Formal Quantitative Analysis of Reaction Networks Using Chemical Organisation Theory

Proceedings of CMSB 2016 will be published as a volume in Springer's Lecture Notes in Computer Science / Lecture Notes in Bioinformatics series (LNCS/LNBI)

Design and Development of Software Tools for Bio-PEPA

This paper surveys the design of software tools for the Bio-PEPA process algebra. Bio-PEPA is a high-level language for modelling biological systems such as metabolic pathways and other biochemical reaction networks. Through providing tools for this modelling language we hope to allow easier use of a range of simulators and model-checkers thereby freeing the modeller from the responsibility of developing a custom simulator for the problem of interest. Further, by providing mappings to a range of different analysis tools the Bio-PEPA language allows modellers to compare analysis results which have been computed using independent numerical analysers, which enhances the reliability and robustness of the results computed.

Organisation-Oriented Coarse Graining and Refinement of Stochastic Reaction Networks

The authors acknowledge support from the European Union through funding under FP7–ICT–2011–8 project HIERATIC 14 (316705). We also thank the anonymous reviewers for their helpful and detailed comments.Peer reviewedPostprin

Organising metabolic networks: cycles in flux distributions

Metabolic networks are among the most widely studied biological systems. The topology and interconnections of metabolic reactions have been well described for many species, but are not sufficient to understand how their activity is regulated in living organisms. The principles directing the dynamic organisation of reaction fluxes remain poorly understood. Cyclic structures are thought to play a central role in the homeostasis of biological systems and in their resilience to a changing environment. In this work, we investigate the role of fluxes of matter cycling in metabolic networks. First, we introduce a methodology for the computation of cyclic and acyclic fluxes in metabolic networks, adapted from an algorithm initially developed to study cyclic fluxes in trophic networks. Subsequently, we apply this methodology to the analysis of three metabolic systems, including the central metabolism of wild type and a deletion mutant of Escherichia coli, erythrocyte metabolism and the central metabolism of the bacterium Methylobacterium extorquens. The role of cycles in driving and maintaining the performance of metabolic functions upon perturbations is unveiled through these examples. This methodology may be used to further investigate the role of cycles in living organisms, their pro-activity and organisational invariance, leading to a better understanding of biological entailment and information processing

Authority in the Age of Modularity

This paper builds upon on-going research into the organisational implications of 'modularity'. Advocates of modularity argue that the Invisible Hand of markets is reaching activities previously controlled through the Visible Hand of hierarchies. This paper argues that there are cognitive limits to the extent of division of labour: what kinds of problems firms solve, and how they solve them, set limits to the extent of division of labour, irrespective of the extent of the market. This paper analyses the cognitive limits to the division of labour relying on an in-depth case study of engineering design activities. On this basis, this paper explains why co-ordinating increasingly specialised bodies of knowledge, and increasingly distributed learning processes, requires the presence of knowledge integrating firms even in the presence of modular products. Such firms, relying on their wide in-house scientific and technological capabilities, have the 'authority' to identify, propose, and implement solutions to complex problems. In so doing, they co-ordinate networks of suppliers of both components and specialised competencies.modularity, division of labour limits, knowledge integrating firms

Mathematical models for chemotaxis and their applications in self-organisation phenomena

Chemotaxis is a fundamental guidance mechanism of cells and organisms, responsible for attracting microbes to food, embryonic cells into developing tissues, immune cells to infection sites, animals towards potential mates, and mathematicians into biology. The Patlak-Keller-Segel (PKS) system forms part of the bedrock of mathematical biology, a go-to-choice for modellers and analysts alike. For the former it is simple yet recapitulates numerous phenomena; the latter are attracted to these rich dynamics. Here I review the adoption of PKS systems when explaining self-organisation processes. I consider their foundation, returning to the initial efforts of Patlak and Keller and Segel, and briefly describe their patterning properties. Applications of PKS systems are considered in their diverse areas, including microbiology, development, immunology, cancer, ecology and crime. In each case a historical perspective is provided on the evidence for chemotactic behaviour, followed by a review of modelling efforts; a compendium of the models is included as an Appendix. Finally, a half-serious/half-tongue-in-cheek model is developed to explain how cliques form in academia. Assumptions in which scholars alter their research line according to available problems leads to clustering of academics and the formation of "hot" research topics.Comment: 35 pages, 8 figures, Submitted to Journal of Theoretical Biolog

Second Generation General System Theory: Perspectives in Philosophy and Approaches in Complex Systems

Following the classical work of Norbert Wiener, Ross Ashby, Ludwig von Bertalanffy and many others, the concept of System has been elaborated in different disciplinary fields, allowing interdisciplinary approaches in areas such as Physics, Biology, Chemistry, Cognitive Science, Economics, Engineering, Social Sciences, Mathematics, Medicine, Artificial Intelligence, and Philosophy. The new challenge of Complexity and Emergence has made the concept of System even more relevant to the study of problems with high contextuality. This Special Issue focuses on the nature of new problems arising from the study and modelling of complexity, their eventual common aspects, properties and approaches—already partially considered by different disciplines—as well as focusing on new, possibly unitary, theoretical frameworks. This Special Issue aims to introduce fresh impetus into systems research when the possible detection and correction of mistakes require the development of new knowledge. This book contains contributions presenting new approaches and results, problems and proposals. The context is an interdisciplinary framework dealing, in order, with electronic engineering problems; the problem of the observer; transdisciplinarity; problems of organised complexity; theoretical incompleteness; design of digital systems in a user-centred way; reaction networks as a framework for systems modelling; emergence of a stable system in reaction networks; emergence at the fundamental systems level; behavioural realization of memoryless functions

Ecological Modelling with the Calculus of Wrapped Compartments

The Calculus of Wrapped Compartments is a framework based on stochastic multiset rewriting in a compartmentalised setting originally developed for the modelling and analysis of biological interactions. In this paper, we propose to use this calculus for the description of ecological systems and we provide the modelling guidelines to encode within the calculus some of the main interactions leading ecosystems evolution. As a case study, we model the distribution of height of Croton wagneri, a shrub constituting the endemic predominant species of the dry ecosystem in southern Ecuador. In particular, we consider the plant at different altitude gradients (i.e. at different temperature conditions), to study how it adapts under the effects of global climate change.Comment: A preliminary version of this paper has been presented in CMC13 (LNCS 7762, pp 358-377, 2013