Toward a curated CellML model repository

Computational Modeling of Mitochondrial Function from a Systems Biology Perspective

The advent of "big data" in biology (e.g., genomics, proteomics, metabolomics), holding the promise to reveal the nature of the formidable complexity in cellular and organ makeup and function, has highlighted the compelling need for analytical and integrative computational methods to interpret and make sense of the patterns and changes in those complex networks. Computational models need to be built on sound physicochemical mechanistic principles in order to integrate, interpret, and simulate high-throughput experimental data. Energy transduction processes have been traditionally studied with thermodynamic, kinetic, or thermo-kinetic models, with the latter proving superior to understand the control and regulation of mitochondrial energy metabolism and its interactions with cytoplasmic and other cellular compartments. In this work, we survey the methods to be followed to build a computational model of mitochondrial energetics in isolation or integrated into a network of cellular processes. We describe the use of analytical tools such as elementary flux modes, linear optimization of metabolic models, and control analysis, to help refine our grasp of biologically meaningful behaviors and model reliability. The use of these tools should improve the design, building, and interpretation of steady-state behaviors of computational models while assessing validation criteria and paving the way to prediction.

MML toolkit and work flow overview: Creating temporo-spatial heart models from CellML

The Modeling Markup Language (MML) framework is a conceptual paradigm to quickly develop and solve biological models utilizing the CellML specification. In this study, we present the open source toolkit developed for this project and a possible workflow to create different scales of cardiac tissue models from a range of CellML models. Models from the CellML repository and other sources were tested for interoperability against the MML framework. Furthermore, to demonstrate the ability of the MML framework to deploy different scales of geometry, a model of atrial electrical activation is also presented.

Modelling heart beat initiation and propagation using the MML framework

The Modeling Markup Language (MML) framework provides a temporo-spatial level modeling tool, consisting of two representation languages with tools which utilize CellML, a mathematical biological model representational language. The purpose of MML is to encourage reuse, sharing and efficiency. In this study, we utilize MML to investigate the role of the hyperpolarizing activated (i(f)) current of the sinoatrial node (SAN), the natural pacemaker of the heart. The if is believed to play an important role in heart automaticity and pacing rate. By using the MML framework and CellML specification, we construct a range of models to examine the role of i(f) in the SAN as well as aspects of wavefront propagation from the SAN into the atria.

The role of theoretical modeling in microcirculation research

Theoretical modeling approaches have made important contributions to research in the biological sciences, including the microcirculation, and their value is increasingly recognized. However, misconceptions about the nature and role of theoretical models persist, and such work is often presented in a way that does not maximize its value, especially for scientists who are not themselves using such models. In this review, a categorization of models as phenomenological, qualitative conceptual, quantitative conceptual, or predictive is proposed, and the characteristics of each type are discussed. Recommendations are made for the presentation of models and for the future development of modeling approaches. The concepts discussed are generally applicable to the theoretical modeling of biological systems and are illustrated by using examples of modeling in microcirculation research.