Systems biology - model simulation - Revision history

Axec@dote.ru at 18:19, 18 March 2022

2022-03-18T18:19:52Z

Axec@dote.ru at 18:19, 18 March 2022

2022-03-18T18:19:13Z

Axec@dote.ru at 17:43, 18 March 2022

2022-03-18T17:43:47Z

Axec@dote.ru at 17:22, 18 March 2022

2022-03-18T17:22:01Z

Axec@dote.ru at 08:02, 18 March 2022

2022-03-18T08:02:06Z

Axec@dote.ru at 07:59, 18 March 2022

2022-03-18T07:59:55Z

Elena.kutumova@biouml.org at 05:04, 16 March 2022

2022-03-16T05:04:28Z

Elena.kutumova@biouml.org at 05:04, 16 March 2022

2022-03-16T05:04:07Z

Elena.kutumova@biouml.org at 05:03, 16 March 2022

2022-03-16T05:03:41Z

Elena.kutumova@biouml.org at 10:05, 14 March 2022

2022-03-14T10:05:00Z

@@ Line 68: / Line 68: @@
 <li>Run simulation.
-<br><br>[[File:detailed_plot_5.png|frameless|upright=4]]<br><br>
+<br><br>[[File:detailed_plot_6.png|frameless|upright=4]]<br><br>
 </ul>
 </font>

@@ Line 59: / Line 59: @@
 <li>In appeared window set table data collection from repository and then column name from combobox. Please note that you can not have two lines with the same titles in one plot! Thus we need to change title
 for experimental line in this example to '''casp8 experimental'''
 <br><br>[[File:detailed_plot_5.png|frameless|upright=4]]<br><br>

@@ Line 5: / Line 5: @@
 <li> Go to the '''Simulation''' tab in the right bottom panel. It has two inner tabs: '''Engine''' and '''Plot'''. First we will need to set variables to plot. Got to '''Plot''' tab and set value for default curve.
-<br><br>[[File:systems_biology_simulation_0.png|frameless|upright=5]]<br><br>
+<br><br>[[File:systems_biology_simulation_0.png|frameless|upright=4]]<br><br>
 <li> Next step is to go to '''Engine''' tab and set simulation properties.
 Depending on the type of your diagram, the appropriate simulation engine will be set in the '''Selected engine''' field. For example, '''ODE Simulation Engine''' is used for ordinary differential equation models. For more information on supported simulation engines, see the [[Simulation]] section.
-<br><br>[[File:systems_biology_simulation_1.png|frameless|upright=5]]<br><br>
+<br><br>[[File:systems_biology_simulation_1.png|frameless|upright=4]]<br><br>
 <li> Select one of the available simulators or use the default one:
@@ Line 20: / Line 20: @@
 *[[JVODE|JVode]] (default)
-<br>[[File:systems_biology_simulation_2.png|frameless|upright=5]]<br><br>
+<br>[[File:systems_biology_simulation_2.png|frameless|upright=4]]<br><br>
 <li> Set simulation options:
@@ Line 28: / Line 28: @@
 *'''Absolute tolerance''', '''Relative Tolerance''' - tolerances for simulation. For example model we use 1.0E-8 values for both tolerances.
-<br>[[File:systems_biology_simulation_3.png|frameless|upright=5]]<br><br>
+<br>[[File:systems_biology_simulation_3.png|frameless|upright=4]]<br><br>
 <li>Click on the '''Simulate''' button [[File:Execute_icon.png]]. The window that opens will show the results of simulation of the variables selected to plot.
-<br><br>[[File:systems_biology_simulation_4.png|frameless|upright=5]]<br><br>
+<br><br>[[File:systems_biology_simulation_4.png|frameless|upright=4]]<br><br>
 </ol>
-==Detailed plot seetings==
+==Detailed plot settings==
 </font>

