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-

Petri net modeling and analysis of an FMS cell

Petri nets have evolved into a powerful tool for the modeling, analysis and design of asynchronous, concurrent systems. This thesis presents the modeling and analysis of a flexible manufacturing system (FMS) cell using Petri nets. In order to improve the productivity of such systems, the building of mathematical models is a crucial step. In this thesis, the theory and application of Petri nets are presented with emphasis on their application to the modeling and analysis of practical automated manufacturing systems. The theory of Petri nets includes their basic notation and properties. In order to illustrate how a Petri net with desirable properties can be modeled, this thesis describes the detailed modeling process for an FMS cell. During the process, top-down refinement, system decomposition, and modular composition ideas are used to achieve the hierarchy and preservation of important system properties. These properties include liveness, boundedness, and reversibility. This thesis also presents two illustrations showing the method adopted to model any manufacturing systems using ordinary Petri nets. The first example deals with a typical resource sharing problem and the second the modeling of Fanuc Machining Center at New Jersey Institute of Technology. Furthermore, this thesis presents the analysis of a timed Petri net for cycle time, system throughput and equipment utilization. The timed (deterministic) Petri net is first converted into an equivalent timed marked graph. Then the standard procedure to find the cycle time for marked graphs is applied. Secondly, stochastic Petri net is analyzed using SPNP software package for obtaining the system throughput and equipment utilization. This thesis is of significance in the sense that it provides industrial engineers and academic researchers with a comprehensive real-life example of applying Petri net theory to modeling and analysis of FMS cells. This will help them develop their own applications

Scheduling and discrete event control of flexible manufacturing systems based on Petri nets

A flexible manufacturing system (FMS) is a computerized production system that can simultaneously manufacture multiple types of products using various resources such as robots and multi-purpose machines. The central problems associated with design of flexible manufacturing systems are related to process planning, scheduling, coordination control, and monitoring. Many methods exist for scheduling and control of flexible manufacturing systems, although very few methods have addressed the complexity of whole FMS operations. This thesis presents a Petri net based method for deadlock-free scheduling and discrete event control of flexible manufacturing systems. A significant advantage of Petri net based methods is their powerful modeling capability. Petri nets can explicitly and concisely model the concurrent and asynchronous activities, multi-layer resource sharing, routing flexibility, limited buffers and precedence constraints in FMSs. Petri nets can also provide an explicit way for considering deadlock situations in FMSs, and thus facilitate significantly the design of a deadlock-free scheduling and control system. The contributions of this work are multifold. First, it develops a methodology for discrete event controller synthesis for flexible manufacturing systems in a timed Petri net framework. The resulting Petri nets have the desired qualitative properties of liveness, boundedness (safeness), and reversibility, which imply freedom from deadlock, no capacity overflow, and cyclic behavior, respectively. This precludes the costly mathematical analysis for these properties and reduces on-line computation overhead to avoid deadlocks. The performance and sensitivity of resulting Petri nets, thus corresponding control systems, are evaluated. Second, it introduces a hybrid heuristic search algorithm based on Petri nets for deadlock-free scheduling of flexible manufacturing systems. The issues such as deadlock, routing flexibility, multiple lot size, limited buffer size and material handling (loading/unloading) are explored. Third, it proposes a way to employ fuzzy dispatching rules in a Petri net framework for multi-criterion scheduling. Finally, it shows the effectiveness of the developed methods through several manufacturing system examples compared with benchmark dispatching rules, integer programming and Lagrangian relaxation approaches

Proceedings of SUMo and CompoNet 2011

International audienc

A computer architecture for intelligent machines

The Theory of Intelligent Machines proposes a hierarchical organization for the functions of an autonomous robot based on the Principle of Increasing Precision With Decreasing Intelligence. An analytic formulation of this theory using information-theoretic measures of uncertainty for each level of the intelligent machine has been developed in recent years. A computer architecture that implements the lower two levels of the intelligent machine is presented. The architecture supports an event-driven programming paradigm that is independent of the underlying computer architecture and operating system. Details of Execution Level controllers for motion and vision systems are addressed, as well as the Petri net transducer software used to implement Coordination Level functions. Extensions to UNIX and VxWorks operating systems which enable the development of a heterogeneous, distributed application are described. A case study illustrates how this computer architecture integrates real-time and higher-level control of manipulator and vision systems

Distributed product development approaches and system for achieving optimal design.

