P. S. Thiagarajan

Message sequence charts

Message sequence charts (MSCs) constitute an attractive visual formalism that is widely used to capture system requirements during the early design stages in domains such as telecommunication software. A version of MSCs called sequence diagrams is one of the behavioral diagram types adopted in the UML. In this chapter we survey MSCs and their extensions. In particular, we discuss high level MSCs, which allow MSCs to be combined in various regular ways, and the more recent mechanism of communicating transaction processes, which can be used to structure sequence charts to capture system behaviors more directly. We also discuss in some detail live sequence charts (LSCs), a multi-modal extension of MSCs with considerably richer expressive power, and the play-in/out method that makes it possible to use LSCs directly as an executable specification.

Elements of General Net Theory

Some of the main features of a theory of systems in which the concept of concurrency plays a central role are presented. This theory is founded upon a systems model called condition/event-systems (CE-systems).

Elementary Net Systems

Our aim will be to introduce and discuss the basic system model of net theory called Condition/Event Systems. We shall start with a brief discussion of the twin notions of states and transitions as viewed within net theory. This will motivate the restrictions placed on the Condition/Event System model. We shall then introduce nets and construct Condition/Event Systems with the help of nets.

OpenComet: an automated tool for comet assay image analysis.

Reactive species such as free radicals are constantly generated in vivo and DNA is the most important target of oxidative stress. Oxidative DNA damage is used as a predictive biomarker to monitor the risk of development of many diseases. The comet assay is widely used for measuring oxidative DNA damage at a single cell level. The analysis of comet assay output images, however, poses considerable challenges. Commercial software is costly and restrictive, while free software generally requires laborious manual tagging of cells. This paper presents OpenComet, an open-source software tool providing automated analysis of comet assay images. It uses a novel and robust method for finding comets based on geometric shape attributes and segmenting the comet heads through image intensity profile analysis. Due to automation, OpenComet is more accurate, less prone to human bias, and faster than manual analysis. A live analysis functionality also allows users to analyze images captured directly from a microscope. We have validated OpenComet on both alkaline and neutral comet assay images as well as sample images from existing software packages. Our results show that OpenComet achieves high accuracy with significantly reduced analysis time.

A theory of regular MSC languages

Message sequence charts (MSCs) are an attractive visual formalism widely used to capture system requirements during the early design stages in domains such as telecommunication software. It is fruitful to have mechanisms for specifying and reasoning about collections of MSCs so that errors can be detected even at the requirements level. We propose, accordingly, a notion of regularity for collections of MSCs and explore its basic properties. In particular, we provide an automata-theoretic characterization of regular MSC languages in terms of finite-state distributed automata called bounded message-passing automata. These automata consist of a set of sequential processes that communicate with each other by sending and receiving messages over bounded FIFO channels. We also provide a logical characterization in terms of a natural monadic second-order logic interpreted over MSCs. A commonly used technique to generate a collection of MSCs is to use a hierarchical message sequence chart (HMSC). We show that the class of languages arising from the so-called bounded HMSCs constitute a proper subclass of the class of regular MSC languages. In fact, we characterize the bounded HMSC languages as the subclass of regular MSC languages that are finitely generated.

Dynamic linear time temporal logic

Abstract A simple extension of the propositional temporal logic of linear time is proposed. The extension consists of strengthening the until operator by indexing it with the regular programs of propositional dynamic logic. It is shown that DLTL, the resulting logic, is expressively equivalent to the monadic second-order theory of ω-sequences. In fact, a sublogic of DLTL which corresponds to propositional dynamic logic with a linear time semantics is already expressively complete. We show that DLTL has an exponential time decision procedure and admits a finitary axiomatization. We also point to a natural extension of the approach presented here to a distributed setting.

A decompositional approach to parameter estimation in pathway modeling

Parameter estimation is a critical problem in modeling biological pathways. It is difficult because of the large number of parameters to be estimated and the limited experimental data available. In this paper, we propose a decompositional approach to parameter estimation. It exploits the structure of a large pathway model to break it into smaller components, whose parameters can then be estimated independently. This leads to significant improvements in computational efficiency. We present our approach in the context of Hybrid Functional Petri Net modeling and evolutionary search for parameter value estimation. However, the approach can be easily extended to other modeling frameworks and is independent of the search method used. We have tested our approach on a detailed model of the Akt and MAPK pathways with two known and one hypothesized crosstalk mechanisms. The entire model contains 84 unknown parameters. Our simulation results exhibit good correlation with experimental data, and they yield positive evidence in support of the hypothesized crosstalk between the two pathways.

A fresh look at free choice nets

A subclass of Petri nets called live and safe free choice nets (LSFC nets) is studied. LSFC nets model distributed systems that can exhibit both nonsequential and nondeterministic behaviours. It is shown that the restricted combination of concurrency and choice as represented by LSFC nets leads to a number of attractive system properties. It is also shown, through examples, that a “less” restrictive combination of concurrency and choice destroys these properties.

Composing Functional and State-Based Performance Models for Analyzing Heterogeneous Real-Time Systems

We present a performance analysis technique for distributed real-time systems in a setting where certain components are modeled in a purely functional manner, while the remaining components require additional modeling of state information. The functional models can be efficiently analyzed but have restricted expressiveness. On the other hand, state-based models are more expressive and offer a richer set of analyzable properties but are computationally more expensive to analyze. We show that by appropriately composing these two classes of models it is possible to leverage on their respective advantages. To this end, we propose an interface between components that are modeled using real-time calculus [Chakraborty, Kiinzli and Thiele, DATE 2003] and those that are modeled using event count automata [Chakraborty, Phan and Thiagarajan, RTSS 2005]. The resulting modeling technique is as expressive as event count automata, but is amenable to more efficient analysis. We illustrate these advantages using a number of examples and a detailed case study.

A theory of bipolar synchronization schemes

The aim is to better understand the relationships between choice and concurrency that lead to the good behaviour of distributed systems. In order to do so, we formulate a model based on Petri nets and develop its theory. The model is called bipolar synchronization schemes (bp schemes) and the theory we construct is mainly devoted to synthesising, in a systematic fashion, all well behaved bp schemes. We also provide a computational interpretation of well behaved bp schemes. Through this interpretation the insights gained by developing the theory of bp schemes can be transferred to concurrent programs.