1. How can I load or save a model?
2. How can I change the concentration unit?
3. How can I create new components?
4. How can I edit new components?
5. How can I create new complexes?
6. How can I edit new complexes?
7. How can I write a new reaction?
8. How can I modify an already existing reaction?
9. How can I create a multistate complex?
10. How can I select a rate constant and what type of rate constant should I select?
11. How can I run the simulation?
12. How can I plot the simulation results?
13. How can I specify the plot type?

Q: How can I load or save a model?

A: To load a model, select the file option from the tool bar, and click on the appropriate (i.e. save or open) option. This will allow you to browse the directory where the file should be saved to or where the file exists in. ( View Picture )

Q: How can I change the concentration unit?

A: To change the concentration unit to micromolar, on the information page click on the Molarity box, and enter 'u'. You can change the unit to nanomolar by entering 'n' in the Molarity box.( View Picture )

Q: How can I create new components?

A: Click on the model on the side panel, and then choose the Components option. Now to create a new component, simply type the Symbol and the Name of the component, and this results in addition of a new component with the specified name to the model.( View Picture )

Q: How can I edit new components?

A: To change the name or the symbol of a component first select the components from the side panel. Now click on the name and/or the symbol and then type the correct name and/or symbol. ( View Picture )

Q: How can I create new complexes?

A: After creating new components choose the Complexes option from the side panel. Now new complexes can be made from the existing components. To make a new complex, one must find and add each one of the components together to form the desired complex. The components are listed on the left most top box. To add a component to a complex simply click on the component of choice, and then click on the forward arrow, which points to the box titled Complex Symbol box. This results in appearance of the component in the Complex Symbol box. Once all the components of the complex are added enter the initial level and check the appropriate box or boxes (i.e. Multistate, Display and Constant). The last step in creating a new complex is to click on the apply button, which results in appearance of the complex symbol, its initial level and its display status in the bottom box. ( View Picture )

Q: How can I edit new complexes?

A: To delete or modify a complex first select the Complexes from the side panel. Now select the complex by clicking on its symbol. Once the symbol is highlighted use the right click on the symbol. This results in the appearance of a drop down box. To Delete the complex select the delete option in the drop down box. To modify the complex (i.e. remove, replace or add components) after selecting the Modify option in the drop down box, using a single left click highlight the component that needs to be removed or replaced. Once the component is highlighted, click on the arrow that points to the top left most box, and this results in deletion of that component from the complex.( View Picture )

Q: How can I write a new reaction?

A: After creating new complexes, from the side panel select Reactions. Once in the Reaction page, right click on the black arrow on the left most edge of the bottom box, and select the add option.
In the Reaction Detail page:

1. Enter the name of the reaction in the Reaction Name box.
2. After selecting each of the substrates for Model Complexes box, click on the top double arrow (i.e. the one that point to the Reaction Substrates box). This results in addition of the selected complex to the Reaction Substrates box. For changing one of the complexes selected click on the arrow pointing to the left to remove and then replace the added complexes.
3. To add the products once again select each one of the products from the Model Complexes box, and then using the arrow, which points to the Reaction Products box, add the complex to the Reaction Product box. To remove any of the complexes from the Reaction Product box click on the arrow pointing to the Model Complexes box until the unwanted complex is removed.
4. Next in the Forward Rate Constant box select a Rate type. After selecting the rate constant type and entering the appropriate rate constant (i.e. Static, Dynamic or Equation), repeat this step for the Reversed Rate Constant.
5. Finally click on the Apply changes button to complete your reaction.

( View Picture )

Q: How can I modify an already existing reaction?

A: To modify or delete a reaction, in the Reaction page, click on the reaction. Select the Edit or the Delete option and modify or delete the reaction in the Reaction Detail page.( View Picture )

Q: How can I create a multistate complex?

A: Under construction

Q: How can I select a rate constant and what type of rate constant should I select?

A: The forward and reversed rate constants can be Static, Dynamic, or a function of time. A static rate remains constant throughout the simulation, whereas the dynamic rate changes as specified the user. The rate that changes as a function of time can be presented by an equation.

Static:

Selecting a Static rate constant requires entering a constant value for the rate of the reaction. This value can be 0 or any positive number.

Dynamic:

After selecting the Dynamic rate type determine the time interval and the corresponding values of rate constant. This can be simply done by clicking on the time column and rate constant column and entering the desired values.

Function:

Under Construction

( View Picture )

Q: How can I run the simulation?

A: After writing(filename.sig) or loading the model (filename.sig) select Run simulation from the tool bar. After checking the Stochastic or/and Deterministic box, click on the Begin Run button. Upon the end of the simulation the simulation results are saved in the same directory as SigTran, ("C:\Program Files\Cell Systems Initiative\SigTran3") and are available for further analysis.( View Picture )

Q: How can I plot the simulation results?

A: To plot the simulation results select the Run Plot option from the toolbar. After selecting the plot type and setting the axis to show the desired parameters, left clicking on the Begin Plot button will result in appearance of the plot of the data.

• Normal : Stochastic results
• Comparison: Stochastic and Deterministic results on same plot
• Frequency: 3D frequency plot

( View Picture )

Q: How can I specify the plot type?

A: You can select one of the three types of plots:

1. Normal
2. Comparison
3. Frequency

A Normal plot allows the user to plot the data, which was acquired through either Stochastic or Deterministic simulation. The Comparison plot as the name suggests allows the comparison of the result of the Stochastic and Deterministic simulation by plotting the two on the same graph. Comparison plots use both the Stochastic and the Deterministic simulations, therefore, in order to be able to run this plot the simulation must be run both stochastically and deterministically. In order to be able to acquire a 3D frequency plot, before the start of the simulation the user must chose the display type to be 3D Relative Frequency. Display type is selected in Model Parameters and Option page. ( View Picture )