CoSMo Platform

CoSMo stands for COmplex System MOdeling platform and is sometimes shortened to CSM.

The CoSMo platform provides the following components to a modeller

* A language to describe models: csmML (Complex Systems Modelling Markup Language). The set of all models that can be described via csmML is called the meta model.
* A simulation engine, which is the kernel of CoSMo simulation platform. This generic simulation engine can be customized with the computational components described by a model that is expressed in csmML. For example the set of plug-ins representing the transition rules are properly interfaced with the simulation engine. The resulting specific simulation engine, equipped with all its components, is a computational model representing the given model. A computational model can then be executed once initial conditions and parameters value are given: the description of this process is called a simulation.
* A language to decribe protocols. A protocol is an executable collection of (often related) simulations. Examples:
o a study of the chaotic behaviour of a model can be started by running a set of simulations on slightly different initial conditions;
o a study of the robustness of a single parameter family of models to parameter perturbation could be conduced through simulation and would be described through a protocol;
o
another central example would be a reconstruction protocol which extracts information from digitized biological raw data and (through e.g. the use of some minimisation algorithm using a validation criteria computed through simulation) reconstructs the associated gene regulatory network (within the framework of a given conceptual model).

With these tools, a modeller can:

* describe a model (via csmML. and plug-ins ),
* run it once (using the simulation engine) i.e. conducing simulations,
* run it many times through a set of simulations i.e. conducing experimentations, or protocols,

Of course, during the modelling process, the modeller will need other software tools. First, before any simulation the modeller could need a software tool to extract from raw data the initial parameter values of the model to be studied.
Then, once the protocol for studying chaotic behaviour is run, the modeller could need

* a software tool to automatically analyse the results of the set of simulations with a statistical packages;
* or to represent them graphically.

These pieces of software that are not mandatory for the platform to be complete but that can be very useful in many cases will be implemented in any programming language and interfaced (possibly loosely) with an existing equipped simulation engine. They are called add-ons:

* in order to be executed some of these add-ons do not need that a simulation has been previously run: they are called pre-simulation tools;
* others act on the results of (sets of) simulations: they are called post-simulation tools.

Some Wordle outputs with the following input dictionary.
Note:

* You can describe all parts of a model in the csmML language (possibly using parameters) but not the transition rules. Transition rules have to be implemented as so-called plug-ins in a general purpose programming language and interfaced with the simulation engine.

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