Reproducibility of experiments is a basic requirement for science. Minimum Information (MI) guidelines have proved a helpful means of enabling reuse of existing work in modern biology. The Minimum Information Required in the Annotation of Models (MIRIAM) guidelines promote the exchange and reuse of biochemical computational models. However, information about a model alone is not sufficient to enable its efficient reuse in a computational setting. Advanced numerical algorithms and complex modeling workflows used in modern computational biology make reproduction of simulations difficult. It is therefore essential to define the core information necessary to perform simulations of those models. The Minimum Information About a Simulation Experiment (MIASE, Glossary in Box 1) describes the minimal set of information that must be provided to make the description of a simulation experiment available to others. It includes the list of models to use and their modifications, all the simulation procedures to apply and in which order, the processing of the raw numerical results, and the description of the final output. MIASE allows for the reproduction of any simulation experiment. The provision of this information, along with a set of required models, guarantees that the simulation experiment represents the intention of the original authors. Following MIASE guidelines will thus improve the quality of scientific reporting, and will also allow collaborative, more distributed efforts in computational modeling and simulation of biological processes.
Box 1. Glossary
Minimum Information About a Simulation Experiment. Reporting guidelines specifying the information to be provided with the description of a simulation in order to permit its correct interpretation and reproduction.
A simulation description that provides all information listed by the MIASE guidelines.
Minimum Information Required in the Annotation of Models. Reporting guidelines specifying the information to be provided with an encoded model in order to permit its correct interpretation and re-use.
A mathematical representation of a biological system that can be manipulated and experimented upon (simulated).
Set of formal statements describing the structure of the components of a modeled system, whether entities or events, encoded in a computer-readable form.
The closeness between independent simulations performed with the same methods on identical models with the same experimental setup.
The closeness between independent simulations performed with the same methods on identical models but with a different experimental setup.
A numerical procedure performed on a model that aims to reproduce the spatial and temporal evolution (the behavior) of the system represented by the model, under prescribed conditions.
A set of procedures, including simulations, to be performed on a model or a group of models, in order to obtain a certain set of given numerical results.