Step 6: Plotting. Step 6: Plotting Just like report, plots can be edited or created from scratch if the predefined plots from the Output Assistant don’t fit your needs. In the object tree on the left in the Output node, you can find the entry called Plots. Selecting this will bring you to the plot definition overview which will probably be empty. (Click here to go to the plot definition overview.) Now you can either create a new plot by clicking on the New button, or you can edit one of the existing plots if there are any. To edit a plot, double click on its entry in the table. In this dialog you can add more curves, delete curves or change the way individual curves are plotted.
In order to add new curves to the plot, you click on the New curve... button. Each curve item gets its own tab in the plot definition dialog and you can edit attributes of the curve by selecting the corresponding tab. Once you are finished with the plot definition, you go back to the Time Course dialog and push the Run button again. Step 4: Creating a Report Definition. Step 4: Creating a Report Definition Sometimes, the predefined report and plots that are provided by the Output Assistant are not what you want. In this case, we can either start with one of the predefined report (or plots) and change it to our needs, or we can create a new report (or plot) from scratch.
In order to create or edit an exisiting report definition, you navigate in the tree to Output->Reports. If you want to edit an exisiting report, just double click on the report you want to edit in the table. If you want to create a new report, click the New button on the bottom and then on the Commit button and then double click on the new entry in the table. You will now find yourself in the dialog for the report definition. (Click here to go to the Report definition dialog.) If you have created a new report the list widget is empty, that means that nothing will be put into the report.
Step 5: Calculating a Time Course. Step 5: Calculating a Time Course In the tree on the left under Tasks you can find the entry called Time Course. Selecting this entry in the tree will bring you to the time course settings dialog. (Click here to go to the Time Course dialog) Here you can set all parameters for calculating a time course like starting time, end time, how many data points are to be stored and, last but not least, the method for calculating the trajectory. Once all values are set, the run button can be used to excecute the timecourse calculation. Sometimes the results of a calculation are to large to be stored in memory, or you might want to have other items in the result that are not in the Result table.
The easiest way to create a report is to choose one of the predefined report with COPASI's Output Assistant which can be started by clicking the buttn with the same name at the bottom of the screen. The dialog features a large number of predefined reports as well as plots. Step 3: Refining the Model. Step 3: Refining the Model Your reaction probably don’t all have a mass-action kinetic, so before you can run the actual simulation, you have to specify the correct kinetics for all the reactions. In order to do this, you navigate in the tree on the left to the reaction that you want to change. Or you can double click on the reaction in the reaction overview table. In the Reaction Settings dialog you can change all attributes of the reaction, especially the kinetics and the associated kinetic parameters. If necessary, you can do the same for the species and the compartment. Just use the tree on the left to navigate to the model element you want to change and make the necessary changes in the dialog on the right.
Step 2: Reaction Input. Step 2: Reaction Input There are several ways to define the set of reactions for the model. The fastest one is probably to type them into the reaction overview table. You find this reaction overview in the tree on the left under Model->Biochemical->Reactions. (Click here to go to the reaction overview.) To create a new reaction just click on the empty cell in the Equation column and start typing. A reaction equation usually consists of three parts.
First comes the set of substrates. After the substrates you either write "->" if it is a irreversible reaction or "=" if it is a reversible reaction. The third part consists of the set of products. There are several things to watch out for when writing reaction equations. Examples of valid reaction equation would be Gluose + Phosphate -> Glucose-6-phosphate or F16BP = F26BP.
It is also possible to either ommit the set of products or the set of substrates, but not both. When you are finished with typing the reaction equation, hit the return key. Step 1: Model Settings. Step 1: Model Settings Once you start COPASI, you are greated with the COPASI Logo on the right and COPASI's Model and Task tree on the left where you can select the individual elements of the model, the tasks etc. If you select the item called Model in the tree, COPASI will display the model dialog to the right of the tree.
On the right side, you can see the settings for this model, which are the name of the model, the units that copasi will use in the model and a description of the model. Here you should give the model a more expressive name and maybe a short description. (Click here to go to the Model Settings dialog.) For a description of the other settings please have a look at the COPASI documentation. Simulation by COPASI - CellDesigner Help. CellDesigner Help Simulation by COPASI To setup COPASI to use with CellDesigner Visit the Copasi web site. Download the Language Binding for Java (e.g. copasi_java_win32_buildxx.zip for Windows 32bit). To simulate a model with COPASI Open the sample file "MAPK.xml". Help Sections Web Image About Us | Site Map | Privacy Policy | Contact Us | ©2010 The Systems Biology Institute All Rights Reserved.
Biomodels: Biomodels Index. BioModels Database. BioModels.net. Computational Systems Biology : CopasiModels. Most of our research is based on modelling biochemical networks. In the course of research, and also of educational activities, we have been collecting a series of models that we have found useful, either written by us or by others. This page is a single entry point for obtaining these models. The file formats stored here are the COPASI format (also known as CopasiML) and SBML, but there are also some in the old Gepasi format (readable by COPASI).
Note that this page does not pretend to be a general repository of models since Biomodels fulfills this purpose. This page is to store models that do not fit in Biomodels or otherwise CopasiML versions of those models. Teusink glycolysis model The famous Teusink et al. model of yeast glycolysis, with parameters adjusted by Pritchard & Kell: YeastGlycolysis.cps (98.04 Kb) (the actual Teusink et al. model is in Biomodels as BIOMD0000000064). Kummer's calcium model Linear pathway with three enzymes data files for parameter estimation.