Development of agent-based models describing the response of Escherichia coli to changes in oxygen availability

The agent-based model involves the representation of each individual molecule of interest as an autonomous agent that exists within the cellular environment and interacts with other molecules according to the biochemical situation. FLAME environmet has beem used for agent-based development. The FLAME framework is an enabling tool to create agent-based models that can be run on high performance computers (HPCs). Models are created based upon extended finite state machines that include message input and output. This information is used by the frame work to automatically generate a simulation program that can run models efficiently on HPCs. In order to develop agent-based model in FLAME, the user need to define at least three xml files as described below:

Model.xml : X-Machine Agent Markup Modelling Language (XMML) A description language for agent-based simulations. XMML should contain the whole structure of the model i.e Agent descriptions, memory variables, functions, messages

Functions.c – should contain the implementations of the functions specified in Model.xml

0.xml – should contain the initial states of the memory variables of the agents i.e Initializations of all parameters

The number of the resulting XML files depends on the number of iterations you specify to run your model (through Main.exe).

Each important molecule is specified in the XMML language and information about its location (abstract co-ordinates), its state, its ability to interact with other molecules and the conditions under which this happens are encoded in its definition.