Gene expression is the synthesis of proteins from the information encoded on DNA. One of the two main steps of gene expression is the translation of messenger RNA (mRNA) into polypeptide sequences of amino acids. Here, by taking into account mRNA degradation, we model the motion of ribosomes along mRNA with a ballistic model where particles advance along a filament without excluded volume interactions. Unidirectional models of transport have previously been used to fit the average density of ribosomes obtained by the experimental ribo-sequencing (Ribo-seq) technique in order to obtain the kinetic rates. The degradation rate is not, however, accounted for and experimental data from different experiments are needed to have enough parameters for the fit. Here, we propose an entirely novel experimental setup and theoretical framework consisting in splitting the mRNAs into categories depending on the number of ribosomes from one to four. We solve analytically the ballistic model for a fixed number of ribosomes per mRNA, study the different regimes of degradation, and propose a criterion for the quality of the inverse fit. The proposed method provides a high sensitivity to the mRNA degradation rate. The additional equations coming from using the monosome (single ribosome) and polysome (arbitrary number) ribo-seq profiles enable us to determine all the kinetic rates in terms of the experimentally accessible mRNA degradation rate.

The analysis of probabilistic schedulability explores all possible combinations of the probabilities of task attributes, which can easily lead to exponential computation time [24]. In this paper, we present a flexible schedulability analysis framework for periodic and sporadic tasks having probabilistic attributes where the computation time scales linearly in the size of analyzed systems. The framework is given in terms of a set of Parameterized Stopwatch Automata (PSA) models, which leads to a large degree of flexibility. Probability distributions for response time are generated using statistical model checking (UPPAAL SMC) while the overall schedulability can be checked using symbolic model checking (UPPAAL). We also define PoMD (percentage of missed deadlines) as a measure of the probabilistic schedulability of systems. To evaluate our approach, we compare the time used for computing response times and the analysis results using similar task models to that of a related analytical approach.

We present the concept of degree of schedulability for mixed-criticality scheduling systems. This concept is given in terms of the two factors 1) Percentage of Missed Deadlines (PoMD), and 2) Degradation of the Quality of Service (DoQoS). The novel aspect is that we consider task arrival patterns that follow user-defined continuous probability distributions. We determine the degree of schedulability of a single scheduling component which can contain both periodic and sporadic tasks using statistical model checking in the form of UPPAAL SMC. We support uniform, exponential, Gaussian and any user-defined probability distribution.

This paper surveys well-established/recent tools and techniques developed for the design of rigorous embedded systems. We will first survey UPPAAL and MODEST, two tools capable of dealing with both timed and stochastic aspects. Then, we will overview the BIP framework for modular design and code generation. Finally, model-based testing will be discussed.

Abstract UPPAAL is a tool suitable for model checking real‐time systems described as networks of timed automata communicating by channel synchronizations and extended with integer variables. Its first version was released in 1995 and its development is still very active. It now features an advanced modeling language, a user‐friendly graphical interface, and a performant model checker engine. In addition, several flavors of the tool have matured in recent years. In this paper, we present how we managed to maintain the tool during 15 years, its current architecture with its challenges, and we give the future directions of the tool. Copyright © 2011 John Wiley & Sons, Ltd.

A specification theory combines notions of specifications and implementations with a satisfaction relation, a refinement relation and a set of operators supporting stepwise design.We develop a complete specification framework for real-time systems using Timed I/O Automata as the specification formalism, with the semantics expressed in terms of Timed I/O Transition Systems.We provide constructs for refinement, consistency checking, logical and structural composition, and quotient of specifications -all indispensable ingredients of a compositional design methodology.The theory is implemented on top of an engine for timed games, Uppaal-tiga, and illustrated with a small case study.

This paper studies the problem of model-based testing of real-time systems that are only partially observable. We model the system under test (SUT) using timed game automata (TGA) which has internal actions, uncontrollable outputs and timing uncertainty of outputs. We define the partial observability of SUT using a set of predicates over the TGA state space, and specify the test purposes in computation tree logic (CTL) formulas. A developed partially observable timed game solver is used to generate winning strategies, which are used as test cases. We propose a conformance testing framework, define a partial observation-based conformance relation, present the test execution algorithms, and prove the soundness and completeness of this test method (i.e., a detected error really violates the conformance relation; and if the SUT violates the test purpose, then a test case can be generated to detect this violation). Experiments on some non-trivial examples show that this method yields encouraging results.

This paper presents a game-theoretic approach to the testing of uncontrollable real-time systems. By modelling the systems with timed I/O game automata and specifying the test purposes as Timed CTL formulas, we employ a recently developed timed game solver UPPAAL-TIGA to synthesize winning strategies, and then use these strategies to conduct black-box conformance testing of the systems. The testing process is proved to be sound and complete with respect to the given test purposes. Case study and preliminary experimental results indicate that this is a viable approach to uncontrollable timed system testing.

We report on an industrial application of UPPAAL, in which a commercial field bus protocol (AF100) is modelled and analysed using the tool. During the case study, a number of imperfections in the protocol logic and its implementation are found and the error sources are debugged based on abstract models of the protocol; respective improvements have been suggested. The authors summarize their experiences in dealing with the complexity of the protocol using various modelling and abstraction features provided in UPPAAL. As an example, they study the bus coupler of AF100, which serves as the data link layer of the protocol.