The Spectrum of Mechanism-oriented Models for Explanations of Biological Phenomena

摘要: Within the diverse interdisciplinary life sciences domains, semantic, workflow, and methodological ambiguities can prevent appreciation of explanations phenomena, handicap use computational models, hamper communication among scientists, engineers, public. Members community commonly, too often loosely, draw on "mechanistic model" similar phrases when referring to processes discovering establishing causal biological phenomena. Ambiguities in modeling simulation terminology methods diminish clarity, credibility, perceived significance research findings. To encourage improved semantic we describe spectrum Mechanism-oriented Models being used develop We cluster them into three broad groups. then expand groups a total seven workflow-related model types having clearly distinguishable features. name each type illustrate with examples drawn from literature. These are intended contribute foundation an ontology mechanism-based sciences. show that it is within model-development workflows different manifest exert their scientific usefulness by enhancing extending forms degrees explanation. The process starts knowledge about phenomenon continues explanatory mathematical descriptions. Those descriptions transformed software perform experimental explorations running examining output. credibility inferences thus linked easy access technical provenance workflow stage.