys</a><br />
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<a href="#tth_sEc13"
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>13 Tutorial</a><br />
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<a href="#tth_sEc14"
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>14 Reporting Bugs and Feature Requests</a><br />
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<a href="#tth_sEc15"
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>15 Credits</a><br />
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<div class="p"><!----></div>
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@ -119,20 +211,20 @@ down menu shown below.
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<div class="p"><!----></div>
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After you have created or opened a project, you can create a
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new model or graph to add to the project. To create a new
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Genetic Circuit Model (see Section ), select
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Genetic Circuit Model (see Section <a href="#GCM">10</a>), select
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New → Genetic Circuit Model from the
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File menu as shown below. You will then be prompted to give a model id. At this
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point, a GCM editor (see Section ) will open in a new
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point, a GCM editor (see Section <a href="#GCMEdit">4</a>) will open in a new
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tab. To create a new SBML model, select New → SBML Model
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from the File menu. You will then be prompted to give a model id.
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At this point, an SBML editor (see Section ) will open
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At this point, an SBML editor (see Section <a href="#SBMLEdit">3</a>) will open
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in a new tab. To create a new TSD graph, select New → TSD Graph
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from the File menu. You will then be prompted to give a name to
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the TSD graph. At this point, a TSD graph editor (see Section )
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the TSD graph. At this point, a TSD graph editor (see Section <a href="#TSDEdit">7</a>)
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will open in a new tab. To create a new probability graph, select
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New → Probability Graph from the File menu. You will then
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be prompted to give a name to the probability graph. At this point, a
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probability graph editor (see Section )
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probability graph editor (see Section <a href="#ProbEdit">8</a>)
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will open in a new tab. Once a model or graph is created, it can
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be opened again later by right clicking on the object in the
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project window and selecting "Edit", or alternatively
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@ -175,16 +267,16 @@ All project objects can be modified by highlighting the object
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and using a right mouse click to open a menu of options as shown
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below. Using this menu, every type of object can be copied, renamed, or
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deleted. For a GCM, the "View/Edit" option opens the
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model in a GCM editor (see Section ). For an SBML model,
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model in a GCM editor (see Section <a href="#GCMEdit">4</a>). For an SBML model,
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the "View/Edit" option opens the model in an SBML editor
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(see Section ). For a TSD graph, the "View/Edit"
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option opens the TSD graph in a TSD graph editor (see Section ).
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(see Section <a href="#SBMLEdit">3</a>). For a TSD graph, the "View/Edit"
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option opens the TSD graph in a TSD graph editor (see Section <a href="#TSDEdit">7</a>).
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For a probability graph, the "View/Edit" option opens
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the probability graph in a probability graph editor
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(see Section ).
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(see Section <a href="#ProbEdit">8</a>).
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For an analysis view, the "Open Analysis View" option opens the
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analysis view (see Section ). For a learn view, the
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"Open Learn View" option opens the learn view (see Section ).
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analysis view (see Section <a href="#Analysis">5</a>). For a learn view, the
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"Open Learn View" option opens the learn view (see Section <a href="#Learn">6</a>).
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<div class="p"><!----></div>
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@ -233,8 +325,8 @@ default xhtml browser.
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<div class="p"><!----></div>
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To perform analysis or learning, right click on a model and
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select "Create Analysis View" (see Section )
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to perform analysis or "Create Learn View" (see Section )
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select "Create Analysis View" (see Section <a href="#Analysis">5</a>)
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to perform analysis or "Create Learn View" (see Section <a href="#Learn">6</a>)
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to perform learning. You will then be prompted to give a name to
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your analysis or learn view. After a name is entered, a tab with
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the newly created view will open. Once a view is created, it can
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@ -257,8 +349,8 @@ analysis view, you can edit the initial concentrations and
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parameters. However, if you wish to be able to edit the
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structure, you should first create an SBML model using Create
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SBML Model option in the right click menu or the Save as SBML button in
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the GCM Editor (see Section ). You can then open and
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edit this model using an SBML editor (see Section ) and
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the GCM Editor (see Section <a href="#GCMEdit">4</a>). You can then open and
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edit this model using an SBML editor (see Section <a href="#SBMLEdit">3</a>) and
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create an analysis view from this edited model.
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<div class="p"><!----></div>
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@ -269,18 +361,18 @@ create an analysis view from this edited model.
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<div class="p"><!----></div>
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The SBML editor as shown below allows the user to create or modify an SBML
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model of a biochemical reaction network. An SBML model includes
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compartments (see Section ),
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species (see Section ),
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reactions (see Section ),
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parameters (see Section ),
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function definitions (see Section ),
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unit definitions (see Section ),
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compartment types (see Section ),
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species types (see Section ),
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initial assignments (see Section ),
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rules (see Section ),
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constraints (see Section ), and
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events (see Section ).
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compartments (see Section <a href="#compartments">3.2.1</a>),
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species (see Section <a href="#species">3.2.2</a>),
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reactions (see Section <a href="#reactions">3.2.3</a>),
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parameters (see Section <a href="#parameters">3.2.4</a>),
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function definitions (see Section <a href="#funcDefn">3.3.1</a>),
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unit definitions (see Section <a href="#unitDefn">3.3.2</a>),
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compartment types (see Section <a href="#compTypes">3.3.3</a>),
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species types (see Section <a href="#specTypes">3.3.4</a>),
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initial assignments (see Section <a href="#initials">3.4.1</a>),
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rules (see Section <a href="#rules">3.4.2</a>),
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constraints (see Section <a href="#constraints">3.4.3</a>), and
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events (see Section <a href="#events">3.4.4</a>).
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Each of these items can be added, removed, or edited.
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To add a new item, click on the appropriate add button. You
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will then be prompted to provide a unique id and some properties
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@ -303,7 +395,7 @@ Note that many checks are done on the fly, so it should be difficult
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to create models with consistency problems. However, if a user does
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not wish to be warned about undeclared units or does not wish to have
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units checked at all can set preferences to turn this off
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(see Section ). The Save and Check SBML button
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(see Section <a href="#Preferences">9</a>). The Save and Check SBML button
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though will still present all the unit warnings and errors.
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Finally, the Save As button can also be used to store the
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model, but in this case, a new model ID will be requested and the
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@ -405,10 +497,10 @@ math formula:
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<div class="p"><!----></div>
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This Main Elements tab shown below is used to specify
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compartments (see Section ),
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species (see Section ),
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reactions (see Section ), and
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parameters (see Section ).
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compartments (see Section <a href="#compartments">3.2.1</a>),
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species (see Section <a href="#species">3.2.2</a>),
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reactions (see Section <a href="#reactions">3.2.3</a>), and
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parameters (see Section <a href="#parameters">3.2.4</a>).
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This tab also includes the Model ID which is fixed to be the same as
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the filename as well as the Model Name which can be used to provide an
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arbitrary string description of the model.
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@ -650,10 +742,10 @@ As shown below, a parameter includes the following:
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<div class="p"><!----></div>
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The Definitions/Types tab shown below allows users to provide
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function definitions (see Section ),
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unit definitions (see Section ),
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compartment types (see Section ), and
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species types (see Section ).
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function definitions (see Section <a href="#funcDefn">3.3.1</a>),
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unit definitions (see Section <a href="#unitDefn">3.3.2</a>),
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compartment types (see Section <a href="#compTypes">3.3.3</a>), and
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species types (see Section <a href="#specTypes">3.3.4</a>).
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<center>
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<img src="screenshots/DefnTypes.png" alt="screenshots/DefnTypes.png" />
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@ -761,10 +853,10 @@ species type includes an ID and an optional name field.
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<div class="p"><!----></div>
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The <tt>Initial Assignments/Rules/Constraints/Events</tt>
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tab as shown below allows users to provide initial assignments
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(see Section ),
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rules (see Section ),
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constraints (see Section ), and
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events (see Section ).
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(see Section <a href="#initials">3.4.1</a>),
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rules (see Section <a href="#rules">3.4.2</a>),
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constraints (see Section <a href="#constraints">3.4.3</a>), and
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events (see Section <a href="#events">3.4.4</a>).
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<center>
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<img src="screenshots/IRCE.png" alt="screenshots/IRCE.png" />
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@ -884,12 +976,12 @@ assignment.
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<div class="p"><!----></div>
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The GCM editor shown below allows the user to create or modify a GCM
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(see Section ). A GCM is a compact graphical representation
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(see Section <a href="#GCM">10</a>). A GCM is a compact graphical representation
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of a genetic circuit which can later be synthesized into an SBML model.
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A GCM includes promoters (see Section ),
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GCM species (see Section ),
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influences (see Section ),
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GCM parameters (see Section ), and an optional
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A GCM includes promoters (see Section <a href="#Promoters">4.1</a>),
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GCM species (see Section <a href="#GCMSpecies">4.2</a>),
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influences (see Section <a href="#Influences">4.3</a>),
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GCM parameters (see Section <a href="#GCMParameters">4.4</a>), and an optional
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SBML file. GCM species, influences,
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and promoters can be added, removed, or edited. Parameters can only be edited.
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An SBML file can also be selected to merge with the SBML generated from a GCM.
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@ -1042,7 +1134,7 @@ allows the user an easy way to change all the parameter values in
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a convenient location. If a parameter in the GCM is set to
|
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default, it will use the value found in the GCM parameter list.
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These defaults can be modified in the user preferences
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(see Section ). The GCM parameters are listed below:
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(see Section <a href="#Preferences">9</a>). The GCM parameters are listed below:
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<div class="p"><!----></div>
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@ -1091,11 +1183,11 @@ factor </td></tr>
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<div class="p"><!----></div>
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The analysis view is used to analyze biochemical reaction
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network models. The analysis view as shown below includes tabs for
|
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simulation options (see Section ),
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abstraction options (see Section ),
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a parameter editor (see Section ),
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a TSD graph editor (see Section ), and a
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probability graph editor (see Section ).
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simulation options (see Section <a href="#simOptions">5.1</a>),
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abstraction options (see Section <a href="#absOptions">5.2</a>),
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a parameter editor (see Section <a href="#paramEdit">5.3</a>),
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a TSD graph editor (see Section <a href="#TSDEdit">7</a>), and a
|
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probability graph editor (see Section <a href="#ProbEdit">8</a>).
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<center>
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<img src="screenshots/analysisView.png" alt="screenshots/analysisView.png" />
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@ -1276,9 +1368,9 @@ to their stop value.
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<div class="p"><!----></div>
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The learn view is used to discover genetic circuit
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connectivity from time series data. The learn view includes tabs
|
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for a data manager (see Section ),
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a learn tool (see Section ), and a
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TSD graph editor (see Section ).
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for a data manager (see Section <a href="#dataManager">6.1</a>),
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a learn tool (see Section <a href="#learnTool">6.2</a>), and a
|
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TSD graph editor (see Section <a href="#TSDEdit">7</a>).
