The Spectrum of Mechanism-Oriented Models and Methods for Explanations of Biological Phenomena

摘要: Developing and improving mechanism-oriented computational models to better explain biological phenomena is a dynamic expanding frontier. As the complexity of targeted has increased, so too diversity in methods terminologies, often at expense clarity, which can make reproduction challenging, even problematic. To encourage improved semantic methodological we describe spectrum Mechanism-oriented Models being used develop explanations phenomena. We cluster into three broad groups. then expand them seven workflow-related model types having distinguishable features. name each type illustrate with examples drawn from literature. These may contribute foundation an ontology mechanism-based biomedical simulation research. show that different manifest exert their scientific usefulness by enhancing extending forms degrees explanation. The process starts knowledge about phenomenon continues explanatory mathematical descriptions. Those descriptions are transformed software perform experimental explorations running examining output. credibility inferences thus linked easy access technical provenance workflow stage.