The ‘Physiome’, physiological modeling, and related endeavors:

The Physiome Project

“The PHYSIOME is the quantitative description of the physiological dynamics or functions of the intact organism. The name comes from "physio-" (life) and "-ome" (as a whole). The PHYSIOME PROJECT is an integrated multi-centric program to design, develop, implement, test and document, archive and disseminate quantitative information and integrative models of the functional behavior of organelles, cells, tissues, organs, and organisms. The long-range goal is to understand and describe the human organism, its physiology and pathophysiology, and to use this understanding in improving human health. But much or most of what must be learned will come from other species. The project aims toward providing models that summarize information on physiological systems, integrating the observations from many laboratories into quantitative, self-consistent, comprehensive descriptions. The goal is to provide to the community of scientists, physicians, teachers, and to medical health professional and industrial communities, functional descriptions of human biological systems in health and disease. A fundamental and major feature of the program is the databasing of the basic observations for retrieval and evaluation.”

National Simulation Resource for Circulatory Transport and Exchange
University of Washington

The National Simulation Resource Facility for Circulatory Transport and Exchange operates as a part of the Department of Bioengineering in the School of Medicine and the College of Engineering…The Resource was created with a focus on studying complex biological systems and networks involved in the transport and exchange of solutes and water in the microvasculature, within whole organs, and within the whole body. While the focus of much of modern biology has been on the study of individual genes, proteins, channels, signaling pathways, and the basic biophysics and biochemistry of cellular and molecular biology, the future trend is a shift of focus to studying systems. The premise is that only by analyzing ever more complete systems can one understand the enchanting beauty and remarkable behaviors of intact, functioning organisms…The analysis of biological systems requires the development of powerful new tools, computational and intellectual, that aid the investigator in the analysis of experimental data, and allow these results to be integrated with the other types of observations present in the literature. Mathematical models can serve as one such vehicle, but, more than that, they allow rapid, sensitive, and semi-automated approaches to designing the most discriminating experiments, expressing data in quantitative and mechanistic terms, and in distinguishing good hypotheses from better ones.”

Center for Computational Medicine & Biology
Johns Hopkins University

“…A focus of the Center is to understand, through development of computational models, how the microscopic properties of biological systems interact to give rise to macroscopic behavior. This is a challenging problem, since the dynamical behavior of all biological systems is determined by interactions between a large number of closely coupled components, each of which may have highly nonlinear properties. Mathematical and computational techniques being developed and applied by Center researchers include modeling of excitable systems, tissue mechanics, and biological fluid flow and transport; applications of nonlinear dynamical systems theory to investigate the parameter dependence of complex biological systems models; applications of the theory of stochastic processes to the modeling of ion channels; molecular dynamics simulations to study dynamics of channels and receptors; and mathematical methods for the representation and analysis of variation in shape of three-dimensional anatomic structures…”

General Neuronal Simulation System (GENESIS)
California Institute of Technology

“GENESIS (short for GEneral NEural SImulation System) is a general purpose simulation platform which was developed to support the simulation of neural systems ranging from complex models of single neurons to simulations of large networks made up of more abstract neuronal components. GENESIS has provided the basis for laboratory courses in neural simulation at both Caltech and the Marine Biological Laboratory in Woods Hole, MA, as well as many other institutions. Most current GENESIS applications involve realistic simulations of biological neural systems. Although the software can also model more abstract networks, other simulators are more suitable for backpropagation and similar connectionist modeling.”

NIH Center for Bioelectric Field Modeling, Simulation and Visualization
University of Utah

 “The NIH Center for Bioelectric Field Modeling, Simulation, and Visualization is a collaboration between the Scientific Computing and Imaging Institute and the Nora Eccles Harrison Cardiovascular Research and Training Institute to conduct research and development in advanced modeling, simulation, and visualization methods for solving bioelectric field problems. Modern medical imaging technologies such as magnetic resonance imaging, ultrasound, and positron emission tomography, provide a wealth of anatomical information to doctors and researchers. Measurements of the electric and magnetic fields from the body, such as electrocardiography (ECG) and magnetoencephalogrphy (MEG), reflect the underlying bioelectrical activity of the tissues and organs. However, without equally advanced modeling and visualization technologies, much of the potential value of this information is lost. Our goal is to couple advanced medical imaging technology with state of the art computer simulation and modeling techniques to produce new methods and tools, which will allow doctors and researchers to tackle immediately important medical problems…To accomplish this goal, we have created an integrated software tool for bioelectric field problems called "Bioelectric Problem Solving Environment" or more regularly, "BioPSE."

The Microcirculation Physiome Project
Johns Hopkins University

“Information on biological systems continues to amass at a rapid rate. While attempts to integrate this information have begun, most of the effort has been aimed at collection of genetic sequence information. As the task of compiling this information nears completion we must begin to layer functional data onto these databases. One attempt at organizing functional information is the Physiome Project. The Physiome Project is an integrated program whose mission is to archive and disseminate quantitative data and models of the functional behavior of biological molecules, cells, tissues, organs, and organisms. Several organ-based efforts, such as the Cardiome, have begun to develop. A functional system such as the microcirculation is a logical extension of the organ based approaches, since much of its structure and function are common between organs, and because its hemodynamic and transport function provides an important coupling between cells, tissues, and organs. Thus, we propose to develop a database of the microcirculation that encompasses anatomical and functional data with mathematical and computational models, computational engines, and tools for integration. The proposed database would include information on microcirculations in the heart, brain, skeletal muscle, lung, kidney, liver, pancreas, spleen, bone, eye, and other organs in health and disease. This database would be directly linked to other appropriate databases, such as gene and protein expression databases, and the rat, mouse and human genome project databases. We refer to this international effort as "The Microcirculation Physiome Project."

Entelos Physiolabs, Inc. (COMMERCIAL SITE)
“Entelos is the leader in predictive biological modeling and disease simulation systems for drug discovery, development, and commercialization. Entelos' mission is to transform the way pharmaceutical and biotech companies do their work, increasing their fundamental understanding of health and disease and improving their odds of success through the use of predictive systems like PhysioLabs.”   

Physiome Sciences (COMMERCIAL SITE)
“Physiome Sciences' mission is to help pharmaceutical companies develop better drugs faster through the use of biological simulations. Physiome is the leading provider of customizable computer-based models of cells, organs and systems that have been designed to incorporate client data and yield proprietary, company-specific insights into drug targets and disease mechanisms. Physiome's unique simulation platform combines process, technology, tools and applications to solve complex biomedical research problems and improve the quality of drug candidates.”