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

Distributed Computing with Adaptive Heuristics

We use ideas from distributed computing to study dynamic environments in which computational nodes, or decision makers, follow adaptive heuristics (Hart 2005), i.e., simple and unsophisticated rules of behavior, e.g., repeatedly "best replying" to others' actions, and minimizing "regret", that have been extensively studied in game theory and economics. We explore when convergence of such simple dynamics to an equilibrium is guaranteed in asynchronous computational environments, where nodes can act at any time. Our research agenda, distributed computing with adaptive heuristics, lies on the borderline of computer science (including distributed computing and learning) and game theory (including game dynamics and adaptive heuristics). We exhibit a general non-termination result for a broad class of heuristics with bounded recall---that is, simple rules of behavior that depend only on recent history of interaction between nodes. We consider implications of our result across a wide variety of interesting and timely applications: game theory, circuit design, social networks, routing and congestion control. We also study the computational and communication complexity of asynchronous dynamics and present some basic observations regarding the effects of asynchrony on no-regret dynamics. We believe that our work opens a new avenue for research in both distributed computing and game theory.Comment: 36 pages, four figures. Expands both technical results and discussion of v1. Revised version will appear in the proceedings of Innovations in Computer Science 201

Task-based adaptive multiresolution for time-space multi-scale reaction-diffusion systems on multi-core architectures

A new solver featuring time-space adaptation and error control has been recently introduced to tackle the numerical solution of stiff reaction-diffusion systems. Based on operator splitting, finite volume adaptive multiresolution and high order time integrators with specific stability properties for each operator, this strategy yields high computational efficiency for large multidimensional computations on standard architectures such as powerful workstations. However, the data structure of the original implementation, based on trees of pointers, provides limited opportunities for efficiency enhancements, while posing serious challenges in terms of parallel programming and load balancing. The present contribution proposes a new implementation of the whole set of numerical methods including Radau5 and ROCK4, relying on a fully different data structure together with the use of a specific library, TBB, for shared-memory, task-based parallelism with work-stealing. The performance of our implementation is assessed in a series of test-cases of increasing difficulty in two and three dimensions on multi-core and many-core architectures, demonstrating high scalability

Simulated single molecule microscopy with SMeagol

SMeagol is a software tool to simulate highly realistic microscopy data based on spatial systems biology models, in order to facilitate development, validation, and optimization of advanced analysis methods for live cell single molecule microscopy data. Availability and Implementation: SMeagol runs on Matlab R2014 and later, and uses compiled binaries in C for reaction-diffusion simulations. Documentation, source code, and binaries for recent versions of Mac OS, Windows, and Ubuntu Linux can be downloaded from http://smeagol.sourceforge.net.Comment: v2: 14 pages including supplementary text. Pre-copyedited, author-produced version of an application note published in Bioinformatics following peer review. The version of record, and additional supplementary material is available online at: https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btw10