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<div class="p"><!----></div>
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<h3><a name="tth_sEc6.1">
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@ -1301,7 +1393,7 @@ current project, and data from the selected view will be copied
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into this learn view. Finally, the Import button brings up a file
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browser, and it allows you to import a data file from outside
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this project. These files can be in time series data (TSD) format
|
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(see Section ), comma separated value (CSV) format, or tab
|
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(see Section <a href="#TSD">11</a>), comma separated value (CSV) format, or tab
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delimited format (DAT).
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<div class="p"><!----></div>
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@ -1330,7 +1422,7 @@ Barker's PhD dissertation (UofUtah 2007)
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. To use this learn tool, adjust
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any options described below, if desired, then press the Save and
|
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Learn button. The resulting genetic circuit is specified using
|
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our Genetic Circuit Model (GCM) Format (see Section ) and is shown
|
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our Genetic Circuit Model (GCM) Format (see Section <a href="#GCM">10</a>) and is shown
|
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graphically using GraphViz's Dotty tool. On this tab, there are also
|
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buttons to save the parameters without learning, view the last learned
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circuit, save the generated circuit into the project, and view the last run
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@ -1609,7 +1701,7 @@ supported file types are:
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<div class="p"><!----></div>
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</li>
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<li> tsd - time series data format (see Section ).
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<li> tsd - time series data format (see Section <a href="#TSD">11</a>).
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<div class="p"><!----></div>
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</li>
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</ul>
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@ -2080,5 +2172,5 @@ Biology in Trento, Italy.
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|||
T<sub><font size="-1">E</font></sub>X
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by <a href="http://hutchinson.belmont.ma.us/tth/">
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||||
T<sub><font size="-1">T</font></sub>H</a>,
|
||||
version 3.81.<br />On 16 Mar 2011, 18:23.</small>
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||||
version 3.81.<br />On 16 Mar 2011, 19:20.</small>
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||||
</html>
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|
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|
@ -7,13 +7,13 @@
|
|||
|
||||
\usepackage{indentfirst,graphics,alltt,epsfig,color}
|
||||
|
||||
\title{LEMA: User's Manual}
|
||||
\title{ATACS User's Manual}
|
||||
|
||||
\author{Chris J. Myers, Kevin Jones, Scott Little, Nicholas Seegmiller, Robert Thacker, David Walter}
|
||||
|
||||
\date{Created: February 20th, 2009\\
|
||||
Last Revised: February 20th, 2009
|
||||
}
|
||||
% \date{Created: February 20th, 2009\\
|
||||
% Last Revised: February 20th, 2009
|
||||
% }
|
||||
|
||||
\begin{document}
|
||||
|
||||
|
|
|
|||
122
docs/LEMA.html
122
docs/LEMA.html
|
|
@ -14,9 +14,9 @@
|
|||
|
||||
|
||||
|
||||
<title> LEMA: User's Manual</title>
|
||||
<title> LEMA User's Manual</title>
|
||||
|
||||
<h1 align="center">LEMA: User's Manual </h1>
|
||||
<h1 align="center">LEMA User's Manual </h1>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
|
|
@ -24,11 +24,71 @@
|
|||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
<h3 align="center">Created: February 20th, 2009<br />
|
||||
Last Revised: March 13th, 2009
|
||||
</h3>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
<h1>Contents </h1><a href="#tth_sEc1"
|
||||
>1 Introduction</a><br />
|
||||
<a href="#tth_sEc2"
|
||||
>2 Project Management</a><br />
|
||||
<a href="#tth_sEc2.1"
|
||||
>2.1 Creating and Opening Projects</a><br />
|
||||
<a href="#tth_sEc2.2"
|
||||
>2.2 Creating Models and Graphs</a><br />
|
||||
<a href="#tth_sEc2.3"
|
||||
>2.3 Importing Models</a><br />
|
||||
<a href="#tth_sEc2.4"
|
||||
>2.4 Editing Project Objects</a><br />
|
||||
<a href="#tth_sEc2.5"
|
||||
>2.5 Viewing Project Objects</a><br />
|
||||
<a href="#tth_sEc2.6"
|
||||
>2.6 Creating Tool Views</a><br />
|
||||
<a href="#tth_sEc3"
|
||||
>3 LHPN Editor</a><br />
|
||||
<a href="#tth_sEc3.1"
|
||||
>3.1 Places</a><br />
|
||||
<a href="#tth_sEc3.2"
|
||||
>3.2 Transitions</a><br />
|
||||
<a href="#tth_sEc3.2.1"
|
||||
>3.2.1 Assignments</a><br />
|
||||
<a href="#tth_sEc3.3"
|
||||
>3.3 Variables</a><br />
|
||||
<a href="#tth_sEc3.4"
|
||||
>3.4 Control Flow</a><br />
|
||||
<a href="#tth_sEc4"
|
||||
>4 Text Editor</a><br />
|
||||
<a href="#tth_sEc5"
|
||||
>5 Verification View</a><br />
|
||||
<a href="#tth_sEc5.1"
|
||||
>5.1 Basic Options</a><br />
|
||||
<a href="#tth_sEc5.2"
|
||||
>5.2 Advanced Options</a><br />
|
||||
<a href="#tth_sEc6"
|
||||
>6 Learn View</a><br />
|
||||
<a href="#tth_sEc6.1"
|
||||
>6.1 Data Manager</a><br />
|
||||
<a href="#tth_sEc6.2"
|
||||
>6.2 Learn Tool</a><br />
|
||||
<a href="#tth_sEc6.2.1"
|
||||
>6.2.1 Basic Options</a><br />
|
||||
<a href="#tth_sEc6.2.2"
|
||||
>6.2.2 Advanced Options</a><br />
|
||||
<a href="#tth_sEc7"
|
||||
>7 TSD Graph Editor</a><br />
|
||||
<a href="#tth_sEc8"
|
||||
>8 Preferences</a><br />
|
||||
<a href="#tth_sEc9"
|
||||
>9 Labeled Hybrid Petri Net Format</a><br />
|
||||
<a href="#tth_sEc10"
|
||||
>10 Time Series Data Format</a><br />
|
||||
<a href="#tth_sEc11"
|
||||
>11 List of Hot Keys</a><br />
|
||||
<a href="#tth_sEc12"
|
||||
>12 Reporting Bugs and Feature Requests</a><br />
|
||||
<a href="#tth_sEc13"
|
||||
>13 Credits</a><br />
|
||||
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
|
|
@ -122,15 +182,15 @@ new model or graph to add to the project. To create a new
|
|||
VHDL-AMS model, select New → VHDL-AMS Model from the
|
||||
File menu as shown below. You will then be prompted to give a model id. At this
|
||||
point, a simple text editor will open in a new tab. To create a new LHPN model
|
||||
(see Section ), select New → Labeled Hybrid Petri Net from
|
||||
(see Section <a href="#LHPN">9</a>), select New → Labeled Hybrid Petri Net from
|
||||
the File menu. You will then be prompted to give a model id. At this point, an
|
||||
LHPN editor (see Section ) will open in a new tab. To create a new
|
||||
LHPN editor (see Section <a href="#LHPNEdit">3</a>) will open in a new tab. To create a new
|
||||
Spice model, select New → Spice Circuit from the File menu. You
|
||||
will then be prompted to give a model id. At this point, a simple text editor
|
||||
will open in a new tab. To create a new TSD graph, select New → TSD
|
||||
Graph from the File menu. You will then
|
||||
be prompted to give a name to the TSD graph. At this point, a TSD graph editor
|
||||
(see Section ) will open in a new tab. Once a model or graph is
|
||||
(see Section <a href="#TSDEdit">7</a>) will open in a new tab. Once a model or graph is
|
||||
created, it can be opened again later by right clicking on the object in the
|
||||
project window and selecting "Edit", or alternatively
|
||||
double-clicking on the object.
|
||||
|
|
@ -167,16 +227,16 @@ All project objects can be modified by highlighting the object
|
|||
and using a right mouse click to open a menu of options as shown
|
||||
below. Using this menu, every type of object can be copied, renamed, or
|
||||
deleted. For an LHPN, the "View/Edit" option opens the
|
||||
model in an LHPN editor (see Section ). For a VHDL-AMS model,
|
||||
model in an LHPN editor (see Section <a href="#LHPNEdit">3</a>). For a VHDL-AMS model,
|
||||
the "View/Edit" option opens the model in a simple text editor. For a TSD
|
||||
graph, the "View/Edit"
|
||||
option opens the TSD graph in a TSD graph editor (see Section ).
|
||||
option opens the TSD graph in a TSD graph editor (see Section <a href="#TSDEdit">7</a>).
|
||||
For a probability graph, the "View/Edit" option opens
|
||||
the probability graph in a histogram editor
|
||||
(see Section ).
|
||||
For a verification view, the "Open Verification View" option opens the
|
||||
verification view (see Section ). For a learn view, the
|
||||
"Open Learn View" option opens the learn view (see Section ).
|
||||
verification view (see Section <a href="#Verification">5</a>). For a learn view, the
|
||||
"Open Learn View" option opens the learn view (see Section <a href="#Learn">6</a>).
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
|
|
@ -219,8 +279,8 @@ LHPN and viewed using the same "View Model" option.
|
|||
|
||||
<div class="p"><!----></div>
|
||||
To perform verification or learning, right click on a model and
|
||||
select "Create Verification View" (see Section )to perform
|
||||
analysis or "Create Learn View" (see Section )
|
||||
select "Create Verification View" (see Section <a href="#Verification">5</a>)to perform
|
||||
analysis or "Create Learn View" (see Section <a href="#Learn">6</a>)
|
||||
to perform learning. A verification or learn view may also be opened by
|
||||
selecting the model in the file tree and selecting Learn or Verification from
|
||||
the Tools menu. You will then be prompted to give a name to
|
||||
|
|
@ -250,10 +310,10 @@ automatically created for verification.
|
|||
<div class="p"><!----></div>
|
||||
The LHPN editor as shown below allows the user to create or modify an LHPN
|
||||
model of an analog or mixed-signal circuit. An LHPN model includes
|
||||
places (see Section ),
|
||||
transitions (see Section ),
|
||||
variables (see Section ), and
|
||||
control flow (see Section ).
|
||||
places (see Section <a href="#places">3.1</a>),
|
||||
transitions (see Section <a href="#transitions">3.2</a>),
|
||||
variables (see Section <a href="#variables">3.3</a>), and
|
||||
control flow (see Section <a href="#controlFlow">3.4</a>).
|
||||
Each of these items can be added, removed, or edited.
|
||||
To add a new item, click on the appropriate add button. You
|
||||
will then be prompted to provide a unique id and some properties
|
||||
|
|
@ -496,8 +556,8 @@ editor.
|
|||
<div class="p"><!----></div>
|
||||
The verification view is used to verify the property stated in the LHPN model.
|
||||
The verification view as shown below includes tabs for
|
||||
basic options (see Section ), and
|
||||
advanced options (see Section ).
|
||||
basic options (see Section <a href="#basOptions">5.1</a>), and
|
||||
advanced options (see Section <a href="#advOptions">5.2</a>).
|
||||
|
||||
<center>
|
||||
<img src="screenshots/verificationView.png" alt="screenshots/verificationView.png" />
|
||||
|
|
@ -659,9 +719,9 @@ The other advanced options include
|
|||
|
||||
<div class="p"><!----></div>
|
||||
The learn view is used to generate an LHPN from time series data. The learn
|
||||
view includes tabs for a data manager (see Section ),
|
||||
a learn tool (see Section ), and a
|
||||
TSD graph editor (see Section ).
|
||||
view includes tabs for a data manager (see Section <a href="#dataManager">6.1</a>),
|
||||
a learn tool (see Section <a href="#learnTool">6.2</a>), and a
|
||||
TSD graph editor (see Section <a href="#TSDEdit">7</a>).
