Translational Systems Biology. Concepts and Practice for the Future of Biomedical Research

Table of Contents

I. Introduction and Overview 1.1 Interesting Times: The Translational Dilemma and the Need for Translational Systems Biology of Inflammation

II. The Current Landscape: Where It Came From, How We Got Here, And What Is Wrong 2.1 A Brief History of the Philosophical Basis of the Scientific Endeavor 2.2 A Brief History of Biomedical Research up to the Molecular Biology Revolution 2.3 Biomedical Reserach Since the Molecular Revolution: An Embarassment of Riches 2.3 Randomized Clinical Trials: A Bridge Too Far? 2.5 Complexity in Biomedical Research: Mysticism Versus Methods 2.6 Human Nature, Politics, and Translational Intertia

III. Translational Systems Biology: How We Propose To Fix The Problems Of The Current Biomedical Research Landscape 3.1 Towards Translational Systems Biology of Inflammation 3.2 Dynamic Knowledge Representation and the Power of Model Making 3.3 A Roadmap for a Rational Future: A Systematic Path for the Design and Implemetation of New Therapeutics

IV. Tools And Implementation Of Translational Systems Biology: This Is How We Do It 4.1 From Data to Knowledge in Translational Systems Biology: An Overview of Computational Approaches Across the Scientific Cycle 4.2 Data-Driven and Statistical Models: Everything Old is New Again 4.3 Mechanistic Modeling of Critical Illness Using Equations 4.4 Agent-Based Modeling and Translational Systems Biology: An Evolution in Parallel 4.5 Getting Science to Scale: Accelerating the Development of Translational Computational Models

V. A New Scientific Cycle for Translational Research and Healthcare Delivery 5.1 What is Old is New Again: The Scientific Cycle in the Twenty-First Century and Beyond

Authors

Yoram Vodovotz University of Pittsburgh, Pittsburgh, PA, USA. Yoram Vodovotz, Ph.D., is currently the President of the Society for Complexity in Acute Illness. His research interests include the biology of acute inflammation in shock states, chronic inflammatory diseases, wound healing, malaria, and restenosis. His work utilizes mathematical modeling to unify and gain insight into the biological interactions that characterize these inflammatory conditions. As the Director of the Center for Inflammation and Regenerative Modeling (CIRM) at the University of Pittsburgh's McGowan Institute for Regenerative Medicine, he has been involved in the mathematical modeling of acute inflammatory states (e.g. septic or hemorrhagic shock, wound healing), including cellular and physiological elements, as part of a large, interdisciplinary collaborative team. He is also a co-founder of Immunetrics, Inc., a company that is commercializing this mathematical modeling work. Gary An University of Chicago, Chicago, IL, USA. Gary An is a trauma/critical care surgeon at The University of Chicago engaged in translational computational research. His work on system-level simulations of trauma and sepsis led him to a more general concern about the ability of biomedical researchers to represent their knowledge and hypotheses in a form that can be "executed,” so that the dynamic consequences of their hypotheses can be seen and evaluated. He is the author of over 59 primary papers and book chapters, is a Senior Fellow of the University of Chicago Computation Institute and current president of the Swarm Development Group for simulation software.