Minimum Information About a Simulation Experiment (MIASE)

Abstract

International audienceReproducibility 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

A call for virtual experiments: Accelerating the scientific process

“…Scientific knowledge must be independently verifiable, even in computational sciences (Morin et al, 2012), and a growing number of scientists are gathering under the banner of reproducible research (LeVeque et al, 2012;Peng, 2011;Waltemath et al, 2011aWaltemath et al, , 2011b. The spectrum of reproducibility (Peng, 2011) ranges from strict "replication" as in re-running a simulation in exact detail, for instance using a virtual machine (Howe, 2012), through "reproduction" in the sense of independent re-implementation of the essential aspects of a carefully described experiment (Drummond, 2009;Ince et al, 2012), to "constructive replication" (Lykken, 1968) based only on a clear statement of the hypothesis, leaving the next researcher free to choose their own experiment and analysis methods.…”

“…More usefully than a script, a protocol description can be given at a higher level of abstraction, providing the details requested by reporting guidelines such as the Minimum Information About a Simulation Experiment (MIASE) (Waltemath et al, 2011a). Different tools that understand the protocol description can reproduce the experiments using their own implementations of algorithms etc., and using their own set of models.…”

“…This limits the relevance of mathematical models for experimental biologists, who often prefer to rely primarily on mental models to develop hypotheses and design tests for them. Despite the growing availability of data and model repositories (Joyce and Palsson, 2006;Le Novere et al, 2006;Li et al, 2010;Lloyd et al, 2008), there has been only a slow uptake of emerging tools and standards for documenting and sharing the protocols for simulation experiments and their results (Cooper et al, 2011b;Waltemath et al, 2011aWaltemath et al, , 2011b.…”

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2

“…We will use this model to demonstrate how a simulation experiment can be described simply and effectively. The simulation example is taken from Waltemath et al [2011a].…”

“…However, the description of the structure of models is not sufficient to enable the reproduction of simulation results. One also needs to describe the procedures the models are subjected to, as described by the Minimum Information About a Simulation Experiment (MIASE) [Waltemath et al, 2011a].…”