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<h3><a name="tth_sEc6.1">
|
||||
|
|
@ -684,7 +744,7 @@ current project, and data from the selected view will be copied
|
|||
into this learn view. Finally, the Import button brings up a file
|
||||
browser, and it allows you to import a data file from outside
|
||||
this project. These files can be in time series data (TSD) format
|
||||
(see Section ), comma separated value (CSV) format, or tab
|
||||
(see Section <a href="#TSD">10</a>), comma separated value (CSV) format, or tab
|
||||
delimited format (DAT).
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
|
@ -709,12 +769,12 @@ to record your changes.
|
|||
The learn tool is used to generate abstract models from the
|
||||
simulation data entered through the data manager described above. To
|
||||
use this learn tool, adjust the basic options(see Section
|
||||
) and advanced options(see Section
|
||||
), if desired, then press the Save and Learn button.
|
||||
<a href="#learnBasOptions">6.2.1</a>) and advanced options(see Section
|
||||
<a href="#learnAdvOptions">6.2.2</a>), if desired, then press the Save and Learn button.
|
||||
The resulting abstract models in the form of Labeled Hybrid Petri Net
|
||||
(see Section ),VHDL-AMS and Verilog-AMS can be viewed by
|
||||
(see Section <a href="#LHPN">9</a>),VHDL-AMS and Verilog-AMS can be viewed by
|
||||
clicking appropriate options in the View Menu. The resulting circuit is
|
||||
specified using our Labeled Hybrid Petri Net Format (see Section )
|
||||
specified using our Labeled Hybrid Petri Net Format (see Section <a href="#LHPN">9</a>)
|
||||
and is shown graphically using GraphViz's Dotty tool. There are also
|
||||
menu options to save the parameters without learning, view the last learned
|
||||
models, save the generated models into the project, and view the last run
|
||||
|
|
@ -1008,7 +1068,7 @@ supported file types are:
|
|||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> tsd - time series data format (see Section ).
|
||||
<li> tsd - time series data format (see Section <a href="#TSD">10</a>).
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
</ul>
|
||||
|
|
@ -1351,5 +1411,5 @@ Virginia State University.
|
|||
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 16 Mar 2011, 18:23.</small>
|
||||
version 3.81.<br />On 16 Mar 2011, 19:20.</small>
|
||||
</html>
|
||||
|
|
|
|||
BIN
docs/LEMA.pdf
BIN
docs/LEMA.pdf
Binary file not shown.
|
|
@ -7,13 +7,13 @@
|
|||
|
||||
\usepackage{indentfirst,graphics,alltt,epsfig,color}
|
||||
|
||||
\title{LEMA: User's Manual}
|
||||
\title{LEMA User's Manual}
|
||||
|
||||
\author{Chris J. Myers, Satish Batchu, Kevin Jones, Scott Little, Nicholas Seegmiller, Robert Thacker, David Walter, Zhen Zhang}
|
||||
|
||||
\date{Created: February 20th, 2009\\
|
||||
Last Revised: March 13th, 2009
|
||||
}
|
||||
% \date{Created: February 20th, 2009\\
|
||||
% Last Revised: March 13th, 2009
|
||||
% }
|
||||
|
||||
\begin{document}
|
||||
|
||||
|
|
|
|||
|
|
@ -14,9 +14,9 @@
|
|||
|
||||
|
||||
|
||||
<title> iBioSim: User's Manual</title>
|
||||
<title> iBioSim User's Manual</title>
|
||||
|
||||
<h1 align="center">iBioSim: User's Manual </h1>
|
||||
<h1 align="center">iBioSim User's Manual </h1>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
|
|
@ -25,11 +25,103 @@
|
|||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
<h3 align="center">Created: August 6th, 2008<br />
|
||||
Last Revised: October 2, 2010
|
||||
</h3>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
<h1>Contents </h1><a href="#tth_sEc1"
|
||||
>1 Introduction</a><br />
|
||||
<a href="#tth_sEc2"
|
||||
>2 Project Management</a><br />
|
||||
<a href="#tth_sEc2.1"
|
||||
>2.1 Creating and Opening Projects</a><br />
|
||||
<a href="#tth_sEc2.2"
|
||||
>2.2 Creating Models and Graphs</a><br />
|
||||
<a href="#tth_sEc2.3"
|
||||
>2.3 Importing Models</a><br />
|
||||
<a href="#tth_sEc2.4"
|
||||
>2.4 Editing Project Objects</a><br />
|
||||
<a href="#tth_sEc2.5"
|
||||
>2.5 Viewing Project Objects</a><br />
|
||||
<a href="#tth_sEc2.6"
|
||||
>2.6 Creating Tool Views</a><br />
|
||||
<a href="#tth_sEc3"
|
||||
>3 SBML Editor</a><br />
|
||||
<a href="#tth_sEc3.1"
|
||||
>3.1 SBML Math Formulas</a><br />
|
||||
<a href="#tth_sEc3.2"
|
||||
>3.2 Main Elements</a><br />
|
||||
<a href="#tth_sEc3.2.1"
|
||||
>3.2.1 Compartments</a><br />
|
||||
<a href="#tth_sEc3.2.2"
|
||||
>3.2.2 Species</a><br />
|
||||
<a href="#tth_sEc3.2.3"
|
||||
>3.2.3 Reactions</a><br />
|
||||
<a href="#tth_sEc3.2.4"
|
||||
>3.2.4 Global Parameters</a><br />
|
||||
<a href="#tth_sEc3.3"
|
||||
>3.3 Definitions/Types</a><br />
|
||||
<a href="#tth_sEc3.3.1"
|
||||
>3.3.1 Function Definitions</a><br />
|
||||
<a href="#tth_sEc3.3.2"
|
||||
>3.3.2 Unit Definitions</a><br />
|
||||
<a href="#tth_sEc3.3.3"
|
||||
>3.3.3 Compartment Types</a><br />
|
||||
<a href="#tth_sEc3.3.4"
|
||||
>3.3.4 Species Types</a><br />
|
||||
<a href="#tth_sEc3.4"
|
||||
>3.4 Initial Assignments/Rules/Constraints/Events</a><br />
|
||||
<a href="#tth_sEc3.4.1"
|
||||
>3.4.1 Initial Assignments</a><br />
|
||||
<a href="#tth_sEc3.4.2"
|
||||
>3.4.2 Rules</a><br />
|
||||
<a href="#tth_sEc3.4.3"
|
||||
>3.4.3 Constraints</a><br />
|
||||
<a href="#tth_sEc3.4.4"
|
||||
>3.4.4 Events</a><br />
|
||||
<a href="#tth_sEc4"
|
||||
>4 GCM Editor</a><br />
|
||||
<a href="#tth_sEc4.1"
|
||||
>4.1 Promoters</a><br />
|
||||
<a href="#tth_sEc4.2"
|
||||
>4.2 GCM Species</a><br />
|
||||
<a href="#tth_sEc4.3"
|
||||
>4.3 Influences</a><br />
|
||||
<a href="#tth_sEc4.4"
|
||||
>4.4 GCM Parameters</a><br />
|
||||
<a href="#tth_sEc4.5"
|
||||
>4.5 GCM Components</a><br />
|
||||
<a href="#tth_sEc5"
|
||||
>5 Analysis View</a><br />
|
||||
<a href="#tth_sEc5.1"
|
||||
>5.1 Simulation Options</a><br />
|
||||
<a href="#tth_sEc5.2"
|
||||
>5.2 Abstraction Options</a><br />
|
||||
<a href="#tth_sEc5.3"
|
||||
>5.3 Parameter Editor</a><br />
|
||||
<a href="#tth_sEc6"
|
||||
>6 Learn View</a><br />
|
||||
<a href="#tth_sEc6.1"
|
||||
>6.1 Data Manager</a><br />
|
||||
<a href="#tth_sEc6.2"
|
||||
>6.2 Learn Tool</a><br />
|
||||
<a href="#tth_sEc7"
|
||||
>7 TSD Graph Editor</a><br />
|
||||
<a href="#tth_sEc8"
|
||||
>8 Probability Graph Editor</a><br />
|
||||
<a href="#tth_sEc9"
|
||||
>9 Preferences</a><br />
|
||||
<a href="#tth_sEc10"
|
||||
>10 Genetic Circuit Model Format</a><br />
|
||||
<a href="#tth_sEc11"
|
||||
>11 Time Series Data Format</a><br />
|
||||
<a href="#tth_sEc12"
|
||||
>12 Tutorial</a><br />
|
||||
<a href="#tth_sEc13"
|
||||
>13 Reporting Bugs and Feature Requests</a><br />
|
||||
<a href="#tth_sEc14"
|
||||
>14 Credits</a><br />
|
||||
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
|
|
@ -142,20 +234,20 @@ down menu shown below.
|
|||
<div class="p"><!----></div>
|
||||
After you have created or opened a project, you can create a
|
||||
new model or graph to add to the project. To create a new
|
||||
Genetic Circuit Model (see Section ), select
|
||||
Genetic Circuit Model (see Section <a href="#GCM">10</a>), select
|
||||
New → Genetic Circuit Model from the
|
||||
File menu as shown below. You will then be prompted to give a model id. At this
|
||||
point, a GCM editor (see Section ) will open in a new
|
||||
point, a GCM editor (see Section <a href="#GCMEdit">4</a>) will open in a new
|
||||
tab. To create a new SBML model, select New → SBML Model
|
||||
from the File menu. You will then be prompted to give a model id.
