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

Ad hoc network security and modeling with stochastic petri nets

Advances in wireless technology and portable computing along with demands for high user mobility have provided a major promotion toward the development of ad hoc networks. These networks feature dynamic topology, self-organization, limited bandwidth and battery power of a node. Unlike the existing commercial wireless systems and fixed infrastructure networks, they do not rely on specialized routers for path discovery and traffic routing. Security is an important issue in such networks. Typically, mobile nodes are significantly more susceptible to physical attacks than their wired counterparts. This research intends to investigate the ad hoc network routing security by proposing a performance enhanced Secure ad hoc On-demand Routing protocol (SOR). Specifically, it presents a method to embed Security Level into ad hoc on-demand routing protocols using node-disjoint multipath, and to use maximum hopcount to restrict the number of routing packets in a specific area. The proposed scheme enables the use of security as a marked factor to improve the relevance of the routes discovered by ad hoc routing protocols. It provides customizable security to the flow of routing protocol messages. In general, SOR offers an alternative way to implement security in on-demand routing protocols. Ad hoc network is too complex to allow analytical study for explicit performance expressions. This research presents a Stochastic Petri net-based approach to modeling and analysis of mobile ad hoc network. This work illustrates how this model is built as a scalable model and used to exploit the characteristics of the networks. The proposed scheme is a powerful analytical model that can be used to derive network performance much more easily than a simulation-based approach. Furthermore, the proposed model is extended to study the performance of ad hoc network security by adding multipath selection and security measurement parameters. This research gives a quantificational measurement to analyze the performance of a modified SPN model under the effect of multipath and attack of a hypothetical compromised node

Fluid Petri Nets for the Performance Evaluation of MapReduce Applications

Big Data applications allow to successfully analyze large amounts of data not necessarily structured, though at the same time they present new challenges. For example, predicting the performance of frameworks such as Hadoop can be a costly task, hence the necessity to provide models that can be a valuable support for designers and developers. This paper provides a new contribution in studying a novel modeling approach based on fluid Petri nets to predict MapReduce jobs execution time. The experiments we performed at CINECA, the Italian supercomputing center, have shown that the achieved accuracy is within 16% of the actual measurements on average

List of requirements on formalisms and selection of appropriate tools

This deliverable reports on the activities for the set-up of the modelling environments for the evaluation activities of WP5. To this objective, it reports on the identified modelling peculiarities of the electric power infrastructure and the information infrastructures and of their interdependencies, recalls the tools that have been considered and concentrates on the tools that are, and will be, used in the project: DrawNET, DEEM and EPSys which have been developed before and during the project by the partners, and M\uf6bius and PRISM, developed respectively at the University of Illinois at Urbana Champaign and at the University of Birmingham (and recently at the University of Oxford)

Performance Analysis of Live-Virtual-Constructive and Distributed Virtual Simulations: Defining Requirements in Terms of Temporal Consistency

This research extends the knowledge of live-virtual-constructive (LVC) and distributed virtual simulations (DVS) through a detailed analysis and characterization of their underlying computing architecture. LVCs are characterized as a set of asynchronous simulation applications each serving as both producers and consumers of shared state data. In terms of data aging characteristics, LVCs are found to be first-order linear systems. System performance is quantified via two opposing factors; the consistency of the distributed state space, and the response time or interaction quality of the autonomous simulation applications. A framework is developed that defines temporal data consistency requirements such that the objectives of the simulation are satisfied. Additionally, to develop simulations that reliably execute in real-time and accurately model hierarchical systems, two real-time design patterns are developed: a tailored version of the model-view-controller architecture pattern along with a companion Component pattern. Together they provide a basis for hierarchical simulation models, graphical displays, and network I/O in a real-time environment. For both LVCs and DVSs the relationship between consistency and interactivity is established by mapping threads created by a simulation application to factors that control both interactivity and shared state consistency throughout a distributed environment

A graphical tool for timed petri nets using object oriented programming

The objective of this effort is to develop a computer tool for drawing, editing and simulating Timed Petri Nets using object oriented programming. The developed C++ based Timed Petri Net Simulation Tool, TimedPNT, is capable of simulating discrete systems with both deterministic and stochastic delays. Preselection is used for conflict resolution. Performance and utilization results are automatically collected. XView™ Toolkit is used for building the TimedPNT\u27s interactive graphical interface in compliance with AT&T\u27s OPENLOOK® standard on a SunSparc™ IPX running SunOSTM 4.1.2. Compliance with the X Window standard makes the developed tool portable to other X Window based systems

MACHS: Mitigating the Achilles Heel of the Cloud through High Availability and Performance-aware Solutions

Cloud computing is continuously growing as a business model for hosting information and communication technology applications. However, many concerns arise regarding the quality of service (QoS) offered by the cloud. One major challenge is the high availability (HA) of cloud-based applications. The key to achieving availability requirements is to develop an approach that is immune to cloud failures while minimizing the service level agreement (SLA) violations. To this end, this thesis addresses the HA of cloud-based applications from different perspectives. First, the thesis proposes a component’s HA-ware scheduler (CHASE) to manage the deployments of carrier-grade cloud applications while maximizing their HA and satisfying the QoS requirements. Second, a Stochastic Petri Net (SPN) model is proposed to capture the stochastic characteristics of cloud services and quantify the expected availability offered by an application deployment. The SPN model is then associated with an extensible policy-driven cloud scoring system that integrates other cloud challenges (i.e. green and cost concerns) with HA objectives. The proposed HA-aware solutions are extended to include a live virtual machine migration model that provides a trade-off between the migration time and the downtime while maintaining HA objective. Furthermore, the thesis proposes a generic input template for cloud simulators, GITS, to facilitate the creation of cloud scenarios while ensuring reusability, simplicity, and portability. Finally, an availability-aware CloudSim extension, ACE, is proposed. ACE extends CloudSim simulator with failure injection, computational paths, repair, failover, load balancing, and other availability-based modules

Recent advances in petri nets and concurrency

CEUR Workshop Proceeding

Using Learning Theory in a Hypermedia-Based Petri Net Modeling Tutorial

The primary aim of this paper is to examine the dominant schools of thought in relation to educational theories and learning styles and in what manner various hypermedia technologies can be integrated into educational theories to enhance the design and delivery of educational content. The specific focus of this paper is to create teaching material for Petri net modeling fundamentals. Guided by the principles of Bloom?s revised taxonomy, a tutorial on Petri net Modeling Fundamentals is developed and implemented. The material in the tutorial is designed specifically to accommodate the lower-order thinking levels of Bloom?s revised taxonomy and the various learning styles proposed in the Felder-Silverman learning style model