Minimum Information About a Simulation Experiment (MIASE)

Herbert M. Sauro,Stefan Hoops,Jacky L. Snoep,Ion I. Moraru ,Peter Hunter,Randall Britten,Edmund J. Crampin,Dagmar Waltemath,Macha Nikolski,Jonathan Cooper,Richard R. Adams ,Vijayalakshmi Chelliah,Edda Klipp,Nicolas Le Novère,Michael Hucka,Upinder S. Bhalla,Henning Schmidt,Alan Garny,David Nickerson,Frank Bergmann ,Dominic P. Tolle ,Olaf Wolkenhauer,Camille Laibe,Poul M. F. Nielsen ,Andrew Miller ,Sven Sahle,Michael T. Cooling,Daniel A. Beard

doi:10.1371/journal.pcbi.1001122

Abstract

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.

Highlights

Reproducibility of experiments is a basic requirement for science
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
Following MIASE guidelines will improve the quality of scientific reporting, and will allow collaborative, more distributed efforts in computational modeling and simulation of biological processes

Summary

Needs for a Standard Description of Simulations Experiments

The rise of systems biology as a new paradigm of biological research has put computational modeling under the spotlight. Defining which information must be provided when describing an experimental procedure is the task of reporting guidelines, federated in the global project Minimum Information for Biological and Biomedical Investigations (MIBBI) [10]. Those reporting guidelines generally result from consultations with a large community and are carefully thought out. Once encoded in a computer readable format, these simulation experiment recipes can be downloaded along with the models, either from public resources or publisher Web sites This will allow one to store descriptions of simulation experiments and reproduce them, and foster their exchange between co-workers, research groups, and even between simulation tools. Experiment descriptions that provide all necessary information specified in the guidelines are considered MIASE compliant

Scope of MIASE

MIASE Enables the Reproduction on Different Experimental Setup

MIASE Applies to Any Simulation Procedure in Life Science

Conclusion and Perspectives

Supporting Information