From types to type requirements: Genericity for model-driven engineering

The final publication is available at Springer via http://dx.doi.org/10.1007/s10270-011-0221-0Model-driven engineering (MDE) is a software engineering paradigm that proposes an active use of models during the development process. This paradigm is inherently type-centric, in the sense that models and their manipulation are defined over the types of specific meta-models. This fact hinders the reuse of existing MDE artefacts with other meta-models in new contexts, even if all these meta-models share common characteristics. To increase the reuse opportunities of MDE artefacts, we propose a paradigm shift from type-centric to requirement-centric specifications by bringing genericity into models, meta-models and model management operations. For this purpose, we introduce so-called concepts gathering structural and behavioural requirements for models and meta-models. In this way, model management operations are defined over concepts, enabling the application of the operations to any meta-model satisfying the requirements imposed by the concept. Model templates rely on concepts to define suitable interfaces, hence enabling the definition of reusable model components. Finally, similar to mixin layers, templates can be defined at the meta-model level as well, to define languages in a modular way, as well as layers of functionality to be plugged-in into other meta-models. These ideas have been implemented in MetaDepth, a multi-level meta-modelling tool that integrates action languages from the Epsilon family for model management and code generation.This work has been sponsored by the Spanish Ministry of Science and Innovation with projects METEORIC (TIN2008-02081) and Go Lite (TIN2011-24139), and by the R&D program of the Community of Madrid with project “e-Madrid” (S2009/TIC-1650)

Simulator for concurrent processing data flow architectures

A software simulator capability of simulating execution of an algorithm graph on a given system under the Algorithm to Architecture Mapping Model (ATAMM) rules is presented. ATAMM is capable of modeling the execution of large-grained algorithms on distributed data flow architectures. Investigating the behavior and determining the performance of an ATAMM based system requires the aid of software tools. The ATAMM Simulator presented is capable of determining the performance of a system without having to build a hardware prototype. Case studies are performed on four algorithms to demonstrate the capabilities of the ATAMM Simulator. Simulated results are shown to be comparable to the experimental results of the Advanced Development Model System

The Signaling Petri Net-Based Simulator: A Non-Parametric Strategy for Characterizing the Dynamics of Cell-Specific Signaling Networks

Reconstructing cellular signaling networks and understanding how they work are major endeavors in cell biology. The scale and complexity of these networks, however, render their analysis using experimental biology approaches alone very challenging. As a result, computational methods have been developed and combined with experimental biology approaches, producing powerful tools for the analysis of these networks. These computational methods mostly fall on either end of a spectrum of model parameterization. On one end is a class of structural network analysis methods; these typically use the network connectivity alone to generate hypotheses about global properties. On the other end is a class of dynamic network analysis methods; these use, in addition to the connectivity, kinetic parameters of the biochemical reactions to predict the network's dynamic behavior. These predictions provide detailed insights into the properties that determine aspects of the network's structure and behavior. However, the difficulty of obtaining numerical values of kinetic parameters is widely recognized to limit the applicability of this latter class of methods

A Petri net design, simulation, and verification tool

Increasing desire for thorough simulation and analysis of engineered products is quickly replacing the prototype and test design model. Petri nets are important instruments for modeling concurrent, distributed, asynchronous, parallel, deterministic, and non-deterministic systems. This tool provides designers with the ability to easily specify a Petri net design with an easy to use user interface, then simulate and analyze the Petri net to determine essential design properties using the reachability tree technique. The tool will construct a reachability tree, then analyze the tree for properties of safeness, boundedness, liveness, and conservativeness

Developing Globally-Asynchronous Locally- Synchronous Systems through the IOPT-Flow Framework

Throughout the years, synchronous circuits have increased in size and com-plexity, consequently, distributing a global clock signal has become a laborious task. Globally-Asynchronous Locally-Synchronous (GALS) systems emerge as a possible solution; however, these new systems require new tools. The DS-Pnet language formalism and the IOPT-Flow framework aim to support and accelerate the development of cyber-physical systems. To do so it offers a tool chain that comprises a graphical editor, a simulator and code gener-ation tools capable of generating C, JavaScript and VHDL code. However, DS-Pnets and IOPT-Flow are not yet tuned to handle GALS systems, allowing for partial specification, but not a complete one. This dissertation proposes extensions to the DS-Pnet language and the IOPT-Flow framework in order to allow development of GALS systems. Addi-tionally, some asynchronous components were created, these form interfaces that allow synchronous blocks within a GALS system to communicate with each other

Representing Resources in Petri Net Models: Hardwiring or Soft-coding?