|
||||
At this point, an SBML editor (see Section ) will open
|
||||
At this point, an SBML editor (see Section <a href="#SBMLEdit">3</a>) will open
|
||||
in a new tab. To create a new TSD graph, select New → TSD Graph
|
||||
from the File menu. You will then be prompted to give a name to
|
||||
the TSD graph. At this point, a TSD graph editor (see Section )
|
||||
the TSD graph. At this point, a TSD graph editor (see Section <a href="#TSDEdit">7</a>)
|
||||
will open in a new tab. To create a new probability graph, select
|
||||
New → Probability Graph from the File menu. You will then
|
||||
be prompted to give a name to the probability graph. At this point, a
|
||||
probability graph editor (see Section )
|
||||
probability graph editor (see Section <a href="#ProbEdit">8</a>)
|
||||
will open in a new tab. Once a model or graph is created, it can
|
||||
be opened again later by right clicking on the object in the
|
||||
project window and selecting "Edit", or alternatively
|
||||
|
|
@ -199,16 +291,16 @@ and using a right mouse click to open a menu of options as shown
|
|||
below. Using this menu, every type of object can be copied, renamed, or
|
||||
deleted (these actions can also be done from the Edit menu).
|
||||
For a GCM, the "View/Edit" option opens the
|
||||
model in a GCM editor (see Section ). For an SBML model,
|
||||
model in a GCM editor (see Section <a href="#GCMEdit">4</a>). For an SBML model,
|
||||
the "View/Edit" option opens the model in an SBML editor
|
||||
(see Section ). For a TSD graph, the "View/Edit"
|
||||
option opens the TSD graph in a TSD graph editor (see Section ).
|
||||
(see Section <a href="#SBMLEdit">3</a>). For a TSD graph, the "View/Edit"
|
||||
option opens the TSD graph in a TSD graph editor (see Section <a href="#TSDEdit">7</a>).
|
||||
For a probability graph, the "View/Edit" option opens
|
||||
the probability graph in a probability graph editor
|
||||
(see Section ).
|
||||
(see Section <a href="#ProbEdit">8</a>).
|
||||
For an analysis view, the "Open Analysis View" option opens the
|
||||
analysis view (see Section ). For a learn view, the
|
||||
"Open Learn View" option opens the learn view (see Section ).
|
||||
analysis view (see Section <a href="#Analysis">5</a>). For a learn view, the
|
||||
"Open Learn View" option opens the learn view (see Section <a href="#Learn">6</a>).
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
|
|
@ -258,8 +350,8 @@ View → Model sub-menu.
|
|||
|
||||
<div class="p"><!----></div>
|
||||
To perform analysis or learning, right click on a model and
|
||||
select "Create Analysis View" (see Section )
|
||||
to perform analysis or "Create Learn View" (see Section )
|
||||
select "Create Analysis View" (see Section <a href="#Analysis">5</a>)
|
||||
to perform analysis or "Create Learn View" (see Section <a href="#Learn">6</a>)
|
||||
to perform learning. You will then be prompted to give a name to
|
||||
your analysis or learn view. After a name is entered, a tab with
|
||||
the newly created view will open. Views can also be created using the
|
||||
|
|
@ -283,8 +375,8 @@ analysis view, you can edit the initial concentrations and
|
|||
parameters. However, if you wish to be able to edit the
|
||||
structure, you should first create an SBML model using Create
|
||||
SBML Model option in the right click menu or the Save as SBML button in
|
||||
the GCM Editor (see Section ). You can then open and
|
||||
edit this model using an SBML editor (see Section ) and
|
||||
the GCM Editor (see Section <a href="#GCMEdit">4</a>). You can then open and
|
||||
edit this model using an SBML editor (see Section <a href="#SBMLEdit">3</a>) and
|
||||
create an analysis view from this edited model.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
|
@ -295,18 +387,18 @@ create an analysis view from this edited model.
|
|||
<div class="p"><!----></div>
|
||||
The SBML editor as shown below allows the user to create or modify an SBML
|
||||
model of a biochemical reaction network. An SBML model includes
|
||||
compartments (see Section ),
|
||||
species (see Section ),
|
||||
reactions (see Section ),
|
||||
parameters (see Section ),
|
||||
function definitions (see Section ),
|
||||
unit definitions (see Section ),
|
||||
compartment types (see Section ),
|
||||
species types (see Section ),
|
||||
initial assignments (see Section ),
|
||||
rules (see Section ),
|
||||
constraints (see Section ), and
|
||||
events (see Section ).
|
||||
compartments (see Section <a href="#compartments">3.2.1</a>),
|
||||
species (see Section <a href="#species">3.2.2</a>),
|
||||
reactions (see Section <a href="#reactions">3.2.3</a>),
|
||||
parameters (see Section <a href="#parameters">3.2.4</a>),
|
||||
function definitions (see Section <a href="#funcDefn">3.3.1</a>),
|
||||
unit definitions (see Section <a href="#unitDefn">3.3.2</a>),
|
||||
compartment types (see Section <a href="#compTypes">3.3.3</a>),
|
||||
species types (see Section <a href="#specTypes">3.3.4</a>),
|
||||
initial assignments (see Section <a href="#initials">3.4.1</a>),
|
||||
rules (see Section <a href="#rules">3.4.2</a>),
|
||||
constraints (see Section <a href="#constraints">3.4.3</a>), and
|
||||
events (see Section <a href="#events">3.4.4</a>).
|
||||
Each of these items can be added, removed, or edited.
|
||||
To add a new item, click on the appropriate add button. You
|
||||
will then be prompted to provide a unique id and some properties
|
||||
|
|
@ -329,7 +421,7 @@ Note that many checks are done on the fly, so it should be difficult
|
|||
to create models with consistency problems. However, if a user does
|
||||
not wish to be warned about undeclared units or does not wish to have
|
||||
units checked at all can set preferences to turn this off
|
||||
(see Section ). The save and check button
|
||||
(see Section <a href="#Preferences">9</a>). The save and check button
|
||||
though will still present all the unit warnings and errors.
|
||||
Finally, the disk with a pencil icon can be used to store the
|
||||
model, but in this case, a new model ID will be requested and the
|
||||
|
|
@ -431,10 +523,10 @@ math formula:
|
|||
|
||||
<div class="p"><!----></div>
|
||||
This Main Elements tab shown below is used to specify
|
||||
compartments (see Section ),
|
||||
species (see Section ),
|
||||
reactions (see Section ), and
|
||||
parameters (see Section ).
|
||||
compartments (see Section <a href="#compartments">3.2.1</a>),
|
||||
species (see Section <a href="#species">3.2.2</a>),
|
||||
reactions (see Section <a href="#reactions">3.2.3</a>), and
|
||||
parameters (see Section <a href="#parameters">3.2.4</a>).
|
||||
This tab also includes the Model ID which is fixed to be the same as
|
||||
the filename as well as the Model Name which can be used to provide an
|
||||
arbitrary string description of the model.
|
||||
|
|
@ -676,10 +768,10 @@ As shown below, a parameter includes the following:
|
|||
|
||||
<div class="p"><!----></div>
|
||||
The Definitions/Types tab shown below allows users to provide
|
||||
function definitions (see Section ),
|
||||
unit definitions (see Section ),
|
||||
compartment types (see Section ), and
|
||||
species types (see Section ).
|
||||
function definitions (see Section <a href="#funcDefn">3.3.1</a>),
|
||||
unit definitions (see Section <a href="#unitDefn">3.3.2</a>),
|
||||
compartment types (see Section <a href="#compTypes">3.3.3</a>), and
|
||||
species types (see Section <a href="#specTypes">3.3.4</a>).
|
||||
|
||||
<center>
|
||||
<img src="screenshots/DefnTypes.png" alt="screenshots/DefnTypes.png" />
|
||||
|
|
@ -787,10 +879,10 @@ species type includes an ID and an optional name field.
|
|||
<div class="p"><!----></div>
|
||||
The <tt>Initial Assignments/Rules/Constraints/Events</tt>
|
||||
tab as shown below allows users to provide initial assignments
|
||||
(see Section ),
|
||||
rules (see Section ),
|
||||
constraints (see Section ), and
|
||||
events (see Section ).
|
||||
(see Section <a href="#initials">3.4.1</a>),
|
||||
rules (see Section <a href="#rules">3.4.2</a>),
|
||||
constraints (see Section <a href="#constraints">3.4.3</a>), and
|
||||
events (see Section <a href="#events">3.4.4</a>).
|
||||
|
||||
<center>
|
||||
<img src="screenshots/IRCE.png" alt="screenshots/IRCE.png" />
|
||||
|
|
@ -910,12 +1002,12 @@ assignment.
|
|||
|
||||
<div class="p"><!----></div>
|
||||
The GCM editor shown below allows the user to create or modify a GCM
|
||||
(see Section ). A GCM is a compact graphical representation
|
||||
(see Section <a href="#GCM">10</a>). A GCM is a compact graphical representation
|
||||
of a genetic circuit which can later be synthesized into an SBML model.
|
||||
A GCM includes promoters (see Section ),
|
||||
GCM species (see Section ),
|
||||
influences (see Section ),
|
||||
GCM parameters (see Section ), and an optional
|
||||
A GCM includes promoters (see Section <a href="#Promoters">4.1</a>),
|
||||
GCM species (see Section <a href="#GCMSpecies">4.2</a>),
|
||||
influences (see Section <a href="#Influences">4.3</a>),
|
||||
GCM parameters (see Section <a href="#GCMParameters">4.4</a>), and an optional
|
||||
SBML file. GCM species, influences,
|
||||
and promoters can be added, removed, or edited. Parameters can only be edited.
|
||||
An SBML file can also be selected to merge with the SBML generated from a GCM.
|
||||
|
|
@ -1070,7 +1162,7 @@ allows the user an easy way to change all the parameter values in
|
|||
a convenient location. If a parameter in the GCM is set to
|
||||
default, it will use the value found in the GCM parameter list.
|
||||
These defaults can be modified in the user preferences
|
||||
(see Section ). The GCM parameters are listed below:
|
||||
(see Section <a href="#Preferences">9</a>). The GCM parameters are listed below:
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
|
|
@ -1154,11 +1246,11 @@ associated.
|
|||
<div class="p"><!----></div>
|
||||
The analysis view is used to analyze biochemical reaction
|
||||
network models. The analysis view as shown below includes tabs for
|
||||
simulation options (see Section ),
|
||||
abstraction options (see Section ),
|
||||
a parameter editor (see Section ),
|
||||
a TSD graph editor (see Section ), and a
|
||||
probability graph editor (see Section ).
|
||||
simulation options (see Section <a href="#simOptions">5.1</a>),
|
||||
abstraction options (see Section <a href="#absOptions">5.2</a>),
|
||||
a parameter editor (see Section <a href="#paramEdit">5.3</a>),
|
||||
a TSD graph editor (see Section <a href="#TSDEdit">7</a>), and a
|
||||
probability graph editor (see Section <a href="#ProbEdit">8</a>).
|
||||
The disk icon in the upper-left is used to save the simulation options
|
||||
while the play button icon is used to run the simulation.
|
||||
|
||||
|
|
@ -1346,9 +1438,9 @@ to their stop value.
|
|||
<div class="p"><!----></div>
|
||||
The learn view is used to discover genetic circuit
|
||||
connectivity from time series data. The learn view includes tabs
|
||||
for a data manager (see Section ),
|
||||
a learn tool (see Section ), and a
|
||||
TSD graph editor (see Section ).
|
||||
for a data manager (see Section <a href="#dataManager">6.1</a>),
|
||||
a learn tool (see Section <a href="#learnTool">6.2</a>), and a
|
||||
TSD graph editor (see Section <a href="#TSDEdit">7</a>).
