Independence Analysis of Firing and Rule-based Net Transformations in Reconfigurable Object Nets

The main idea behind Reconfigurable Object Nets (RONs) is to support the visual specification of controlled rule-based net transformations of place/transition nets (P/T nets). RONs are high-level nets with two types of tokens: object nets (place/transition nets) and net transformation rules (a dedicated type of graph transformation rules). Firing of high-level transitions may involve firing of object net transitions, transporting object net tokens through the high-level net, and applying net transformation rules to object nets, e.g. to model net reconfigurations. A visual editor and simulator for RONs has been developed as a plug-in for ECLIPSE using the ECLIPSE Modeling Framework (EMF) and Graphical Editor Framework (GEF) plug-ins. The problem in this context is to analyze under which conditions net transformations and token firing can be executed in arbitrary order. This problem has been solved formally in a previous paper. In this contribution we present an extension of our RON tool which implements the analysis of conflicts between parallel enabled transitions, between parallel applicable net transformation rules (Church-Rosser property), and between transition firing and net transformation steps. The conflict analysis is applied to a RON simulating a distributed producer-consumer system

BioSimulator.jl: Stochastic simulation in Julia

Biological systems with intertwined feedback loops pose a challenge to mathematical modeling efforts. Moreover, rare events, such as mutation and extinction, complicate system dynamics. Stochastic simulation algorithms are useful in generating time-evolution trajectories for these systems because they can adequately capture the influence of random fluctuations and quantify rare events. We present a simple and flexible package, BioSimulator.jl, for implementing the Gillespie algorithm, $\tau$-leaping, and related stochastic simulation algorithms. The objective of this work is to provide scientists across domains with fast, user-friendly simulation tools. We used the high-performance programming language Julia because of its emphasis on scientific computing. Our software package implements a suite of stochastic simulation algorithms based on Markov chain theory. We provide the ability to (a) diagram Petri Nets describing interactions, (b) plot average trajectories and attached standard deviations of each participating species over time, and (c) generate frequency distributions of each species at a specified time. BioSimulator.jl's interface allows users to build models programmatically within Julia. A model is then passed to the simulate routine to generate simulation data. The built-in tools allow one to visualize results and compute summary statistics. Our examples highlight the broad applicability of our software to systems of varying complexity from ecology, systems biology, chemistry, and genetics. The user-friendly nature of BioSimulator.jl encourages the use of stochastic simulation, minimizes tedious programming efforts, and reduces errors during model specification.Comment: 27 pages, 5 figures, 3 table

The DS-Pnet modeling formalism for cyber-physical system development

This work presents the DS-Pnet modeling formalism (Dataflow, Signals and Petri nets), designed for the development of cyber-physical systems, combining the characteristics of Petri nets and dataflows to support the modeling of mixed systems containing both reactive parts and data processing operations. Inheriting the features of the parent IOPT Petri net class, including an external interface composed of input and output signals and events, the addition of dataflow operations brings enhanced modeling capabilities to specify mathematical data transformations and graphically express the dependencies between signals. Data-centric systems, that do not require reactive controllers, are designed using pure dataflow models. Component based model composition enables reusing existing components, create libraries of previously tested components and hierarchically decompose complex systems into smaller sub-systems. A precise execution semantics was defined, considering the relationship between dataflow and Petri net nodes, providing an abstraction to define the interface between reactive controllers and input and output signals, including analog sensors and actuators. The new formalism is supported by the IOPT-Flow Web based tool framework, offering tools to design and edit models, simulate model execution on the Web browser, plus model-checking and software/hardware automatic code generation tools to implement controllers running on embedded devices (C,VHDL and JavaScript). A new communication protocol was created to permit the automatic implementation of distributed cyber-physical systems composed of networks of remote components communicating over the Internet. The editor tool connects directly to remote embedded devices running DS-Pnet models and may import remote components into new models, contributing to simplify the creation of distributed cyber-physical applications, where the communication between distributed components is specified just by drawing arcs. Several application examples were designed to validate the proposed formalism and the associated framework, ranging from hardware solutions, industrial applications to distributed software applications

Process Calculi Abstractions for Biology

Several approaches have been proposed to model biological systems by means of the formal techniques and tools available in computer science. To mention just a few of them, some representations are inspired by Petri Nets theory, and some other by stochastic processes. A most recent approach consists in interpreting the living entities as terms of process calculi where the behavior of the represented systems can be inferred by applying syntax-driven rules. A comprehensive picture of the state of the art of the process calculi approach to biological modeling is still missing. This paper goes in the direction of providing such a picture by presenting a comparative survey of the process calculi that have been used and proposed to describe the behavior of living entities. This is the preliminary version of a paper that was published in Algorithmic Bioprocesses. The original publication is available at http://www.springer.com/computer/foundations/book/978-3-540-88868-

A Taxonomy of Workflow Management Systems for Grid Computing

With the advent of Grid and application technologies, scientists and engineers are building more and more complex applications to manage and process large data sets, and execute scientific experiments on distributed resources. Such application scenarios require means for composing and executing complex workflows. Therefore, many efforts have been made towards the development of workflow management systems for Grid computing. In this paper, we propose a taxonomy that characterizes and classifies various approaches for building and executing workflows on Grids. We also survey several representative Grid workflow systems developed by various projects world-wide to demonstrate the comprehensiveness of the taxonomy. The taxonomy not only highlights the design and engineering similarities and differences of state-of-the-art in Grid workflow systems, but also identifies the areas that need further research.Comment: 29 pages, 15 figure

Design, construction, and application of a generic visual language generation environment

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