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Minimum information about a simulation experiment

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logo of MIASE
logo of MIASE

The Minimum Information About a Simulation Experiment (MIASE) is an effort to standardize the description of simulation experiments in the field of systems biology.

MIASE is a registered project of the MIBBI (Minimum Information for Biological and Biomedical Investigations)[1].

History

The MIASE project was launched in 2007 by Dagmar Köhn and Nicolas Le Novere and first presented on the 12th SBML Forum Meeting in October 2007. Since then, MIASE was discussed on various meetings, not only within the SBML community. MIASE has become a community effort involving people from various standardisation communities as well as developers of simulation tools. In April 2009, MIASE was part of the "CellML, SBGN, SBO, BioPAX, and MIASE Super-Workshop 2009".

The Guidelines

The MIASE guidelines describe the Minimum Information needed about a simulation experiment in order to repeat it. They do, for example, contain information about:

Information about the models simulated

MIASE recommends to explicitly define all models used in a simulation by providing a specific name and the source of each model. In order to get a desired simulation result, it is often not sufficient to use models as such. That is why, changes that have to be applied to the model before simulation have to be described. Examples of such changes can be the assignment of a new value (e.g. constant, initial concentration), or the change of a mathematical expression (e.g. using different enzyme kinetics), and simulation settings (type of simulation and the corresponding parameters).

Information about the simulations to run

The simulation tasks to be undertaken in order to complete the simulation experiment need to be specified. Typically, that will involve describing how a simulation procedure has to be applied to a specific model, and in which order. Each simulation can be characterized by certain types of simulation procedures to be run (steady-state, timecourse etc.) and the simulation algorithms used to perform them. The information has to be sufficiently detailed so that no arbitrary choices have to be made when setting up the simulations. KiSAO[2] is a classification of simulation algorithms and methods for the simulation of quantitative models. It will be used for the unambiguous reference to a simulation algorithm in the simulation settings.

Information about the outputs produced

It is often necessary to define the transformations that have to be applied to the raw output of the simulation tasks, and how to provide the final results. These results can be numerical or graphical. For instance, a model of a periodic process can provide just time courses showing oscillations; or it can, on the contrary, provide phase diagrams, which are more explicit in describing the relationship between variables. An even more striking example of the necessity for output definitions is the bifurcation diagram.


See also

References

  1. ^ http://www.mibbi.org/ Minimum Information for Biological and Biomedical Investigations
  2. ^ http://www.ebi.ac.uk/compneur-srv/kisao/ Kinetic Simulation Algorithm Ontology
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