3,053 research outputs found

    BioSimulator.jl: Stochastic simulation in Julia

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    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, τ\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

    Domain specific software design for decision aiding

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    McDonnell Aircraft Company (MCAIR) is involved in many large multi-discipline design and development efforts of tactical aircraft. These involve a number of design disciplines that must be coordinated to produce an integrated design and a successful product. Our interpretation of a domain specific software design (DSSD) is that of a representation or framework that is specialized to support a limited problem domain. A DSSD is an abstract software design that is shaped by the problem characteristics. This parallels the theme of object-oriented analysis and design of letting the problem model directly drive the design. The DSSD concept extends the notion of software reusability to include representations or frameworks. It supports the entire software life cycle and specifically leads to improved prototyping capability, supports system integration, and promotes reuse of software designs and supporting frameworks. The example presented in this paper is the task network architecture or design which was developed for the MCAIR Pilot's Associate program. The task network concept supported both module development and system integration within the domain of operator decision aiding. It is presented as an instance where a software design exhibited many of the attributes associated with DSSD concept

    The pros and cons of using SDL for creation of distributed services

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    In a competitive market for the creation of complex distributed services, time to market, development cost, maintenance and flexibility are key issues. Optimizing the development process is very much a matter of optimizing the technologies used during service creation. This paper reports on the experience gained in the Service Creation projects SCREEN and TOSCA on use of the language SDL for efficient service creation

    Design and Development of Software Tools for Bio-PEPA

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    This paper surveys the design of software tools for the Bio-PEPA process algebra. Bio-PEPA is a high-level language for modelling biological systems such as metabolic pathways and other biochemical reaction networks. Through providing tools for this modelling language we hope to allow easier use of a range of simulators and model-checkers thereby freeing the modeller from the responsibility of developing a custom simulator for the problem of interest. Further, by providing mappings to a range of different analysis tools the Bio-PEPA language allows modellers to compare analysis results which have been computed using independent numerical analysers, which enhances the reliability and robustness of the results computed.

    Generic kinematic simulation for verification of laser deposition tool paths

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    The development of 3D visual simulation tool for machine simulation is a key approach in saving time and reducing cost. It is an important step before a manufacturing operation is performed on a part, as a tool to detect collision and validate the operation results. There are several kinds of manufacturing equipment being used and hence there is a need for the development of a generalized method to visually simulate a variety of machines. This paper presents the research conducted on describing machine configuration in a generic format which not only gives useful information, but can also be used as a tool to generate the parent list and the dependency list, which would aid in the simulation process. This format is also used to describe the type of motion - linear and rotational motion of the machines parts. In this study, a generic movement description file is also presented, which is utilized to compute the machine motion for various axes. This work concentrates on laser deposition in order to demonstrate a manufacturing operation. This 3D simulation tool has been tested on various manufacturing equipment and the results are shown in the paper. This thesis is composed of two papers. In paper I, a basic version of the algorithm for simulation and generic machine configuration format have been presented. This paper only describes linear motion for machine axes. Paper II discusses in detail about the algorithm, provides results for both translational and rotational motion and enhances the deposition simulation as well as the display scene --Abstract, page iv

    Queuing Network Modeling of Human Multitask Performance and its Application to Usability Testing of In-Vehicle Infotainment Systems.

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    Human performance of a primary continuous task (e.g., steering a vehicle) and a secondary discrete task (e.g., tuning radio stations) simultaneously is a common scenario in many domains. It is of great importance to have a good understanding of the mechanisms of human multitasking behavior in order to design the task environments and user interfaces (UIs) that facilitate human performance and minimize potential safety hazards. In this dissertation I investigated and modeled human multitask performance with a vehicle-steering task and several typical in-vehicle secondary tasks. Two experiments were conducted to investigate how various display designs and control modules affect the driver's eye glance behavior and performance. A computational model based on the cognitive architecture of Queuing Network-Model Human Processor (QN-MHP) was built to account for the experiment findings. In contrast to most existing studies that focus on visual search in single task situations, this dissertation employed experimental work that investigates visual search in multitask situations. A modeling mechanism for flexible task activation (rather than strict serial activations) was developed to allow the activation of a task component to be based on the completion status of other task components. A task switching scheme was built to model the time-sharing nature of multitasking. These extensions offer new theoretical insights into visual search in multitask situations and enable the model to simulate parallel processing both within one task and among multiple tasks. The validation results show that the model could account for the observed performance differences from the empirical data. Based on this model, a computer-aided engineering toolkit was developed that allows the UI designers to make quantitative prediction of the usability of design concepts and prototypes. Scientifically, the results of this dissertation research offer additional insights into the mechanisms of human multitask performance. From the engineering application and practical value perspective, the new modeling mechanism and the new toolkit have advantages over the traditional usability testing methods with human subjects by enabling the UI designers to explore a larger design space and address usability issues at the early design stages with lower cost both in time and manpower.PHDIndustrial and Operations EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/113590/1/fredfeng_1.pd

    Computer-Integrated Design and Manufacture of Integrated Circuits

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    Contains research goals and objectives, reports on sixteen research projects and a list of publications.Defense Advanced Research Projects Agency/U.S. Navy Contract N00174-93-K-0035Defense Advanced Research Projects Agency/U.S. Army Contract DABT 63-95-C-0088Multisponsored Projects Industrial/MIT Leaders for Manufacturing Progra
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