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<h3><a name="tth_sEc6.1">
|
||||
|
|
@ -1371,7 +1463,7 @@ current project, and data from the selected view will be copied
|
|||
into this learn view. Finally, the Import button brings up a file
|
||||
browser, and it allows you to import a data file from outside
|
||||
this project. These files can be in time series data (TSD) format
|
||||
(see Section ), comma separated value (CSV) format, or tab
|
||||
(see Section <a href="#TSD">11</a>), comma separated value (CSV) format, or tab
|
||||
delimited format (DAT).
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
|
@ -1400,7 +1492,7 @@ Barker's PhD dissertation (UofUtah 2007)
|
|||
. To use this learn tool, adjust
|
||||
any options described below, if desired, then press the play button
|
||||
icon. The resulting genetic circuit is specified using
|
||||
our Genetic Circuit Model (GCM) Format (see Section ) and is shown
|
||||
our Genetic Circuit Model (GCM) Format (see Section <a href="#GCM">10</a>) and is shown
|
||||
graphically using GraphViz's Dotty tool. On this tab, one can also
|
||||
save the parameters without learning, view the last learned
|
||||
circuit, save the generated circuit into the project, and view the last run
|
||||
|
|
@ -1679,7 +1771,7 @@ supported file types are:
|
|||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> tsd - time series data format (see Section ).
|
||||
<li> tsd - time series data format (see Section <a href="#TSD">11</a>).
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
</ul>
|
||||
|
|
@ -2088,5 +2180,5 @@ the University of Texas in Austin.
|
|||
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 16 Mar 2011, 18:22.</small>
|
||||
version 3.81.<br />On 16 Mar 2011, 19:20.</small>
|
||||
</html>
|
||||
|
|
|
|||
BIN
docs/iBioSim.pdf
BIN
docs/iBioSim.pdf
Binary file not shown.
|
|
@ -7,14 +7,14 @@
|
|||
|
||||
\usepackage{indentfirst,graphics,alltt,epsfig,color}
|
||||
|
||||
\title{iBioSim: User's Manual}
|
||||
\title{iBioSim User's Manual}
|
||||
|
||||
\author{Chris J. Myers, Nathan Barker, Kevin Jones, Hiroyuki Kuwahara,\\ Curtis
|
||||
Madsen, Nam Nguyen, Nicolas Roehner, Tyler Patterson}
|
||||
|
||||
\date{Created: August 6th, 2008\\
|
||||
Last Revised: October 2, 2010
|
||||
}
|
||||
% \date{Created: August 6th, 2008\\
|
||||
% Last Revised: October 2, 2010
|
||||
% }
|
||||
|
||||
\begin{document}
|
||||
|
||||
|
|
|
|||
|
|
@ -14,9 +14,9 @@
|
|||
|
||||
|
||||
|
||||
<title> iBioSim: Installation Instructions</title>
|
||||
<title> iBioSim Installation Instructions</title>
|
||||
|
||||
<h1 align="center">iBioSim: Installation Instructions </h1>
|
||||
<h1 align="center">iBioSim Installation Instructions </h1>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
|
|
@ -24,11 +24,19 @@
|
|||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
<h3 align="center">Created: August 11th, 2008<br />
|
||||
Last Revised: August 14th, 2008
|
||||
</h3>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
<h1>Contents </h1><a href="#tth_sEc1"
|
||||
>1 General Requirements</a><br />
|
||||
<a href="#tth_sEc2"
|
||||
>2 Installation on Windows</a><br />
|
||||
<a href="#tth_sEc3"
|
||||
>3 Installation on Linux</a><br />
|
||||
<a href="#tth_sEc4"
|
||||
>4 Installation on MacOS</a><br />
|
||||
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
|
|
@ -208,5 +216,5 @@ double-clicking on it.
|
|||
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 16 Mar 2011, 18:23.</small>
|
||||
version 3.81.<br />On 16 Mar 2011, 19:20.</small>
|
||||
</html>
|
||||
|
|
|
|||
Binary file not shown.
|
|
@ -7,13 +7,13 @@
|
|||
|
||||
\usepackage{indentfirst,graphics,alltt,epsfig,color}
|
||||
|
||||
\title{iBioSim: Installation Instructions}
|
||||
\title{iBioSim Installation Instructions}
|
||||
|
||||
\author{Chris J. Myers}
|
||||
|
||||
\date{Created: August 11th, 2008\\
|
||||
Last Revised: August 14th, 2008
|
||||
}
|
||||
% \date{Created: August 11th, 2008\\
|
||||
% Last Revised: August 14th, 2008
|
||||
% }
|
||||
|
||||
\begin{document}
|
||||
|
||||
|
|
|
|||
731
docs/iBioSim_Tutorial.html
Normal file
731
docs/iBioSim_Tutorial.html
Normal file
|
|
@ -0,0 +1,731 @@
|
|||
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"
|
||||
"http://www.w3.org/TR/REC-html40/loose.dtd">
|
||||
<html>
|
||||
<meta name="GENERATOR" content="TtH 3.81">
|
||||
<style type="text/css"> div.p { margin-top: 7pt;}</style>
|
||||
<style type="text/css"><!--
|
||||
td div.comp { margin-top: -0.6ex; margin-bottom: -1ex;}
|
||||
td div.comb { margin-top: -0.6ex; margin-bottom: -.6ex;}
|
||||
td div.hrcomp { line-height: 0.9; margin-top: -0.8ex; margin-bottom: -1ex;}
|
||||
td div.norm {line-height:normal;}
|
||||
span.roman {font-family: serif; font-style: normal; font-weight: normal;}
|
||||
span.overacc2 {position: relative; left: .8em; top: -1.2ex;}
|
||||
span.overacc1 {position: relative; left: .6em; top: -1.2ex;} --></style>
|
||||
|
||||
|
||||
|
||||
<title> iBioSim Tutorial</title>
|
||||
|
||||
<h1 align="center">iBioSim Tutorial </h1>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
<h3 align="center">Chris J. Myers </h3>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
<h1>Contents </h1><a href="#tth_sEc1"
|
||||
>1 Introduction</a><br />
|
||||
<a href="#tth_sEc2"
|
||||
>2 SBML Editor</a><br />
|
||||
<a href="#tth_sEc3"
|
||||
>3 GCM Editor</a><br />
|
||||
<a href="#tth_sEc4"
|
||||
>4 Analysis</a><br />
|
||||
<a href="#tth_sEc5"
|
||||
>5 Probabilistic Analysis</a><br />
|
||||
<a href="#tth_sEc6"
|
||||
>6 GCM Learning</a><br />
|
||||
<a href="#tth_sEc7"
|
||||
>7 Genetic Circuit Design</a><br />
|
||||
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<h2><a name="tth_sEc1">
|
||||
1</a> Introduction</h2>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
The example described in this tutorial constructs a simple model for
|
||||
the <em>cI</em> and <em>cII</em> genes and the P<sub>R</sub> and P<sub>RE</sub>
|
||||
promoters from the phage λ decision circuit. This example
|
||||
illustrates many of the features of <tt>iBioSim</tt>.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<h2><a name="tth_sEc2">
|
||||
2</a> SBML Editor</h2>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
After starting <tt>iBioSim</tt>, complete the following steps to create
|
||||
an SBML model for this example:
|
||||
|
||||
<ol type="1">
|
||||
<li> Select <tt>File</tt> → <tt>New</tt> → <tt>Project</tt>.
|
||||
Browse to desired path and create a project named <tt>demo</tt>.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<img src="screenshots/project.png" alt="screenshots/project.png" />
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> Select <tt>File</tt> → <tt>New</tt> → <tt>SBML Model</tt>.
|
||||
Enter <tt>lambda</tt> as the SBML model ID at which point an SBML
|
||||
editor will open.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<img src="screenshots/newModel.png" alt="screenshots/newModel.png" />
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> Highlight the <tt>default</tt> compartment, select <tt>Edit
|
||||
Compartment</tt>, and change its ID to <tt>Cytoplasm</tt>. Also, change
|
||||
the units to <tt>volume</tt>.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<img src="screenshots/compartment.png" alt="screenshots/compartment.png" />
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> Select <tt>Add Species</tt> and enter <tt>CI</tt> as the ID,
|
||||
<tt>The lambda repressor</tt> as the name, change the units
|
||||
to <tt>mole</tt>, and set the <tt>Has Only Substance Units</tt> flag to
|
||||
true. Select <tt>Add Species</tt> again and enter <tt>CI2</tt> as the ID,
|
||||
<tt>CI dimer</tt> as the name, change the units to <tt>mole</tt>, and set the
|
||||
<tt>Has Only Substance Units</tt> flag to true.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<img src="screenshots/species.png" alt="screenshots/species.png" />
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> Select <tt>Add Parameter</tt> and enter <tt>nd</tt> as the ID,
|
||||
<tt>Number of molecules in dimer</tt> as the name, the value to be 2,
|
||||
and change the units to <tt>dimensionless</tt>.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<img src="screenshots/parameter.png" alt="screenshots/parameter.png" />
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> Select <tt>Definitions/Types</tt> tab, and select <tt>Add Unit</tt>
|
||||
and enter <tt>per_second</tt> as the ID. Select <tt>Add to List</tt>,
|
||||
select <tt>second</tt> as the kind, change the exponent to −1,
|
||||
and click <tt>Add</tt>. Click <tt>Add</tt> in the <tt>Unit Definition Editor</tt>.
|
||||
Repeat these steps to create a <tt>per_second_mole</tt> unit
|
||||
(i.e., (second)<sup>−1</sup>(mole)<sup>−1</sup>).