The research in this dissertation attempts to provide theoretic approaches and design systems to support engineers who are located in different places and belong to different teams or companies to work collaboratively to perform product development.The second challenge is addressed by developing a collaborative design process modeling technique based on Petri-net. Petri-net is used to describe complex design processes and to construct different design process alternatives. These alternative Petri-net models are then analyzed to evaluate design process alternatives and to select the appropriate process.In this dissertation, three major challenges are identified in realization of a collaborative design paradigm: (i) development of design method that supports multidisciplinary xi design teams to collaboratively solve coupled design problems, (ii) development of process modeling techniques to support representation and improve complex collaborative design process, and (iii) implementation of a testbed system that demonstrates the feasibility of enhancing current design system to satisfy with the needs of organizing collaborative design process for collaborative decision making and associated design activities.New paradigms, along with accompanying approaches and software systems are necessary to support collaborative design work, in a distributed design environment, of multidisciplinary engineering teams who have different knowledge, experience, and skills. Current research generally focuses on the development of online collaborative tools, and software frameworks that integrate and coordinate these tools. However, a gap exists between the needs of a distributed collaborative design paradigm and current collaborative design tools. On one side, design methodologies facilitating engineering teams' decision making is not well developed. In a distributed collaborative design paradigm, each team holds its own perspective towards the product realization problem, and each team seeks design decisions that can maximize the design performance in its own discipline. Design methodologies that coordinate the separate design decisions are essential to achieve successful collaboration. On the other side, design of products is becoming more complex. Organizing a complex design process is a major obstacle in the application of a distributed collaborative design paradigm in practice. Therefore, the principal research goal in this dissertation is to develop a collaborative multidisciplinary decision making methodology and design process modeling technique that bridges the gap between a collaborative design paradigm and current collaborative design systems.To overcome the first challenge, decision templates are constructed to exchange design information among interacting disciplines. Three game protocols from game theory are utilized to categorize the collaboration in decision makings. Design formulations are used to capture the design freedom among coupled design activities.The third challenge, implementation of collaborative design testbed, is addressed by integration of existing Petri-net modeling tools into the design system. The testbed incorporates optimization software, collaborative design tools, and management software for product and process design to support group design activities.Two product realization examples are presented to demonstrate the applicability of the research and collaborative testbed. A simplified manipulator design example is used for explanation of collaborative decision making and design process organization. And a reverse engineering design example is introduced to verify the application of collaborative design paradigm with design support systems in practice

Quantitative Analysis of Apache Storm Applications: The NewsAsset Case Study

The development of Information Systems today faces the era of Big Data. Large volumes of information need to be processed in real-time, for example, for Facebook or Twitter analysis. This paper addresses the redesign of NewsAsset, a commercial product that helps journalists by providing services, which analyzes millions of media items from the social network in real-time. Technologies like Apache Storm can help enormously in this context. We have quantitatively analyzed the new design of NewsAsset to assess whether the introduction of Apache Storm can meet the demanding performance requirements of this media product. Our assessment approach, guided by the Unified Modeling Language (UML), takes advantage, for performance analysis, of the software designs already used for development. In addition, we converted UML into a domain-specific modeling language (DSML) for Apache Storm, thus creating a profile for Storm. Later, we transformed said DSML into an appropriate language for performance evaluation, specifically, stochastic Petri nets. The assessment ended with a successful software design that certainly met the scalability requirements of NewsAsset