Daniel Cook, MD, PhD

Research Professor, Physiology/Biophysics

Adjunct Research Professor, Biomedical Informatics and Medical Education



Developing tools for the representation and analysis of complex dynamic systems


Dr. Cook has been developing tools for the representation and analysis of complex dynamic systems for 40 years. He earned a BSME in mechanical engineering from the University of Michigan and spent 4 years as a Boeing while earning his Masters degree in Mechanical Engineering from the UW. To follow-up his masters thesis project on the simulation of glucose-induced insulin secretion, he entered the UW’s Medical Scientist Training Program to earn his MD and a PhD in Physiology & Biophysics. After making seminal discoveries in the electrophysiology of insulin secretion,

Dr. Cook returned to his interests in the computational representation and analysis of complex systems. He authored two graphics-based applications for diagramming and analyzing cell networks and based one program, Chalkboard, on a linguistic metaphor of entity interactions using noun/verb constructs. He then connected with Dr. Cornelius Rosse and the FMA project to learn state-of-the-art knowledge representation and query methods as part of the DARPA-sponsored Virtual Soldier Project.

In subsequent collaborations with Drs. John Gennari, James Brinkley, and others, he is developing informatics methods for the declarative representation of physics-based biosimulation models as needed by, for example, the European Virtual Physiological Human and IUPS Physiome projects. The major contributions to this effort are an ontology of classical physics, the Ontology of Physics for Biology (OPB), and light-weight OWL representations (SemSim models) that map the biological and mathematical content of individual simulation models to the FMA and OPB.