The Simple Biomodel Example

Here we use a simple, but realistic, model of an experimental graph. The model is similar to what is found in the formats MAGETAB or ISATAB. We show how a model like that can be adapted to the Node interface, required by the library and, from that, how to generate the table representing the graph.

As you'll see in the code, this is the typical approach to adapt your model:

  1. Define node wrappers for your object model (see node_wrappers package). Leave getInputs()/getOutputs() temporarily unimplemented.
  2. Define a Node Wrapper Factory (see node_wrappers/NodeFactory). Complete getInputs()/getOutputs() by using your factory
  3. Define a custom implementation of TableBuilder, so that you can instantiate it with the initial nodes that allow to reach of your experimental graph (See SimpleModelTableBuilder).
  4. Use the table builder and get the result from getTable() (See SimpleBioModelTest).