MOLNs: A cloud platform for interactive, reproducible and scalable spatial stochastic computational experiments in systems biology using PyURDME

Computational experiments using spatial stochastic simulations have led to important new biological insights, but they require specialized tools, a complex software stack, as well as large and scalable compute and data analysis resources due to the large computational cost associated with Monte Carlo computational workflows. The complexity of setting up and managing a large-scale distributed computation environment to support productive and reproducible modeling can be prohibitive for practitioners in systems biology. This results in a barrier to the adoption of spatial stochastic simulation tools, effectively limiting the type of biological questions addressed by quantitative modeling. In this paper, we present PyURDME, a new, user-friendly spatial modeling and simulation package, and MOLNs, a cloud computing appliance for distributed simulation of stochastic reaction-diffusion models. MOLNs is based on IPython and provides an interactive programming platform for development of sharable and reproducible distributed parallel computational experiments

A Rewriting-Logic-Based Technique for Modeling Thermal Systems

This paper presents a rewriting-logic-based modeling and analysis technique for physical systems, with focus on thermal systems. The contributions of this paper can be summarized as follows: (i) providing a framework for modeling and executing physical systems, where both the physical components and their physical interactions are treated as first-class citizens; (ii) showing how heat transfer problems in thermal systems can be modeled in Real-Time Maude; (iii) giving the implementation in Real-Time Maude of a basic numerical technique for executing continuous behaviors in object-oriented hybrid systems; and (iv) illustrating these techniques with a set of incremental case studies using realistic physical parameters, with examples of simulation and model checking analyses.Comment: In Proceedings RTRTS 2010, arXiv:1009.398

Viewpoint Development of Stochastic Hybrid Systems

Nowadays, due to the explosive spreading of networked and highly distributed systems, mastering system complexity becomes a critical issue. Two development and verification paradigms have become more popular: viewpoints and randomisation. The viewpoints offer large freedom and introduce concurrency and compositionality in the development process. Randomisation is now a traditional method for reducing complexity (comparing with deterministic models) and it offers finer analytical analysis tools (quantification over non-determinism, multi-valued logics, etc). In this paper, we propose a combination of these two paradigms introducing a viewpoint methodology for systems with stochastic behaviours

Simulation of networks of spiking neurons: A review of tools and strategies

We review different aspects of the simulation of spiking neural networks. We start by reviewing the different types of simulation strategies and algorithms that are currently implemented. We next review the precision of those simulation strategies, in particular in cases where plasticity depends on the exact timing of the spikes. We overview different simulators and simulation environments presently available (restricted to those freely available, open source and documented). For each simulation tool, its advantages and pitfalls are reviewed, with an aim to allow the reader to identify which simulator is appropriate for a given task. Finally, we provide a series of benchmark simulations of different types of networks of spiking neurons, including Hodgkin-Huxley type, integrate-and-fire models, interacting with current-based or conductance-based synapses, using clock-driven or event-driven integration strategies. The same set of models are implemented on the different simulators, and the codes are made available. The ultimate goal of this review is to provide a resource to facilitate identifying the appropriate integration strategy and simulation tool to use for a given modeling problem related to spiking neural networks.Comment: 49 pages, 24 figures, 1 table; review article, Journal of Computational Neuroscience, in press (2007

Generating a Performance Stochastic Model from UML Specifications

Since its initiation by Connie Smith, the process of Software Performance Engineering (SPE) is becoming a growing concern. The idea is to bring performance evaluation into the software design process. This suitable methodology allows software designers to determine the performance of software during design. Several approaches have been proposed to provide such techniques. Some of them propose to derive from a UML (Unified Modeling Language) model a performance model such as Stochastic Petri Net (SPN) or Stochastic process Algebra (SPA) models. Our work belongs to the same category. We propose to derive from a UML model a Stochastic Automata Network (SAN) in order to obtain performance predictions. Our approach is more flexible due to the SAN modularity and its high resemblance to UML' state-chart diagram

Scalable Approach to Uncertainty Quantification and Robust Design of Interconnected Dynamical Systems

Development of robust dynamical systems and networks such as autonomous aircraft systems capable of accomplishing complex missions faces challenges due to the dynamically evolving uncertainties coming from model uncertainties, necessity to operate in a hostile cluttered urban environment, and the distributed and dynamic nature of the communication and computation resources. Model-based robust design is difficult because of the complexity of the hybrid dynamic models including continuous vehicle dynamics, the discrete models of computations and communications, and the size of the problem. We will overview recent advances in methodology and tools to model, analyze, and design robust autonomous aerospace systems operating in uncertain environment, with stress on efficient uncertainty quantification and robust design using the case studies of the mission including model-based target tracking and search, and trajectory planning in uncertain urban environment. To show that the methodology is generally applicable to uncertain dynamical systems, we will also show examples of application of the new methods to efficient uncertainty quantification of energy usage in buildings, and stability assessment of interconnected power networks