Documentation
Documentation is a little sparse at the moment. Using the plug-in should be fairly intuitive with only one gotcha that I can think of at present. What is more important is a reference for the language's syntax which you can find in the Bio-PASTA 2009 paper. This should hopefully allow a modeller to write a Bio-PEPA model in the new syntax that the 0.1.x plug-in supports. This paper has one edit from the paper available on the PASTA website in the model. Where it used to saykineticLawOf beta : r*P;it now reads
kineticLawOf beta : r*P@main;The example didn't reference the component P in a particular location - something the plug-in highlighted once I added the model to a project.
Creating a Bio-PEPA model in the Bio-PEPA Eclipse Plug-In
If you can't see the Bio-PEPA drop down menu option click on the editor tab for your model.
Models (Eclipse sees them as files) must exist within a project. So once you have a working copy of Eclipse with the Bio-PEPA Eclipse Plug-In installed (see here for details) you need to create a new project. You can either seelct Other... from the New sub-menu in the drop down menu File (1) or right click in the Navigator panel (2)
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From there you want to select the Project option under General (see below).
and n the next page you can enter a project name and click Finish.
Having created your project you can now create the Bio-PEPA file in a similar way, in fact the option for a new file can also be seen above the selected Project option in the image above. In the next page of the wizard you will then have the ability to select a filename for your file. The extension (as can be seen below) is important and is how the plug-in recognises the file as a Bio-PEPA model.
All going well, you should have an environment similar to the one below. The single error you can see in the picture is because the file doesn't contain a Bio-PEPA model. Write your model and once you save the plug-in will attempt to parse it and return any errors.
