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 Comprehensive Workflow for General-Purpose Neural Modeling with Highly Configurable Neuromorphic Hardware Systems

In this paper we present a methodological framework that meets novel requirements emerging from upcoming types of accelerated and highly configurable neuromorphic hardware systems. We describe in detail a device with 45 million programmable and dynamic synapses that is currently under development, and we sketch the conceptual challenges that arise from taking this platform into operation. More specifically, we aim at the establishment of this neuromorphic system as a flexible and neuroscientifically valuable modeling tool that can be used by non-hardware-experts. We consider various functional aspects to be crucial for this purpose, and we introduce a consistent workflow with detailed descriptions of all involved modules that implement the suggested steps: The integration of the hardware interface into the simulator-independent model description language PyNN; a fully automated translation between the PyNN domain and appropriate hardware configurations; an executable specification of the future neuromorphic system that can be seamlessly integrated into this biology-to-hardware mapping process as a test bench for all software layers and possible hardware design modifications; an evaluation scheme that deploys models from a dedicated benchmark library, compares the results generated by virtual or prototype hardware devices with reference software simulations and analyzes the differences. The integration of these components into one hardware-software workflow provides an ecosystem for ongoing preparative studies that support the hardware design process and represents the basis for the maturity of the model-to-hardware mapping software. The functionality and flexibility of the latter is proven with a variety of experimental results

A survey of simulation techniques in commerce and defence

Despite the developments in Modelling and Simulation (M&S) tools and techniques over the past years, there has been a gap in the M&S research and practice in healthcare on developing a toolkit to assist the modellers and simulation practitioners with selecting an appropriate set of techniques. This study is a preliminary step towards this goal. This paper presents some results from a systematic literature survey on applications of M&S in the commerce and defence domains that could inspire some improvements in the healthcare. Interim results show that in the commercial sector Discrete-Event Simulation (DES) has been the most widely used technique with System Dynamics (SD) in second place. However in the defence sector, SD has gained relatively more attention. SD has been found quite useful for qualitative and soft factors analysis. From both the surveys it becomes clear that there is a growing trend towards using hybrid M&S approaches

An empirical learning-based validation procedure for simulation workflow

Simulation workflow is a top-level model for the design and control of simulation process. It connects multiple simulation components with time and interaction restrictions to form a complete simulation system. Before the construction and evaluation of the component models, the validation of upper-layer simulation workflow is of the most importance in a simulation system. However, the methods especially for validating simulation workflow is very limit. Many of the existing validation techniques are domain-dependent with cumbersome questionnaire design and expert scoring. Therefore, this paper present an empirical learning-based validation procedure to implement a semi-automated evaluation for simulation workflow. First, representative features of general simulation workflow and their relations with validation indices are proposed. The calculation process of workflow credibility based on Analytic Hierarchy Process (AHP) is then introduced. In order to make full use of the historical data and implement more efficient validation, four learning algorithms, including back propagation neural network (BPNN), extreme learning machine (ELM), evolving new-neuron (eNFN) and fast incremental gaussian mixture model (FIGMN), are introduced for constructing the empirical relation between the workflow credibility and its features. A case study on a landing-process simulation workflow is established to test the feasibility of the proposed procedure. The experimental results also provide some useful overview of the state-of-the-art learning algorithms on the credibility evaluation of simulation models