An introduction to Biomodel engineering, illustrated for signal transduction pathways

BioModel Engineering is the science of designing, constructing and analyzing computational models of biological systems. It is inspired by concepts from software engineering and computing science. This paper illustrates a major theme in BioModel Engineering, namely that identifying a quantitative model of a dynamic system means building the structure, finding an initial state, and parameter fitting. In our approach, the structure is obtained by piecewise construction of models from modular parts, the initial state is obtained by analysis of the structure and parameter fitting comprises determining the rate parameters of the kinetic equations. We illustrate this with an example in the area of intracellular signalling pathways

Integrated Modeling and Verification of Real-Time Systems through Multiple Paradigms

Complex systems typically have many different parts and facets, with different characteristics. In a multi-paradigm approach to modeling, formalisms with different natures are used in combination to describe complementary parts and aspects of the system. This can have a beneficial impact on the modeling activity, as different paradigms an be better suited to describe different aspects of the system. While each paradigm provides a different view on the many facets of the system, it is of paramount importance that a coherent comprehensive model emerges from the combination of the various partial descriptions. In this paper we present a technique to model different aspects of the same system with different formalisms, while keeping the various models tightly integrated with one another. In addition, our approach leverages the flexibility provided by a bounded satisfiability checker to encode the verification problem of the integrated model in the propositional satisfiability (SAT) problem; this allows users to carry out formal verification activities both on the whole model and on parts thereof. The effectiveness of the approach is illustrated through the example of a monitoring system.Comment: 27 page

A comparative analysis of business process modelling techniques

Business process modelling is an increasingly popular research area for both organisations and academia due to its usefulness in facilitating human understanding and communication. Several modelling techniques have been proposed and used to capture the characteristics of business processes. However, available techniques view business processes from different perspectives and have different features and capabilities. Furthermore, to date limited guidelines exist for selecting appropriate modelling techniques based on the characteristics of the problem and its requirements. This paper presents a comparative analysis of some popular business process modelling techniques. The comparative framework is based on five criteria: flexibility, ease of use, understandability, simulation support and scope. The study highlights some of the major paradigmatic differences between the techniques. The proposed framework can serve as the basis for evaluating further modelling techniques and generating selection procedures

Formal Methods for Systems Engineering Behavior Models

International audienceSafety analysis in Systems Engineering (SE) processes, as usually implemented, rarely relies on formal methods such as model checking since such techniques, however powerful and mature, are deemed too complex for efficient use. This paper thus aims at improving the verification practice in SE design: considering the widely-used model of EFFBDs (Enhanced Function Flow Block Diagrams), it formally establishes its syntax and behavioral semantics. It also proposes a structural translation of EFFBDs to transition time Petri nets (TPNs); this translation is then proved to preserve the behavioral semantics (i.e. timed bisimilarity). After proving results on the boundedness of the resulting TPNs, it was possible to extend a number of fundamental properties (such as the decidability of liveness, state-access, etc.) from bounded TPNs to so-called \emph{bounded EFFBDs}. Finally, these results led to implement and integrate an operational formal verification tool within a development platform, used in systems design for defense applications, where the underlying complexity is totally concealed from the end-us

09091 Abstracts Collection -- Formal Methods in Molecular Biology

From 23. February to 27. February 2009, the Dagstuhl Seminar 09091 ``Formal Methods in Molecular Biology \u27\u27 was held in Schloss Dagstuhl~--~Leibniz Center for Informatics. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available

Modeling and Analyzing Cyber-Physical Systems Using Hybrid Predicate Transition Nets

Cyber-Physical Systems (CPSs) are software controlled physical devices that are being used everywhere from utility features in household devices to safety-critical features in cars, trains, aircraft, robots, smart healthcare devices. CPSs have complex hybrid behaviors combining discrete states and continuous states capturing physical laws. Developing reliable CPSs are extremely difficult. Formal modeling methods are especially useful for abstracting and understanding complex systems and detecting and preventing early system design problems. To ensure the dependability of formal models, various analysis techniques, including simulation and reachability analysis, have been proposed in recent decades. This thesis aims to provide a unified formal modeling and analysis methodology for studying CPSs. Firstly, this thesis contributes to the modeling and analysis of discrete, continuous, and hybrid systems. This work enhances modeling of discrete systems using predicate transition nets (PrTNs) by fully realizing the underlying specification through incorporating the first-order logic with set theory, improving the type system, and providing incremental model composition. This work enhances the technique of analyzing discrete systems using PrTN by improving the simulation algorithm and its efficient implementation. This work also improves the analysis of discrete systems using SPIN by providing a more accurate and complete translation method. Secondly, this work contributes to the modeling and analysis of hybrid systems by proposing an extension of PrTNs, hybrid predicate transition nets (HPrTNs). The proposed method incorporates a novel concept of token evolution, which nicely addresses the continuous state evolution and the conflicts present in other related works. This work presents a powerful simulation capability that can handle linear, non-linear dynamics, transcendental functions through differential equations. This work also provides a complementary technique for reachability analysis through the translation of HPrTN models for analysis using SpaceEx

Simulation Modelling Practice and Theory

The influx of data in the world today needs analysis that no one method can handle. Some reports estimated the influx of data would reach 163 zitabytes by 2025, hence the need for simulation and modeling theory and practice. Simulation and modeling tools and techniques are most important in this day and age. While simulation carries the needed work, tools for visualizing the results help in the decision-making process. Simulation ranges from a simple queue to molecular dynamics, including seismic reliability analysis, structural integrity assessment, games, reliability engineering, and system safety. This book will introduce practitioners, researchers, and novice users to simulation and modeling, and to the world of imagination