@@ Line 1: / Line 1: @@
 <font size=3>
-To simulate SBML model, do the following:
+==Quick model simulation==
 <ol>
 <li> Go to the '''Simulation''' tab in the right bottom panel. It has two inner tabs: '''Engine''' and '''Plot'''. First we will need to set variables to plot. Got to '''Plot''' tab and set value for default curve.
-<br><br>[[File:systems_biology_simulation_0.png]]<br><br>
+<br><br>[[File:systems_biology_simulation_0.png|frameless|upright=5]]<br><br>
 <li> Next step is to go to '''Engine''' tab and set simulation properties.
 Depending on the type of your diagram, the appropriate simulation engine will be set in the '''Selected engine''' field. For example, '''ODE Simulation Engine''' is used for ordinary differential equation models. For more information on supported simulation engines, see the [[Simulation]] section.
-<br><br>[[File:systems_biology_simulation_1.png]]<br><br>
+<br><br>[[File:systems_biology_simulation_1.png|frameless|upright=5]]<br><br>
 <li> Select one of the available simulators or use the default one:
@@ Line 19: / Line 20: @@
 *[[JVODE|JVode]] (default)
-<br>[[File:systems_biology_simulation_2.png]]<br><br>
+<br>[[File:systems_biology_simulation_2.png|frameless|upright=5]]<br><br>
 <li> Set simulation options:
@@ Line 27: / Line 28: @@
 *'''Absolute tolerance''', '''Relative Tolerance''' - tolerances for simulation. For example model we use 1.0E-8 values for both tolerances.
-<br>[[File:systems_biology_simulation_3.png]]<br><br>
+<br>[[File:systems_biology_simulation_3.png|frameless|upright=5]]<br><br>
 <li>Click on the '''Simulate''' button [[File:Execute_icon.png]]. The window that opens will show the results of simulation of the variables selected to plot.
-<br><br>[[File:systems_biology_simulation_4.png]]<br><br>
+<br><br>[[File:systems_biology_simulation_4.png|frameless|upright=5]]<br><br>
 </ol>
 </font>

@@ Line 25: / Line 25: @@
 *'''Completion time''' - the point in model time when the simulation ends.
 *'''Time increment''' - the gap between the time points at which the simulation results will be written.
 <br>[[File:systems_biology_simulation_3.png]]<br><br>

@@ Line 19: / Line 19: @@
 <li> Set simulation options:
-*Initial time - initial value of the model time. It is strongly recommended to use only the value 0 here.
+*'''Initial time''' - initial value of the model time. It is strongly recommended to use only the value 0 here.
-*Completion time - the point in model time when the simulation ends.
+*'''Completion time''' - the point in model time when the simulation ends.
-*Time increment - the gap between the time points at which the simulation results will be written.
+*'''Time increment''' - the gap between the time points at which the simulation results will be written.
 <br>[[File:systems_biology_simulation_figure_3.png]]<br><br>

@@ Line 1: / Line 1: @@
-[[File:systems_biology_simulation_figure_1.png|thumb|'''Figure 1'''. Select the appropriate simulation engine.]]
+<font size=3>
-[[File:systems_biology_simulation_figure_2.png|thumb|'''Figure 2'''. Select one of the available simulators.]]
-[[File:systems_biology_simulation_figure_3.png|thumb|'''Figure 3'''. Set simulation options.]]
-[[File:systems_biology_simulation_figure_4.png|thumb|'''Figure 4'''. The results of simulation.]]
 To simulate SBML model, do the following:
 <ol>
-<li> Go to the '''Simulation''' tab in the right bottom panel. Depending on the type of your diagram, the appropriate simulation engine will be set in the '''Selected engine''' field (Figure 1). For example, '''ODE Simulation Engine''' is used for ordinary differential equation models. For more information on supported simulation engines, see the [[Simulation]] section.
+<li> Go to the '''Simulation''' tab in the right bottom panel. Depending on the type of your diagram, the appropriate simulation engine will be set in the '''Selected engine''' field. For example, '''ODE Simulation Engine''' is used for ordinary differential equation models. For more information on supported simulation engines, see the [[Simulation]] section.
-<li> Select one of the available simulators or use the default one (Figure 2):
 *[[Euler]]
 *[[Dormand-Prince]]
@@ Line 15: / Line 15: @@
 *[[RADAU V|Radau V]]
 *[[JVODE|JVode]] (default)
-<li> Set simulation options (Figure 3):
 *Initial time - initial value of the model time. It is strongly recommended to use only the value 0 here.
 *Completion time - the point in model time when the simulation ends.
 *Time increment - the gap between the time points at which the simulation results will be written.
-<li>Click on the '''Simulate''' button [[File:Execute_icon.png]]. The window that opens will show the results of simulation of the variables selected to plot (Figure 4).
 </ol>