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Protocol Files
iDynoMiCS uses plain-text XML files in order to define the simulation to run; these files are called protocol files. In a protocol file, an XML mark-up is used to define the simulation parameters, including details such as run time, simulated solutes, simulated agents, and included reactions. In this section we describe how this mark-up is used. The overall simulation information is contained within the <idynomics> and </idynomics> opening and closing tags, and comments are specified with the following syntax: <!-- this is a comment -->.
From December 2013, we are encouraging users to generate their protocol files using the new online protocol file generator. This eases the process of specifying a simulation. However, this does not replace the detail in this tutorial, and the two should be used together while you are becoming familiar with iDynoMiCS.
We will go through each part of an example protocol file and explain what each part of the mark-up does. For more example protocol files useful as templates when defining your own simulations, look in the iDynoMiCS\protocol directory. The included example_2D.xml and example_3D.xml files are also useful references in creating your own protocol files because they include extensive documentation of each part of the file. Note also in those files that many user-definable labels are prefixed with My so that it is clear which labels are reserved and which are free; we follow that convention in this tutorial.
This is a large section of the tutorial and is split into the following sections. We suggest you work through each in order. If you are reading the PDF version of this tutorial on screen, clicking on the section will take you to the relevant page on the iDynoMiCS wiki on github. The information in this document is however the same as that found on the wiki.