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<img src="screenshots/units.png" alt="screenshots/units.png" />
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> Select <tt>Main Elements</tt> tab. Select <tt>Add Reaction</tt> and
|
||||
enter <tt>Dimerize_CI</tt> as the ID, <tt>Reaction to dimerize CI</tt> as
|
||||
the name, and change reversible to <tt>true</tt>.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<img src="screenshots/reaction.png" alt="screenshots/reaction.png" />
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> Select <tt>Add Reactant</tt> and select <tt>CI</tt> as the species,
|
||||
change <tt>Stoichiometry</tt> to <tt>Stoichiometry math</tt>, and set its
|
||||
value to <tt>nd</tt>.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<img src="screenshots/reactant.png" alt="screenshots/reactant.png" />
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> Select <tt>Add Product</tt> and select <tt>CI2</tt> as the species.
|
||||
Leave the stoichiometry as 1.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<img src="screenshots/product.png" alt="screenshots/product.png" />
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> Highlight <tt>kf</tt> and select <tt>Edit Selected Parameter</tt>, change
|
||||
<tt>kf</tt> to <tt>k2f</tt>, and change the units to <tt>per_second_mole</tt>.
|
||||
Highlight <tt>kr</tt> and select <tt>Edit Selected Parameter</tt>, change
|
||||
<tt>kr</tt> to <tt>k2r</tt>, and change the units to <tt>per_second</tt>.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<img src="screenshots/localParam.png" alt="screenshots/localParam.png" />
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> Select <tt>Use Mass Action</tt>, select <tt>Add</tt>,
|
||||
and select <tt>Save and Check SBML</tt>. There should be no errors.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<img src="screenshots/kineticLaw.png" alt="screenshots/kineticLaw.png" />
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> Highlight <tt>lambda.sbml</tt>, using right mouse button, select
|
||||
<tt>View Network</tt>.
|
||||
Highlight <tt>lambda.sbml</tt>, using right mouse button, select
|
||||
<tt>View in Browser</tt>.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<img src="screenshots/viewNet.png" alt="screenshots/viewNet.png" /><br />
|
||||
|
||||
<table>
|
||||
<tr><td align="center"><img src="screenshots/viewNetwork.png" alt="screenshots/viewNetwork.png" /> </td><td align="center"><img src="screenshots/viewBrowser.png" alt="screenshots/viewBrowser.png" />
|
||||
</td></tr></table>
|
||||
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> Go back to the SBML editor complete the construction of the
|
||||
chemical reaction network shown below:
|
||||
|
||||
<br clear="all" /><table border="0" width="95%"><tr><td>
|
||||
<table border="0" cellspacing="0" cellpadding="0">
|
||||
<tr><td width="50%"></td><td nowrap="nowrap" align="right" colspan="1"><table border="0" cellspacing="0" cellpadding="2"><tr><td nowrap="nowrap" align="left">
|
||||
PRE + <span class="roman">RNAP</span> </td></tr></table></td><td nowrap="nowrap" align="left">
|
||||
<table border="0" cellspacing="0" cellpadding="2"><tr><td nowrap="nowrap" align="left">
|
||||
</td><td nowrap="nowrap" align="center">
|
||||
<small>KPRE2</small><!--sup
|
||||
--><br />↔ <br />
|
||||
<small></small> <br /></td><td nowrap="nowrap" align="center">
|
||||
</td></tr></table></td><td nowrap="nowrap" align="left">
|
||||
<table border="0" cellspacing="0" cellpadding="2"><tr><td nowrap="nowrap" align="left">
|
||||
PRE_<span class="roman">RNAP</span> </td></tr></table></td><td width="50%"></td></tr>
|
||||
<tr><td width="50%"></td><td nowrap="nowrap" align="right" colspan="1"><table border="0" cellspacing="0" cellpadding="2"><tr><td nowrap="nowrap" align="left">
|
||||
PRE + <span class="roman">CII</span> + <span class="roman">RNAP</span> </td></tr></table></td><td nowrap="nowrap" align="left">
|
||||
<table border="0" cellspacing="0" cellpadding="2"><tr><td nowrap="nowrap" align="left">
|
||||
</td><td nowrap="nowrap" align="center">
|
||||
<small>KPRE4</small><!--sup
|
||||
--><br />↔ <br />
|
||||
<small></small> <br /></td><td nowrap="nowrap" align="center">
|
||||
</td></tr></table></td><td nowrap="nowrap" align="left">
|
||||
<table border="0" cellspacing="0" cellpadding="2"><tr><td nowrap="nowrap" align="left">
|
||||
PRE_<span class="roman">CII</span>_<span class="roman">RNAP</span> </td></tr></table></td><td width="50%"></td></tr>
|
||||
<tr><td width="50%"></td><td nowrap="nowrap" align="right" colspan="1"><table border="0" cellspacing="0" cellpadding="2"><tr><td nowrap="nowrap" align="left">
|
||||
PRE_<span class="roman">RNAP</span> </td></tr></table></td><td nowrap="nowrap" align="left">
|
||||
<table border="0" cellspacing="0" cellpadding="2"><tr><td nowrap="nowrap" align="left">
|
||||
</td><td nowrap="nowrap" align="center">
|
||||
<small>kPREb</small><!--sup
|
||||
--><br />→ <br />
|
||||
<small></small> <br /></td><td nowrap="nowrap" align="center">
|
||||
</td></tr></table></td><td nowrap="nowrap" align="left">
|
||||
<table border="0" cellspacing="0" cellpadding="2"><tr><td nowrap="nowrap" align="left">
|
||||
PRE_<span class="roman">RNAP</span> + n<span class="roman">CI</span> </td></tr></table></td><td width="50%"></td></tr>
|
||||
<tr><td width="50%"></td><td nowrap="nowrap" align="right" colspan="1"><table border="0" cellspacing="0" cellpadding="2"><tr><td nowrap="nowrap" align="left">
|
||||
PRE_<span class="roman">CII</span>_<span class="roman">RNAP</span> </td></tr></table></td><td nowrap="nowrap" align="left">
|
||||
<table border="0" cellspacing="0" cellpadding="2"><tr><td nowrap="nowrap" align="left">
|
||||
</td><td nowrap="nowrap" align="center">
|
||||
<small>kPRE</small><!--sup
|
||||
--><br />→ <br />
|
||||
<small></small> <br /></td><td nowrap="nowrap" align="center">
|
||||
</td></tr></table></td><td nowrap="nowrap" align="left">
|
||||
<table border="0" cellspacing="0" cellpadding="2"><tr><td nowrap="nowrap" align="left">
|
||||
PRE_<span class="roman">CII</span>_<span class="roman">RNAP</span> + n<span class="roman">CI</span> </td></tr></table></td><td width="50%"></td></tr>
|
||||
<tr><td width="50%"></td><td nowrap="nowrap" align="right" colspan="1"><table border="0" cellspacing="0" cellpadding="2"><tr><td nowrap="nowrap" align="left">
|
||||
PR + <span class="roman">RNAP</span> </td></tr></table></td><td nowrap="nowrap" align="left">
|
||||
<table border="0" cellspacing="0" cellpadding="2"><tr><td nowrap="nowrap" align="left">
|
||||
</td><td nowrap="nowrap" align="center">
|
||||
<small>KOR9</small><!--sup
|
||||
--><br />↔ <br />
|
||||
<small></small> <br /></td><td nowrap="nowrap" align="center">
|
||||
</td></tr></table></td><td nowrap="nowrap" align="left">
|
||||
<table border="0" cellspacing="0" cellpadding="2"><tr><td nowrap="nowrap" align="left">
|
||||
PR_<span class="roman">RNAP</span> </td></tr></table></td><td width="50%"></td></tr>
|
||||
<tr><td width="50%"></td><td nowrap="nowrap" align="right" colspan="1"><table border="0" cellspacing="0" cellpadding="2"><tr><td nowrap="nowrap" align="left">
|
||||
PR + 2 <span class="roman">CI</span><span class="roman">2</span> </td></tr></table></td><td nowrap="nowrap" align="left">
|
||||
<table border="0" cellspacing="0" cellpadding="2"><tr><td nowrap="nowrap" align="left">
|
||||
</td><td nowrap="nowrap" align="center">
|
||||
<small>KOR10</small><!--sup
|
||||
--><br />↔ <br />
|
||||
<small></small> <br /></td><td nowrap="nowrap" align="center">
|
||||
</td></tr></table></td><td nowrap="nowrap" align="left">
|
||||
<table border="0" cellspacing="0" cellpadding="2"><tr><td nowrap="nowrap" align="left">
|
||||
PR_2 <span class="roman">CI</span><span class="roman">2</span> </td></tr></table></td><td width="50%"></td></tr>
|
||||
<tr><td width="50%"></td><td nowrap="nowrap" align="right" colspan="1"><table border="0" cellspacing="0" cellpadding="2"><tr><td nowrap="nowrap" align="left">
|
||||
PR_<span class="roman">RNAP</span> </td></tr></table></td><td nowrap="nowrap" align="left">
|
||||
<table border="0" cellspacing="0" cellpadding="2"><tr><td nowrap="nowrap" align="left">
|
||||
</td><td nowrap="nowrap" align="center">
|
||||
<small>kPR</small><!--sup
|
||||
--><br />→ <br />
|
||||
<small></small> <br /></td><td nowrap="nowrap" align="center">
|
||||
</td></tr></table></td><td nowrap="nowrap" align="left">
|
||||
<table border="0" cellspacing="0" cellpadding="2"><tr><td nowrap="nowrap" align="left">
|
||||
PR_<span class="roman">RNAP</span> + n<span class="roman">CII</span> </td></tr></table></td><td width="50%"></td></tr>
|
||||
<tr><td width="50%"></td><td nowrap="nowrap" align="right" colspan="1"><table border="0" cellspacing="0" cellpadding="2"><tr><td nowrap="nowrap" align="left">
|
||||
2 <span class="roman">CI</span> </td></tr></table></td><td nowrap="nowrap" align="left">
|
||||
<table border="0" cellspacing="0" cellpadding="2"><tr><td nowrap="nowrap" align="left">
|
||||
</td><td nowrap="nowrap" align="center">
|
||||
<small>K2</small><!--sup
|
||||
--><br />↔ <br />
|
||||
<small></small> <br /></td><td nowrap="nowrap" align="center">
|
||||
</td></tr></table></td><td nowrap="nowrap" align="left">
|
||||
<table border="0" cellspacing="0" cellpadding="2"><tr><td nowrap="nowrap" align="left">
|
||||
<span class="roman">CI</span><span class="roman">2</span> </td></tr></table></td><td width="50%"></td></tr>
|
||||
<tr><td width="50%"></td><td nowrap="nowrap" align="right" colspan="1"><table border="0" cellspacing="0" cellpadding="2"><tr><td nowrap="nowrap" align="left">
|
||||
<span class="roman">CI</span> </td></tr></table></td><td nowrap="nowrap" align="left">
|
||||
<table border="0" cellspacing="0" cellpadding="2"><tr><td nowrap="nowrap" align="left">
|
||||
</td><td nowrap="nowrap" align="center">
|
||||
<small>k1</small><!--sup
|
||||
--><br />→ <br />
|
||||
<small></small> <br /></td><td nowrap="nowrap" align="center">
|
||||
</td></tr></table></td><td nowrap="nowrap" align="left">
|
||||
<table border="0" cellspacing="0" cellpadding="2"><tr><td nowrap="nowrap" align="left">
|
||||