©2011 IEEE. Reprinted, with permission, from : Reggie Davidrajuh; Representing Resources in Petri Net Models : Hardwiring or Soft-coding?, 2011 IEEE International Conference on Service Operations, Logistics, and Informatics (SOLI), 2011; Beijing, China. This material is posted here with permission of the IEEE. Such permission of the IEEE does not in any way imply IEEE endorsement of any of the University of Stavanger's products or services. Internal or personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution must be obtained from the IEEE by writing to pubs‐[email protected]. By choosing to view this document, you agree to all provisions of the copyright laws protecting it.This paper presents an interesting design problem in developing a new tool for discrete-event dynamic systems (DEDS). A new tool known as GPenSIM was developed for modeling and simulation of DEDS; GPenSIM is based on Petri Nets. The design issue this paper talks about is whether to represent resources in DEDS hardwired as a part of the Petri net structure (which is the widespread practice) or to soft code as common variables in the program code. This paper shows that soft coding resources give benefits such as simpler and skinny models

Open and Extensible Business Process Simulator

Äriprotesesside haldamise üheks väga oluliseks osaks on protsesside simuleerimine. Simuleerimine annab hea võimaluse kontrollida protsesside toimimist ning leida muutmist vajavaid kitsaskohti. Käesolevas magistritöös vaatleme olemasolevaid protsesside simuleerimise keskkondi, mida peetakse hetkel selle valdkonna tippudeks (näiteks TIBCO, IBM WebSphere jt), ning uurime nendes esinevaid probleeme seoses funktsionaalsuse ja laiendatavuse puudumisega. Praktiliselt kõikidel uuritud vahenditel oli probleeme keerukama ülesehitusega protsesside simuleerimisel ning puudub võimalus töövahendit äridomeeni spetsiifikast lähtuvalt vajadusel muuta või täiendada. Magistritöö põhiosa on jagatud kaheks. Esimeses osas toome välja protsessielementide teisendused defacto standard modelleerimisnotatsioonist BPMN, madalama taseme modelleerimiselementideks CPN keeles. Teisenduse kasulikkus seisneb selles, et CPN keeles olev protsess on simuleeritav vahendiga CPN Tools, ning konverteerimist on võimalik kohendada vastavalt vajadustele. Näiteks on võimalus lisada ärispetsiifilisi simulatsiooniandmeid või kasutada mittestandardseid tööde jaotamise mustreid. Magistritöö teises osas töötame välja täiesti uue protsesside konverteerimise arhitektuuri, mis on kättesaadav avatud lähtekoodina, ning on kergesti laiendatav. Siinkohal tähendab laiendatavus seda, et välja töötatud arhitektuuri on võimalik kasutada erinevatest modelleerimiskeeltest protsesside konverteerimiseks CPN keelde. Näidisena oleme loonud ka prototüübi, mis on suuteline teisendama enamlevinud BPMN elemente simuleerimisvalmidusega CPN elementideks. Edasiste töödena näeme me võimalust laiendada olemasolevat prototüüpi toetamaks kõiki BPMN elemente ning keerulisi simulatsiooniandmeid. Prototüüpi on võimalik ka edasi arendada simuleerimise veebiteenuseks, mida saaksid edukalt kasutada erinevad modelleerimiskeskkonnad simulatsioonide läbiviimiseks.Existing business process simulation tools suffer from two limitations: (i) they allow one to simulate processes that are designed only in the same tool; and (ii) the simulation engine is built-in and it is not extensible. The aim of this thesis is to move towards overcoming these two limitations. The contribution of the thesis is twofold. First we provide some of the commonly used Business Process Notation (BPMN) mappings to Coloured Petri Net (CPN) modules while considering the need to use these converted models for simulation purposes. This means that the mappings have to be able to handle simulation data and can generate simulation output into log files. Secondly we provide a new process model converter architecture that is open and extensible and it is responsible for generating a ready to simulate CPN models

Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle

<p>Abstract</p> <p>Background</p> <p>In systems biology the experimentalist is presented with a selection of software for analyzing dynamic properties of signaling networks. These tools either assume that the network is in steady-state or require highly parameterized models of the network of interest. For biologists interested in assessing how signal propagates through a network under specific conditions, the first class of methods does not provide sufficiently detailed results and the second class requires models which may not be easily and accurately constructed. A tool that is able to characterize the dynamics of a signaling network using an unparameterized model of the network would allow biologists to quickly obtain insights into a signaling network's behavior.</p> <p>Results</p> <p>We introduce <it>PathwayOracle</it>, an integrated suite of software tools for computationally inferring and analyzing structural and dynamic properties of a signaling network. The feature which differentiates <it>PathwayOracle </it>from other tools is a method that can predict the response of a signaling network to various experimental conditions and stimuli using only the connectivity of the signaling network. Thus signaling models are relatively easy to build. The method allows for tracking signal flow in a network and comparison of signal flows under different experimental conditions. In addition, <it>PathwayOracle </it>includes tools for the enumeration and visualization of coherent and incoherent signaling paths between proteins, and for experimental analysis – loading and superimposing experimental data, such as microarray intensities, on the network model.</p> <p>Conclusion</p> <p><it>PathwayOracle </it>provides an integrated environment in which both structural and dynamic analysis of a signaling network can be quickly conducted and visualized along side experimental results. By using the signaling network connectivity, analyses and predictions can be performed quickly using relatively easily constructed signaling network models. The application has been developed in Python and is designed to be easily extensible by groups interested in adding new or extending existing features. <it>PathwayOracle </it>is freely available for download and use.</p