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

Dynamic Influence Networks for Rule-based Models

We introduce the Dynamic Influence Network (DIN), a novel visual analytics technique for representing and analyzing rule-based models of protein-protein interaction networks. Rule-based modeling has proved instrumental in developing biological models that are concise, comprehensible, easily extensible, and that mitigate the combinatorial complexity of multi-state and multi-component biological molecules. Our technique visualizes the dynamics of these rules as they evolve over time. Using the data produced by KaSim, an open source stochastic simulator of rule-based models written in the Kappa language, DINs provide a node-link diagram that represents the influence that each rule has on the other rules. That is, rather than representing individual biological components or types, we instead represent the rules about them (as nodes) and the current influence of these rules (as links). Using our interactive DIN-Viz software tool, researchers are able to query this dynamic network to find meaningful patterns about biological processes, and to identify salient aspects of complex rule-based models. To evaluate the effectiveness of our approach, we investigate a simulation of a circadian clock model that illustrates the oscillatory behavior of the KaiC protein phosphorylation cycle.Comment: Accepted to TVCG, in pres

Prediction and predictability of global epidemics: the role of the airline transportation network

The systematic study of large-scale networks has unveiled the ubiquitous presence of connectivity patterns characterized by large scale heterogeneities and unbounded statistical fluctuations. These features affect dramatically the behavior of the diffusion processes occurring on networks, determining the ensuing statistical properties of their evolution pattern and dynamics. In this paper, we investigate the role of the large scale properties of the airline transportation network in determining the global evolution of emerging disease. We present a stochastic computational framework for the forecast of global epidemics that considers the complete world-wide air travel infrastructure complemented with census population data. We address two basic issues in global epidemic modeling: i) We study the role of the large scale properties of the airline transportation network in determining the global diffusion pattern of emerging diseases; ii) We evaluate the reliability of forecasts and outbreak scenarios with respect to the intrinsic stochasticity of disease transmission and traffic flows. In order to address these issues we define a set of novel quantitative measures able to characterize the level of heterogeneity and predictability of the epidemic pattern. These measures may be used for the analysis of containment policies and epidemic risk assessment.Comment: 20 pages, 5 figure

NetEvo: A computational framework for the evolution of dynamical complex networks

NetEvo is a computational framework designed to help understand the evolution of dynamical complex networks. It provides flexible tools for the simulation of dynamical processes on networks and methods for the evolution of underlying topological structures. The concept of a supervisor is used to bring together both these aspects in a coherent way. It is the job of the supervisor to rewire the network topology and alter model parameters such that a user specified performance measure is minimised. This performance measure can make use of current topological information and simulated dynamical output from the system. Such an abstraction provides a suitable basis in which to study many outstanding questions related to complex system design and evolution

The state of MIIND

MIIND (Multiple Interacting Instantiations of Neural Dynamics) is a highly modular multi-level C++ framework, that aims to shorten the development time for models in Cognitive Neuroscience (CNS). It offers reusable code modules (libraries of classes and functions) aimed at solving problems that occur repeatedly in modelling, but tries not to impose a specific modelling philosophy or methodology. At the lowest level, it offers support for the implementation of sparse networks. For example, the library SparseImplementationLib supports sparse random networks and the library LayerMappingLib can be used for sparse regular networks of filter-like operators. The library DynamicLib, which builds on top of the library SparseImplementationLib, offers a generic framework for simulating network processes. Presently, several specific network process implementations are provided in MIIND: the Wilson–Cowan and Ornstein–Uhlenbeck type, and population density techniques for leaky-integrate-and-fire neurons driven by Poisson input. A design principle of MIIND is to support detailing: the refinement of an originally simple model into a form where more biological detail is included. Another design principle is extensibility: the reuse of an existing model in a larger, more extended one. One of the main uses of MIIND so far has been the instantiation of neural models of visual attention. Recently, we have added a library for implementing biologically-inspired models of artificial vision, such as HMAX and recent successors. In the long run we hope to be able to apply suitably adapted neuronal mechanisms of attention to these artificial models

Sustaining Economic Exploitation of Complex Ecosystems in Computational Models of Coupled Human-Natural Networks

Understanding ecological complexity has stymied scientists for decades. Recent elucidation of the famously coined "devious strategies for stability in enduring natural systems" has opened up a new field of computational analyses of complex ecological networks where the nonlinear dynamics of many interacting species can be more realistically mod-eled and understood. Here, we describe the first extension of this field to include coupled human-natural systems. This extension elucidates new strategies for sustaining extraction of biomass (e.g., fish, forests, fiber) from ecosystems that account for ecological complexity and can pursue multiple goals such as maximizing economic profit, employment and carbon sequestration by ecosystems. Our more realistic modeling of ecosystems helps explain why simpler "maxi-mum sustainable yield" bioeconomic models underpinning much natural resource extraction policy leads to less profit, biomass, and biodiversity than predicted by those simple models. Current research directions of this integrated natu-ral and social science include applying artificial intelligence, cloud computing, and multiplayer online games

Simulation α of EEG using brain network model

In this paper, we developed a large-scale brain network model comprising of four cerebral areas in the left hemisphere, and each area is modelled as an oscillator Jansen and Rit (JR) model. Our model is based on the structural connectivity of human connectome (SC) which was a hybrid from CoCoMac neuroinformatics database and diffusion spectrum imaging (DSI.) This brain network model was designed and implemented on the neuroinformatics platform using The Virtual Brain (TVB v1.5.3). The results demonstrated that incorporating the large-scale connectivity of brain regions and neural mass of JR model can generate signals similar to the α oscillation in frequency range of (7-12HZ) of EEG

From Social Simulation to Integrative System Design

As the recent financial crisis showed, today there is a strong need to gain "ecological perspective" of all relevant interactions in socio-economic-techno-environmental systems. For this, we suggested to set-up a network of Centers for integrative systems design, which shall be able to run all potentially relevant scenarios, identify causality chains, explore feedback and cascading effects for a number of model variants, and determine the reliability of their implications (given the validity of the underlying models). They will be able to detect possible negative side effect of policy decisions, before they occur. The Centers belonging to this network of Integrative Systems Design Centers would be focused on a particular field, but they would be part of an attempt to eventually cover all relevant areas of society and economy and integrate them within a "Living Earth Simulator". The results of all research activities of such Centers would be turned into informative input for political Decision Arenas. For example, Crisis Observatories (for financial instabilities, shortages of resources, environmental change, conflict, spreading of diseases, etc.) would be connected with such Decision Arenas for the purpose of visualization, in order to make complex interdependencies understandable to scientists, decision-makers, and the general public.Comment: 34 pages, Visioneer White Paper, see http://www.visioneer.ethz.c