() </td></tr></table></td><td width="50%"></td></tr>
|
||||
<tr><td width="50%"></td><td nowrap="nowrap" align="right" colspan="1"><table border="0" cellspacing="0" cellpadding="2"><tr><td nowrap="nowrap" align="left">
|
||||
<span class="roman">CII</span> </td></tr></table></td><td nowrap="nowrap" align="left">
|
||||
<table border="0" cellspacing="0" cellpadding="2"><tr><td nowrap="nowrap" align="left">
|
||||
</td><td nowrap="nowrap" align="center">
|
||||
<small>k10</small><!--sup
|
||||
--><br />→ <br />
|
||||
<small></small> <br /></td><td nowrap="nowrap" align="center">
|
||||
</td></tr></table></td><td nowrap="nowrap" align="left">
|
||||
<table><tr><td nowrap="nowrap" align="right" colspan="1">()</td></tr></table></td><td width="50%"></td></tr></table>
|
||||
</td></tr></table>
|
||||
|
||||
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
<center>
|
||||
<table border="1">
|
||||
<tr><td align="center"><table border="0" cellspacing="0" cellpadding="0"><tr><td nowrap="nowrap" align="center">
|
||||
Constant </td></tr></table></td><td align="center"><table border="0" cellspacing="0" cellpadding="0"><tr><td nowrap="nowrap" align="center">
|
||||
Value </td></tr></table></td><td align="center"><table border="0" cellspacing="0" cellpadding="0"><tr><td nowrap="nowrap" align="center">
|
||||
Constant </td></tr></table></td><td align="center"><table border="0" cellspacing="0" cellpadding="0"><tr><td nowrap="nowrap" align="center">
|
||||
Value </td></tr></table></td><td align="center"><table border="0" cellspacing="0" cellpadding="0"><tr><td nowrap="nowrap" align="center">
|
||||
Constant </td></tr></table></td><td align="center"><table border="0" cellspacing="0" cellpadding="0"><tr><td nowrap="nowrap" align="center">
|
||||
Value </td></tr></table></td></tr><tr><td></td></tr>
|
||||
<tr><td align="center"><table border="0" cellspacing="0" cellpadding="0"><tr><td nowrap="nowrap" align="center">
|
||||
KPRE2 </td></tr></table></td><td align="center"><table border="0" cellspacing="0" cellpadding="0"><tr><td nowrap="nowrap" align="center">
|
||||
0.01 M<sup>−1</sup> </td></tr></table></td><td align="center"><table border="0" cellspacing="0" cellpadding="0"><tr><td nowrap="nowrap" align="center">
|
||||
KPRE4 </td></tr></table></td><td align="center"><table border="0" cellspacing="0" cellpadding="0"><tr><td nowrap="nowrap" align="center">
|
||||
0.00161 M<sup>−2</sup> </td></tr></table></td><td align="center"><table border="0" cellspacing="0" cellpadding="0"><tr><td nowrap="nowrap" align="center">
|
||||
kPREb </td></tr></table></td><td align="center"><table border="0" cellspacing="0" cellpadding="0"><tr><td nowrap="nowrap" align="center">
|
||||
0.00004 <span class="roman">sec</span><sup>−1</sup> </td></tr></table></td></tr>
|
||||
<tr><td align="center"><table border="0" cellspacing="0" cellpadding="0"><tr><td nowrap="nowrap" align="center">
|
||||
kPRE </td></tr></table></td><td align="center"><table border="0" cellspacing="0" cellpadding="0"><tr><td nowrap="nowrap" align="center">
|
||||
0.015 <span class="roman">sec</span><sup>−1</sup> </td></tr></table></td><td align="center"><table border="0" cellspacing="0" cellpadding="0"><tr><td nowrap="nowrap" align="center">
|
||||
KOR9 </td></tr></table></td><td align="center"><table border="0" cellspacing="0" cellpadding="0"><tr><td nowrap="nowrap" align="center">
|
||||
0.69422 M<sup>−1</sup> </td></tr></table></td><td align="center"><table border="0" cellspacing="0" cellpadding="0"><tr><td nowrap="nowrap" align="center">
|
||||
KOR10 </td></tr></table></td><td align="center"><table border="0" cellspacing="0" cellpadding="0"><tr><td nowrap="nowrap" align="center">
|
||||
0.06568 M<sup>−2</sup> </td></tr></table></td></tr>
|
||||
<tr><td align="center"><table border="0" cellspacing="0" cellpadding="0"><tr><td nowrap="nowrap" align="center">
|
||||
kPR </td></tr></table></td><td align="center"><table border="0" cellspacing="0" cellpadding="0"><tr><td nowrap="nowrap" align="center">
|
||||
0.014 <span class="roman">sec</span><sup>−1</sup> </td></tr></table></td><td align="center"><table border="0" cellspacing="0" cellpadding="0"><tr><td nowrap="nowrap" align="center">
|
||||
K2 </td></tr></table></td><td align="center"><table border="0" cellspacing="0" cellpadding="0"><tr><td nowrap="nowrap" align="center">
|
||||
0.1 M<sup>−1</sup> </td></tr></table></td><td align="center"><table border="0" cellspacing="0" cellpadding="0"><tr><td nowrap="nowrap" align="center">
|
||||
k1 </td></tr></table></td><td align="center"><table border="0" cellspacing="0" cellpadding="0"><tr><td nowrap="nowrap" align="center">
|
||||
0.0007 <span class="roman">sec</span><sup>−1</sup> </td></tr></table></td></tr>
|
||||
<tr><td align="center"><table border="0" cellspacing="0" cellpadding="0"><tr><td nowrap="nowrap" align="center">
|
||||
k10 </td></tr></table></td><td align="center"><table border="0" cellspacing="0" cellpadding="0"><tr><td nowrap="nowrap" align="center">
|
||||
0.002 <span class="roman">sec</span><sup>−1</sup> </td></tr></table></td><td align="center"><table border="0" cellspacing="0" cellpadding="0"><tr><td nowrap="nowrap" align="center">
|
||||
n </td></tr></table></td><td align="center"><table border="0" cellspacing="0" cellpadding="0"><tr><td nowrap="nowrap" align="center">
|
||||
10 </td></tr></table></td><td align="center"><table border="0" cellspacing="0" cellpadding="0"><tr><td nowrap="nowrap" align="center">
|
||||
</td></tr></table></td><td align="center"><table border="0" cellspacing="0" cellpadding="0"><tr><td nowrap="nowrap" align="center">
|
||||
</td></tr></table></td></tr></table>
|
||||
<br />
|
||||
Set an initial amount of 1.0 for PRE and OR, 30.0 for RNAP, and 0.0
|
||||
for the rest.
|
||||
</center>
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
</ol>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<h2><a name="tth_sEc3">
|
||||
3</a> GCM Editor</h2>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
This section describes how to construct a GCM model for this example:
|
||||
|
||||
<ol type="1">
|
||||
<li> Select <tt>File</tt> → <tt>New</tt> →
|
||||
<tt>Genetic Circuit Model</tt>.
|
||||
Enter <tt>CI_CII</tt> as the GCM model ID at which point a GCM
|
||||
editor will open.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<img src="screenshots/newModel.png" alt="screenshots/newModel.png" />
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> Select <tt>Add Promoter</tt>, enter <tt>PR</tt> as the ID, and press
|
||||
<tt>Ok</tt>. Next, add the <tt>PRE</tt> promoter in the same way.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<img src="screenshots/promoter.png" alt="screenshots/promoter.png" />
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> Select <tt>Add Species</tt>, enter <tt>CI</tt> as the ID, and press
|
||||
<tt>Ok</tt>. Next, add the <tt>CII</tt> species in the same way.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<img src="screenshots/GCMspecies.png" alt="screenshots/GCMspecies.png" />
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> Select <tt>Add Influence</tt>, change the input to <tt>CI</tt>, change
|
||||
the output to <tt>CII</tt>, change the promoter to <tt>PR</tt>, and the
|
||||
type to <tt>repression</tt>. Next, add an activation influence between
|
||||
<tt>CII</tt> and <tt>CI</tt> on promoter <tt>PRE</tt>.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<img src="screenshots/influence.png" alt="screenshots/influence.png" />
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> Select <tt>Save GCM</tt>, highlight <tt>CI_CII.gcm</tt> file, and
|
||||
right click to select <tt>View Genetic Circuit</tt>.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
<table>
|
||||
<tr><td align="center"><img src="screenshots/viewGenNet.png" alt="screenshots/viewGenNet.png" /></td><td align="center"><img src="screenshots/viewGCM.png" alt="screenshots/viewGCM.png" />
|
||||
</td></tr></table>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
</ol>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<h2><a name="tth_sEc4">
|
||||
4</a> Analysis</h2>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
The following instructions describe how to analyze the GCM file just
|
||||
created. The SBML file can also be simulated using the following steps.
|
||||
|
||||
<ol type="1">
|
||||
<li> Select <tt>Save GCM</tt>, highlight <tt>CI_CII.gcm</tt> file,
|
||||
right click to select <tt>Create Analysis View</tt>, and set the
|
||||
analysis ID to <tt>sim</tt>.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<img src="screenshots/GCMAnalysis.png" alt="screenshots/GCMAnalysis.png" />
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> In the newly opened window, select <tt>ODE</tt>.
|
||||
Also, in this window, change the time limit to 2100.0 and print interval
|
||||
to 10.0. Finally, select <tt>Save and Run</tt> at the bottom of the window.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<img src="screenshots/analysisView.png" alt="screenshots/analysisView.png" />
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> After the simulation completes, click on the <tt>TSD Graph</tt> tab.
|
||||
Double click on the graph to bring up the graph editor.
|
||||
Highlight Average, if not already highlighted, select CI and CII,
|
||||
change the Title to "ODE Simulation Results",
|
||||
change the X-Axis Label to "Time
|
||||
(seconds)", and change the Y-Axis Label to "Number of Molecules".
|
||||
Press the OK button. Click on Export and enter file name of <tt>ode.jpg</tt>.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<img src="screenshots/odeResults.png" alt="screenshots/odeResults.png" /><br />
|
||||
<img src="screenshots/odeSimResults.png" alt="screenshots/odeSimResults.png" />
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> Select the simulation options tab again, select <tt>Monte
|
||||
Carlo</tt>, change the number of runs to 100, and set the simulation ID
|
||||
to <tt>ssa</tt>. Click on <tt>Save and Run</tt>. Click on the <tt>TSD
|
||||
Graph</tt> tab.
|
||||
Double click on the graph to bring up the graph editor.
|
||||
Open the ssa simulation directory, and highlight <tt>run-1</tt>.
