We present a core Ontology of Biomodelling (OBM), which formally defines principle entities of modelling of biological systems, and follows a structural approach for the engineering of biochemical network models. OBM is fully interoperable with relevant resources, e.g. GO, SBML, ChEBI, and the recording of biomodelling knowledge with Ontology of Biomedical investigations (OBI) ensures efficient...

1 Computational Biomodelling Laboratory Department of Information Technologies Åbo Akademi University, Turku 20520, Finland [email protected] 2 Dipartimento di Informatica, Sistemistica e Comunicazione Università degli Studi di Milano – Bicocca Viale Sarca 336/14, 20126 Milano, Italy [email protected] 3 Key Laboratory of Image Processing and Intelligent Control Department of Control Scie...

1 Key Laboratory of Image Processing and Intelligent Control Department of Control Science and Engineering Huazhong University of Science and Technology Wuhan 430074, Hubei, People’s Republic of China [email protected], [email protected] 2 Computational Biomodelling Laboratory Åbo Akademi University Department of Information Technologies 20520 Turku, Finland [email protected] 3 Research Gr...

Andrea Tinelli* *Corresponding author:Andrea Tinelli, The International Translational Medicine and Biomodelling Research Group, Department of Applied Mathematics, Moscow Institute of Physics and Technology (State University), Moscow Region, Russia. Division of Experimental Endoscopic Surgery, Imaging, Technology and Minimally Invasive Therapy of Centre for Interdisciplinary Research Applied to ...

1 Computational Biomodelling Laboratory Åbo Akademi University Department of Information Technologies 20520 Turku, Finland [email protected] 2 Università degli Studi di Milano – Bicocca Dipartimento di Informatica, Sistemistica e Comunicazione Viale Sarca 336/14, 20126 Milano, Italy [email protected] 3 Key Laboratory of Image Processing and Intelligent Control Department of Control Scien...

In this paper we present the foundation of a unified, object-oriented, three-dimensional biomodelling environment, which allows us to integrate multiple submodels at scales from subcellular to those of tissues and organs. Our current implementation combines a modified discrete model from statistical mechanics, the Cellular Potts Model, with a continuum reaction-diffusion model and a state autom...