ProBMoT is an implementation of the process-based modeling approach to modeling dynamical systems.
In the core of the process-based modeling approach is a formalism for representing models of dynamical systems as well as knowledge for modeling dynamical systems in a particular domain of interest. The process-based model formalism allows for representing models of dynamical systems at two levels of abstraction. At the higher level, the model is represented as sets of processes that govern the dynamics of the observed system and entities involved in the processes. At the lower level, each process includes a model of its dynamical influence on the variables of the observed system. The process-based modeling software can automatically combine the models of individual processes into a set of coupled differential equations used to simulate the behavior of the observed system. Thus, process-based models at the higher abstraction level reveal the structure of the observed systems in terms of entities and process interactions among them, providing explanation of the model behavior obtained by a lower-level declaration of the model equations.
To start establishing process-based models, we first have to formalize the modeling knowledge by establishing templates of generic entities that appear in the generic processes that govern the dynamics of systems in the particular domain. This modular knowledge representation allows for automated modeling of an observed system following a compositional approach. For a given modeling task, the generic templates are being instantiated into specific components (entities and processes) that can be used as building blocks for process-based models. Combinations of these building blocks represent candidate process-based models of the observed system. Automated modeling tool than searches for a process-based model with an optimal fit between the simulated and observed behavior of the system at hand.
More info @ http://probmot.ijs.si/
Dependencies: Java JDK 7+
Make sure that you have Java JDK version 7 or higher installed on your system and that the PATH system variable contains the path to the Java compiler from the JDK.
Please read the user guide for preparing the inputs and running ProBMoT, which is available at http://probmot.ijs.si/userguide.html.
This ProBMoT distribution contains input files for running ProBMoT in two domains of modeling population dynamics aquatic ecosystems and modeling biochemical dynamics of endocytosis. The folder 'examples' contains all the example files, while further description thereof can be found at http://probmot.ijs.si/examples.html.
To test the correctness of the installation you can run a simple task of simulating an aquatic ecosystem model using the command
java -jar probmot-1.2.jar examples/aquatic/taskSimulate.xml
that should produce the following terminal output
/time_stamp/ [main] INFO xml.TaskSpec - Task 'examples/aquatic/taskSimulate.xml' read successfully /time_stamp/ [main] INFO traverse.Traverse - Library 'examples/aquatic/AquaticEcosystem.pbl' compiled successfully /time_stamp/ [main] INFO traverse.Traverse - Incomplete Model 'examples/aquatic/BledComplete.pbm' compiled successfully /time_stamp/ [main] INFO temp.Dataset - Dataset 'examples/aquatic/data/96.data' read successfully - /time_stamp/ [main] INFO traverse.Traverse - Library 'examples/aquatic/AquaticEcosystem.pbl' compiled successfully /time_stamp/ [main] INFO traverse.Traverse - Incomplete Model 'examples/aquatic/BledComplete.pbm' compiled successfully /time_stamp/ [main] INFO temp.Dataset - Dataset 'examples/aquatic/data/96.data' read successfully - /time_stamp/ [main] INFO task.Task - Task started /time_stamp/ [main] INFO task.Task - Task ended
For further description of the output files produced consult the user guide and examples description on the ProBMoT website.