|
||||
Select CI and CII, change Title to "SSA Simulation Results",
|
||||
change the X-Axis Label to "Time (seconds)", and change the Y-Axis
|
||||
Label to "Number of Molecules". Press the OK button. Click on
|
||||
Export and enter file name of <tt>ssa-1.jpg</tt>.
|
||||
Repeat these steps to generate graphs for the average (<tt>
|
||||
average.jpg</tt>) and standard deviation (<tt>stddev.jpg</tt>).
|
||||
Note that you can use the "Deselect All" button to
|
||||
remove all items from the graph.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<img src="screenshots/ssaResults.png" alt="screenshots/ssaResults.png" /><br />
|
||||
<img src="screenshots/ssaSimResults.png" alt="screenshots/ssaSimResults.png" />
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> Click on the parameter editor tab. Highlight the <tt>PR</tt>
|
||||
species, and select <tt>Edit Species</tt>. Select <tt>Custom</tt> for
|
||||
the initial amount of <tt>PR</tt> and change it to 5.
|
||||
Click on the simulation options tab and change the simulation ID to
|
||||
<tt>ssa5</tt>.
|
||||
Press the Save and Run button.
|
||||
Click on the <tt>TSD Graph</tt> tab and following the steps above,
|
||||
create the
|
||||
following plots <tt>ssa-1_5.jpg</tt>, <tt>average_5.jpg</tt>, and
|
||||
<tt>stddev_5.jpg</tt>.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<img src="screenshots/paramEdit.png" alt="screenshots/paramEdit.png" /><br />
|
||||
<img src="screenshots/ssaSimResults5.png" alt="screenshots/ssaSimResults5.png" />
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> Now go back to the parameter editor tab,
|
||||
and change the initial amount for <tt>PR</tt> to <tt>Sweep</tt>, set
|
||||
the start to 2, stop to 8, step to 3. Press the save and run
|
||||
button. Click on the <tt>TSD Graph</tt> tab and double click on the graph to
|
||||
open the graph editor. Notice the new simulations id's
|
||||
generated for each of the run with PR of 2, PR of 5, and PR of
|
||||
8. Deselect all from the current graph, and go and add the
|
||||
average value of <tt>CI</tt> from each of these simulation runs.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<img src="screenshots/sweep.png" alt="screenshots/sweep.png" /><br />
|
||||
<img src="screenshots/sweepPR.png" alt="screenshots/sweepPR.png" />
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> Go back to the Parameter Editor tab and change <tt>PR</tt> back to
|
||||
<tt>Original</tt> value type. Go back to the Simulation Options tab,
|
||||
select <tt>Abstraction</tt> and change the simulation ID to <tt>abs</tt>.
|
||||
Press <tt>Save and Run</tt> and note that the simulation time should be
|
||||
substantially faster.
|
||||
Go back to the <tt>TSD Graph</tt> tab and double click on the graph to bring up
|
||||
the graph editor. Deselect all and add the average value of <tt>CI</tt>
|
||||
from both the <tt>abs</tt> and <tt>ssa</tt> simulations.
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
</ol>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<img src="screenshots/absResults.png" alt="screenshots/absResults.png" />
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<h2><a name="tth_sEc5">
|
||||
5</a> Probabilistic Analysis</h2>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
This example illustrates how <tt>iBioSim</tt> can be used for
|
||||
probabilistic analysis.
|
||||
|
||||
<ol type="1">
|
||||
<li> Go back to the GCM editor for <tt>CI_CII</tt>.
|
||||
Select <tt>Save as SBML Template</tt> and give it the name <tt>
|
||||
CI_CIIenv</tt>. Use the <tt>SBML File</tt> pulldown menu to select
|
||||
<tt>CI_CIIenv.sbml</tt> to associate with this GCM. Press the
|
||||
<tt>Save GCM</tt> button.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<img src="screenshots/linkSBML.png" alt="screenshots/linkSBML.png" />
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> Double click on the <tt>CI_CIIenv.sbml</tt> file to open it in an
|
||||
SBML editor. Select the <tt>Initial
|
||||
Assignments/Rules/Constraints/Events</tt> tab, and select <tt>Add
|
||||
Constraint</tt>. Add a constraint with ID <tt>CI20</tt>, constraint
|
||||
<tt>geq(CI, 20)</tt>, and message <tt>CI greater than 20 molecules</tt>.
|
||||
Repeat these steps to add constraints for CII ≥ 30, and t ≥ 200. Be sure to press the <tt>Save SBML</tt> button when you are done.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<img src="screenshots/constraint.png" alt="screenshots/constraint.png" />
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> Go back to your analysis view by clicking on the <tt>sim</tt> tab.
|
||||
Remove the simulation ID and press <tt>Save and Run</tt>. Click on the
|
||||
<tt>Probability Graph</tt> tab.
|
||||
Double click on the graph to bring up the probability graph
|
||||
editor. Change the title to <tt>Probability Results</tt> and the
|
||||
Y-axis label to <tt>Percent</tt>. Click on the <tt>sim-rep</tt> file on the
|
||||
left-hand side. Select <tt>CI20</tt>, <tt>CII30</tt>, and <tt>t200</tt> to
|
||||
graph them. Press <tt>Ok</tt>.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<img src="screenshots/editProbGraph.png" alt="screenshots/editProbGraph.png" />
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> Export the graph as a jpg file by selecting the <tt>Export</tt>
|
||||
button and entering the filename <tt>prob.jpg</tt>.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<img src="screenshots/probResults.png" alt="screenshots/probResults.png" />
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
</ol>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<h2><a name="tth_sEc6">
|
||||
6</a> GCM Learning</h2>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
This section describes how a GCM can be learned from time series data.
|
||||
|
||||
<ol type="1">
|
||||
<li> Highlight <tt>CI_CII.gcm</tt>, right click on it, and select
|
||||
<tt>Create Learn View</tt>. Give the learn view the ID <tt>learn</tt>.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<img src="screenshots/createLearn.png" alt="screenshots/createLearn.png" />
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> At this point a <tt>Learn View</tt> will open, and you could begin
|
||||
to add your experimental data. In this demo, we will just utilize our
|
||||
simulation data as synthetic experimental data. To do this, click
|
||||
<tt>Copy From View</tt>, and select <tt>sim/ssa</tt>. Highlight
|
||||
<tt>sim/ssa/run-1.tsd</tt>, and you should see the simulation data for
|
||||
<tt>CI</tt> and <tt>CII</tt> appear on the right in the data editor.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<img src="screenshots/dataManager.png" alt="screenshots/dataManager.png" />
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> Click on the <tt>Learn</tt> tab. Here you can edit the various
|
||||
learning options. For example, you can either use auto generated
|
||||
levels or user generated levels for your data encoding. Select
|
||||
<tt>Use User Generated Levels</tt> which will make the levels below
|
||||
editable. You can also select how many bins to use. Change the
|
||||
number of bins for both <tt>CI</tt> and <tt>CII</tt> to 3. At this point,
|
||||
you can ask the tool to suggest levels by clicking on the <tt>Suggest
|
||||
Levels</tt> button. Finally, press <tt>Save and Learn</tt> which will
|
||||
bring up the GCM that has been learned from this experimental data
|
||||
using Graphviz's dotty program.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<img src="screenshots/learn.png" alt="screenshots/learn.png" />
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
</ol>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<h2><a name="tth_sEc7">
|
||||
7</a> Genetic Circuit Design</h2>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
This last section describes how <tt>iBioSim</tt> can be used to design
|
||||
genetic logic gates.
|
||||
|
||||
<ol type="1">
|
||||
<li> Select <tt>File → New → Genetic Circuit
|
||||
Model</tt> and give it the ID <tt>gate</tt>.
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> Add promoters <tt>P1</tt> and <tt>P2</tt>, species <tt>A</tt>, <tt>B</tt>,
|
||||
and <tt>C</tt> (make <tt>A</tt> and <tt>B</tt> type <tt>boundary</tt> and <tt>
|
||||
C</tt> type normal), and repression influences from <tt>A</tt> to <tt>C</tt> on
|
||||
<tt>P1</tt> and <tt>B</tt> to <tt>C</tt> on <tt>P2</tt>. Save as an SBML
|
||||
template named <tt>gateEnv</tt>, and associate that SBML file with this
|
||||
GCM. Finally, save the GCM.
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> Open <tt>gateEnv.sbml</tt> in an SBML editor. Click on the<br />
|
||||
<tt>Initial Assignments/Rules/Constraints/Events</tt> tab, and
|
||||
select <tt>Add Event</tt>.
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> In the event editor, give a trigger of <tt>geq(t,2000)</tt>.
|
||||
Press <tt>Add Assignment</tt>, select variable <tt>A</tt>, and enter
|
||||
60 in the <tt>Assignment</tt> field. Press <tt>Add</tt> for the event
|
||||
assignment and <tt>Add</tt> for the event. Repeat these steps to
|
||||
create an assignment to <tt>B</tt> of 60 at time 4000. Note that
|
||||
you may ignore the warnings. These can be suppressed by
|
||||
changing your preferences and deselecting <tt>Check for
|
||||
undeclared units in SBML</tt>. Be sure to press <tt>Save SBML</tt>
|
||||
when you are done.
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> Highlight <tt>gate.gcm</tt>, right-click, and select <tt>Create
|
||||
Analysis View</tt>. Give it the ID <tt>simGate</tt>.
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> In the analysis view, change the options to
|
||||
<tt>Monte Carlo</tt>, time limit of 6000, print interval of 30,
|
||||
runs of 100.
|
||||
Press <tt>Save and Run</tt>.
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> Select the <tt>TSD Graph</tt> tab and graph the averages of <tt>
|
||||
A</tt>, <tt>B</tt>, and <tt>C</tt>. The behavior should be that of a Nand
|
||||
gate.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<img src="screenshots/nandResults.png" alt="screenshots/nandResults.png" />
|
||||
|
||||
<div class="p"><!----></div>
|
||||
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
|
||||
<li> Go back to the GCM editor for <tt>gate</tt>. Change the promoter
|
||||
on the influence from <tt>B</tt> to <tt>C</tt> to <tt>P1</tt>, and save the
|
||||
GCM. Go back to your analysis view and press <tt>Save and Run</tt>.
|
||||
The behavior should now be that of a Nor gate.
|
||||
|
||||
<div class="p"><!----></div>
|
||||
<img src="screenshots/norResults.png" alt="screenshots/norResults.png" />
|
||||
<div class="p"><!----></div>
|
||||
</li>
|
||||
</ol>
|
||||
|
||||
<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 16 Mar 2011, 18:25.</small>
|
||||
</html>
|
||||
BIN
docs/iBioSim_Tutorial.pdf
Normal file
BIN
docs/iBioSim_Tutorial.pdf
Normal file
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