A critical review on modelling formalisms and simulation tools in computational biosystems

Integration of different kinds of biological processes is an ultimate goal for whole-cell modelling. We briefly review modelling formalisms that have been used in Systems Biology and identify the criteria that must be addressed by an integrating framework capable of modelling, analysing and simulating different biological networks. Aware that no formalism can fit all purposes we realize Petri nets as a suitable model for Metabolic Engineering and take a deeper perspective on the role of this formalism as an integrating framework for regulatory and metabolic networks.Research supported by PhD grant SFRH/BD/35215/2007 from the Fundacao para a Ciencia e a Tecnologia (FCT) and the MIT-Portugal program

Peer-Based Programming Model for Coordination Patterns

International audienceModern distributed software systems must integrate in near-time parallel processes and heterogeneous information sources provided by active, autonomous software systems. Such lively information sources are e.g. sensory data, weather data, traffic data, or booking data, operated by independent distributed sites. The complex integration requires the coordination of these data flows to guarantee consistent global semantics. Design, implementation, analysis and control of distributed concurrent systems are notoriously complex tasks. Petri Nets are widely used to model concurrent activities. However, a higher-level programming abstraction is needed. We propose a new programming model for modeling concurrent coordination patterns, which is based on the idea of “peer workers” that represent re-usable coordination and application components. These components encapsulate behavior, structure distributed data and control flow, and allow integration of pre-existing service functions. A domain-specific language is presented. The usability of the peer-based programming model is evaluated with the Split/Join pattern

Protos 7.0: simulation made accessible

Many consider simulation to be a highly specialist activity: it is difficult to undertake and is even more difficult to understand its outcomes. The new version of the business process modeling tool Protos attempts to more closely integrate modeling and simulation facilities into one tool. The assumed benefit is that business professionals may more easily undertake simulation experiments when they are enabled with the same tool to extend their existing process models to carry out simulation experiments. This paper explains how the existing engine of the Petri-net based tool ExSpect is integrated into Protos 7.0. It also shows the extended user interface of Protos and the simulation reports it generates

CPN Tools for editing, simulating, and analysing coloured Petri nets

Abstract. CPN Tools is a tool for editing, simulating and analysing Coloured Petri Nets. The GUI is based on advanced interaction techniques, such as toolglasses, marking menus, and bi-manual interaction. Feedback facilities provide contextual error messages and indicate dependency relationships between net elements. The tool features incremental syntax checking and code generation which take place while a net is being constructed. A fast simulator efficiently handles both untimed and timed nets. Full and partial state spaces can be generated and analysed, and a standard state space report contains information such as boundedness properties and liveness properties. The functionality of the simulation engine and state space facilities are similar to the corresponding components in Design/CPN, which is a widespread tool for Coloured Petri Nets.

CPN tools for editing, simulating, and analysing coloured Petri nets

CPN Tools is a tool for editing, simulating and analysing Coloured Petri Nets. The GUI is based on advanced interaction techniques, such as toolglasses, marking menus, and bi-manual interaction. Feedback facilities provide contextual error messages and indicate dependency relationships between net elements. The tool features incremental syntax checking and code generation which take place while a net is being constructed. A fast simulator efficiently handles both untimed and timed nets. Full and partial state spaces can be generated and analysed, and a standard state space report contains information such as boundedness properties and liveness properties. The functionality of the simulation engine and state space facilities are similar to the corresponding components in Design/CPN, which is a widespread tool for Coloured Petri Nets

Designing Case Handling Systems

A case handling system is an information system supporting the handling of cases. The (sub) tasks for a particular case are performed by persons or software agents and the result of a task is the updating of the case data. Case handling systems consist of three parts: (1) a workflow engine that executes the process of a case, (2) a document manager that manipulates the case data and (3) a database manager for manipulation of the global data, i.e., the data that is independent of a particular case. In this paper we present a new methodology for the first four phases of the development of a case handling system: (1) user requirements, (2) functional architecture, (3) software architecture, and (4) the prototyping phase. The methodology is supported by a tool consisting of a Petri net based workflow engine, a standard document manager and a standard database system