The Realistic Modeling of Biological Systems: A Workshop Synopsis

Abstract

There is a growing awareness for the need to understand the basic design principles of living systems. In May of 2005, a diverse group of researchers from the fields of biomedicine, physics, mathematics, engineering, and computer science were brought together in Mizpe Hayamim, Israel to contemplate the current and future trends in computational modeling of biology. In the following work we provide an overview of the discussions that took place and describe some of the research projects that were presented. We also discuss how these seemingly disparate efforts may be integrated and directed at the development of meaningful computational models of biological systems. The wide range of techniques presented in Mizpe Hayamim served to demonstrate not only the breadth of scale found in biology but also the diversity in criteria for the development and application of numerical models in the field. One of the key issues remains the reconciliation of different model types and their effective use as a single composite representation. By attempting to formulate a unifying theme that transcends traditional boundaries between disciplines, it is hoped that this workshop provided a first rallying point that will promote a new level of interaction and synergy in the field.

Accelerating reaction–diffusion simulations with general-purpose graphics processing units

“…Often, spatial distributions play an important role in the dynamic evolution of biomolecular systems. The analysis of such systems requires accurate yet highly performant simulation algorithms that can handle spatially inhomogeneous reaction-diffusion (Broderick and Rubin, 2006). Unfortunately, stochastic simulation methods for this problem are computationally extremely expensive and it thus becomes necessary to build parallel versions of existing algorithms (Ballarini et al, 2009).…”

Modeling Biological Systems Using Functional State Spaces

“…Such hybrid frameworks might contain a range of representations, such as Structure-Behavior-Function (SBF) representations, which one study suggests may enable more accurate inferences about biological systems for complex and abstract questions than purely textual, or textual and diagrammatic, representations, and that no one representation is best for all types of inferences [12]. Other efforts have also attempted to achieve the reconciliation of different model types into a single composite representation by formulating a unifying theme that transcends traditional boundaries between disciplines [13]. It remains to be determined which lessons from those efforts might be reused in defining biological systems in terms of this hierarchy of functional state spaces.…”

Systems biology of complex symptom profiles: Capturing interactivity across behavior, brain and immune regulation

“…Systems biology in its simplest form can be described as an integrative science. Fundamentally it is directed at the identification of organizing principles that govern the context-specific emergence of function from the interactions that occur between constituent parts (Broderick and Rubin, 2006; Chuang, Hofree and Ideker, 2010). Our current understanding suggests that many of these principles appear to be conserved across scales of biology.…”