Petri nets for systems and synthetic biology

We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which uni¯es the qualita- tive, stochastic and continuous paradigms. Each perspective adds its con- tribution to the understanding of the system, thus the three approaches do not compete, but complement each other. We illustrate our approach by applying it to an extended model of the three stage cascade, which forms the core of the ERK signal transduction pathway. Consequently our focus is on transient behaviour analysis. We demonstrate how quali- tative descriptions are abstractions over stochastic or continuous descrip- tions, and show that the stochastic and continuous models approximate each other. Although our framework is based on Petri nets, it can be applied more widely to other formalisms which are used to model and analyse biochemical networks

Non-null Infinitesimal Micro-steps: a Metric Temporal Logic Approach

Many systems include components interacting with each other that evolve with possibly very different speeds. To deal with this situation many formal models adopt the abstraction of "zero-time transitions", which do not consume time. These however have several drawbacks in terms of naturalness and logic consistency, as a system is modeled to be in different states at the same time. We propose a novel approach that exploits concepts from non-standard analysis to introduce a notion of micro- and macro-steps in an extension of the TRIO metric temporal logic, called X-TRIO. We use X-TRIO to provide a formal semantics and an automated verification technique to Stateflow-like notations used in the design of flexible manufacturing systems.Comment: 20 pages, 2 figures, submitted to the conference "FORMATS: Formal Modelling and Analysis of Timed Systems" 201

Capturing Assumptions while Designing a Verification Model for Embedded Systems

A formal proof of a system correctness typically holds under a number of assumptions. Leaving them implicit raises the chance of using the system in a context that violates some assumptions, which in return may invalidate the correctness proof. The goal of this paper is to show how combining informal and formal techniques in the process of modelling and formal verification helps capturing these assumptions. As we focus on embedded systems, the assumptions are about the control software, the system on which the software is running and the system’s environment. We present them as a list written in natural language that supplements the formally verified embedded system model. These two together are a better argument for system correctness than each of these given separately

Probabilistic Model Checking for Energy Analysis in Software Product Lines

In a software product line (SPL), a collection of software products is defined by their commonalities in terms of features rather than explicitly specifying all products one-by-one. Several verification techniques were adapted to establish temporal properties of SPLs. Symbolic and family-based model checking have been proven to be successful for tackling the combinatorial blow-up arising when reasoning about several feature combinations. However, most formal verification approaches for SPLs presented in the literature focus on the static SPLs, where the features of a product are fixed and cannot be changed during runtime. This is in contrast to dynamic SPLs, allowing to adapt feature combinations of a product dynamically after deployment. The main contribution of the paper is a compositional modeling framework for dynamic SPLs, which supports probabilistic and nondeterministic choices and allows for quantitative analysis. We specify the feature changes during runtime within an automata-based coordination component, enabling to reason over strategies how to trigger dynamic feature changes for optimizing various quantitative objectives, e.g., energy or monetary costs and reliability. For our framework there is a natural and conceptually simple translation into the input language of the prominent probabilistic model checker PRISM. This facilitates the application of PRISM's powerful symbolic engine to the operational behavior of dynamic SPLs and their family-based analysis against various quantitative queries. We demonstrate feasibility of our approach by a case study issuing an energy-aware bonding network device.Comment: 14 pages, 11 figure