A Petri nets-based framework for whole-cell modeling

Design patterns for the construction of computational biological models

Computational biological models have proven to be an invaluable tool for understanding and predicting the behaviour of many biological systems. While it may not be too challenging for experienced researchers to construct such models from scratch, it is not a straightforward task for early stage researchers. Design patterns are well-known techniques widely applied in software engineering as they provide a set of typical solutions to common problems in software design. In this paper, we collect and discuss common patterns that are usually used during the construction and execution of computational biological models. We adopt Petri nets as a modelling language to provide a visual illustration of each pattern; however, the ideas presented in this paper can also be implemented using other modelling formalisms. We provide two case studies for illustration purposes and show how these models can be built up from the presented smaller modules. We hope that the ideas discussed in this paper will help many researchers in building their own future models.

Surveying membrane landscapes: a new look at the bacterial cell surface

Recent studies applying advanced imaging techniques are changing the way we understand bacterial cell surfaces, bringing new knowledge on everything from single-cell heterogeneity in bacterial populations to their drug sensitivity and mechanisms of antimicrobial resistance. In both Gram-positive and Gram-negative bacteria, the outermost surface of the bacterial cell is being imaged at nanoscale; as a result, topographical maps of bacterial cell surfaces can be constructed, revealing distinct zones and specific features that might uniquely identify each cell in a population. Functionally defined assembly precincts for protein insertion into the membrane have been mapped at nanoscale, and equivalent lipid-assembly precincts are suggested from discrete lipopolysaccharide patches. As we review here, particularly for Gram-negative bacteria, the applications of various modalities of nanoscale imaging are reawakening our curiosity about what is conceptually a 3D cell surface landscape: what it looks like, how it is made and how it provides resilience to respond to environmental impacts.

Modelling and measuring complexity of traditional and ancient technologies using Petri nets

Technologies and their production systems are used by archaeologists and anthropologists to study complexity of socio-technical systems. However, there are several issues that hamper agreement about what constitutes complexity and how we can systematically compare the complexity of production systems. In this work, we propose a novel approach to assess the behavioural and structural complexity of production systems using Petri nets. Petri nets are well-known formal models commonly used in, for example, biological and business process modelling, as well as software engineering. The use of Petri nets overcomes several obstacles of current approaches in archaeology and anthropology, such as the incompatibility of the intrinsic sequential logic of the available methods with inherently non-sequential processes, and the inability to explicitly model activities and resources separately. We test the proposed Petri net modelling approach on two traditional production systems of adhesives made by Ju/'hoan makers from Nyae, Namibia from Ammocharis coranica and Ozoroa schinzii plants. We run simulations in which we assess the complexity of these two adhesive production systems in detail and show how Petri net dynamics reveal the structural and behavioural complexity of different production scenarios. We show that concurrency may be prevalent in the production system of adhesive technologies and discuss how changes in location during the process may serve to control the behavioural complexity of a production system. The approach presented in this paper paves the way for future systematic visualization, analysis, and comparison of ancient production systems, accounting for the inherent complex, concurrent, and action/resource-oriented aspects of such processes.

Coloured fuzzy Petri nets for modelling and analysing membrane systems

Membrane systems are a very powerful computational modelling formalism inspired by the internal organisation of living cells. Modelling of membrane systems is challenged by composing many structurally similar components, which may result in very large models. Furthermore, some components may suffer from a lack of precise kinetic parameters. FPN^C (coloured fuzzy Petri nets) combine coloured Petri nets with fuzzy kinetic parameters, and thus offer an approach to address these challenges. In this paper, we use FPN^C to model and simulate membrane systems which are enriched by fuzzy kinetic parameters. We also introduce a methodology and workflow utilising FPN^C for modelling and simulating general biological systems which have to cope with incomplete knowledge of their kinetic data.