An Agent-Oriented Conceptual Framework for Systems Biology. In: Priami C, Merelli E, Gonzalez P, Omicini A, editors. Transactions on Computational Systems Biology III. Berlin: Springer Berlin Heidelberg; 2005. pp. 105-22. [DOI: 10.1007/11599128_8]

Clustering Based Parameter Estimation of Thyroid Hormone Pathway

An ordinary differential equation (ODE) model of the working of the thyroid system for euthyroidism has been presented. As clinical data for thyroid hormones is relatively scarce, such modelling offers potential benefits over wet lab procedures. Genetic algorithms developed for determining of parameters of the ODE system using the available data have been presented and evaluated. This approach enables subject specific parameter estimation towards characterisation of individual thyroid operation. Initially, a simple steady state model was used. Later a cosinor model for the circadian variation of thyroid hormones was used to obtain more reliable results, as indicated through sensitivity analysis in conjunction with other statistical methods. Our parameter determination method has been tested on groups of patients with similar observed values of thyroid stimulating hormone (TSH), free T ₃ and free T ₄ (identified through clustering) to determine their parameter values jointly. This approach appears to produce parameter sets with lower variation than parameters determined independently, thus leading to better parameter determination.

Agent-Based Modeling in Molecular Systems Biology

Molecular systems orchestrating the biology of the cell typically involve a complex web of interactions among various components and span a vast range of spatial and temporal scales. Computational methods have advanced our understanding of the behavior of molecular systems by enabling us to test assumptions and hypotheses, explore the effect of different parameters on the outcome, and eventually guide experiments. While several different mathematical and computational methods are developed to study molecular systems at different spatiotemporal scales, there is still a need for methods that bridge the gap between spatially-detailed and computationally-efficient approaches. In this review, we summarize the capabilities of agent-based modeling (ABM) as an emerging molecular systems biology technique that provides researchers with a new tool in exploring the dynamics of molecular systems/pathways in health and disease.

Agent-Based Modelling in Multicellular Systems Biology

This chapter aims at discussing the content of multi-agent based simulation (MABS) applied to computational biology i.e., to modelling and simulating biological systems by means of computational models, methodologies, and frameworks. In particular, the adoption of agent-based modelling (ABM) in the field of multicellular systems biology is explored, focussing on the challenging scenarios of developmental biology. After motivating why agent-based abstractions are critical in representing multicellular systems behaviour, MABS is discussed as the source of the most natural and appropriate mechanism for analysing the self-organising behaviour of systems of cells. As a case study, an application of MABS to the development of Drosophila Melanogaster is finally presented, which exploits the ALCHEMIST platform for agent-based simulation.

Agent-based models of cellular systems

Software agents are particularly suitable for engineering models and simulations of cellular systems. In a very natural and intuitive manner, individual software components are therein delegated to reproduce "in silico" the behavior of individual components of alive systems at a given level of resolution. Individuals' actions and interactions among individuals allow complex collective behavior to emerge. In this chapter we first introduce the readers to software agents and multi-agent systems, reviewing the evolution of agent-based modeling of biomolecular systems in the last decade. We then describe the main tools, platforms, and methodologies available for programming societies of agents, possibly profiting also of toolkits that do not require advanced programming skills.

An agent-based multilayer architecture for bioinformatics grids

Due to the huge volume and complexity of biological data available today, a fundamental component of biomedical research is now in silico analysis. This includes modelling and simulation of biological systems and processes, as well as automated bioinformatics analysis of high-throughput data. The quest for bioinformatics resources (including databases, tools, and knowledge) becomes therefore of extreme importance. Bioinformatics itself is in rapid evolution and dedicated Grid cyberinfrastructures already offer easier access and sharing of resources. Furthermore, the concept of the Grid is progressively interleaving with those of Web Services, semantics, and software agents. Agent-based systems can play a key role in learning, planning, interaction, and coordination. Agents constitute also a natural paradigm to engineer simulations of complex systems like the molecular ones. We present here an agent-based, multilayer architecture for bioinformatics Grids. It is intended to support both the execution of complex in silico experiments and the simulation of biological systems. In the architecture a pivotal role is assigned to an "alive" semantic index of resources, which is also expected to facilitate users' awareness of the bioinformatics domain.