A performance comparison of data and memory allocation strategies for sequence aligners on NUMA architectures

Over the last several years, many sequence alignment tools have appeared and become popular for the fast evolution of next generation sequencing technologies. Obviously, researchers that use such tools are interested in getting maximum performance when they execute them in modern infrastructures. Today’s NUMA (Non-uniform memory access) architectures present major challenges in getting such applications to achieve good scalability as more processors/cores are used. The memory system in NUMA systems shows a high complexity and may be the main cause for the loss of an application’s performance. The existence of several memory banks in NUMA systems implies a logical increase in latency associated with the accesses of a given processor to a remote bank. This phenomenon is usually attenuated by the application of strategies that tend to increase the locality of memory accesses. However, NUMA systems may also suffer from contention problems that can occur when concurrent accesses are concentrated on a reduced number of banks. Sequence alignment tools use large data structures to contain reference genomes to which all reads are aligned. Therefore, these tools are very sensitive to performance problems related to the memory system. The main goal of this study is to explore the trade-offs between data locality and data dispersion in NUMA systems. We have performed experiments with several popular sequence alignment tools on two widely available NUMA systems to assess the performance of different memory allocation policies and data partitioning strategies. We find that there is not one method that is best in all cases. However, we conclude that memory interleaving is the memory allocation strategy that provides the best performance when a large number of processors and memory banks are used. In the case of data partitioning, the best results are usually obtained when the number of partitions used is greater, sometimes combined with an interleave policy.     

A dynamic over games drives selfish agents to win–win outcomes

Understanding human institutions, animal cultures and other social systems requires flexible formalisms that describe how their members change them from within. We introduce a framework for modelling how agents change the games they participate in. We contrast this between-game ‘institutional evolution’ with the more familiar within-game ‘behavioural evolution’. We model institutional change by following small numbers of persistent agents as they select and play a changing series of games. Starting from an initial game, a group of agents trace trajectories through game space by navigating to increasingly preferable games until they converge on ‘attractor’ games. Agents use their ‘institutional preferences'' for game features (such as stability, fairness and efficiency) to choose between neighbouring games. We use this framework to pose a pressing question: what kinds of games does institutional evolution select for; what is in the attractors? After computing institutional change trajectories over the two-player space, we find that attractors have disproportionately fair outcomes, even though the agents who produce them are strictly self-interested and indifferent to fairness. This seems to occur because game fairness co-occurs with the self-serving features these agents do actually prefer. We thus present institutional evolution as a mechanism for encouraging the spontaneous emergence of cooperation among small groups of inherently selfish agents, without space, reputation, repetition, or other more familiar mechanisms. Game space trajectories provide a flexible, testable formalism for modelling the interdependencies of behavioural and institutional evolutionary processes, as well as a mechanism for the evolution of cooperation.     

Predicting Positive and Negative Relationships in Large Social Networks

In a social network, users hold and express positive and negative attitudes (e.g. support/opposition) towards other users. Those attitudes exhibit some kind of binary relationships among the users, which play an important role in social network analysis. However, some of those binary relationships are likely to be latent as the scale of social network increases. The essence of predicting latent binary relationships have recently began to draw researchers'' attention. In this paper, we propose a machine learning algorithm for predicting positive and negative relationships in social networks inspired by structural balance theory and social status theory. More specifically, we show that when two users in the network have fewer common neighbors, the prediction accuracy of the relationship between them deteriorates. Accordingly, in the training phase, we propose a segment-based training framework to divide the training data into two subsets according to the number of common neighbors between users, and build a prediction model for each subset based on support vector machine (SVM). Moreover, to deal with large-scale social network data, we employ a sampling strategy that selects small amount of training data while maintaining high accuracy of prediction. We compare our algorithm with traditional algorithms and adaptive boosting of them. Experimental results of typical data sets show that our algorithm can deal with large social networks and consistently outperforms other methods.     

Exploring Entrainment Patterns of Human Emotion in Social Media

Emotion entrainment, which is generally defined as the synchronous convergence of human emotions, performs many important social functions. However, what the specific mechanisms of emotion entrainment are beyond in-person interactions, and how human emotions evolve under different entrainment patterns in large-scale social communities, are still unknown. In this paper, we aim to examine the massive emotion entrainment patterns and understand the underlying mechanisms in the context of social media. As modeling emotion dynamics on a large scale is often challenging, we elaborate a pragmatic framework to characterize and quantify the entrainment phenomenon. By applying this framework on the datasets from two large-scale social media platforms, we find that the emotions of online users entrain through social networks. We further uncover that online users often form their relations via dual entrainment, while maintain it through single entrainment. Remarkably, the emotions of online users are more convergent in nonreciprocal entrainment. Building on these findings, we develop an entrainment augmented model for emotion prediction. Experimental results suggest that entrainment patterns inform emotion proximity in dyads, and encoding their associations promotes emotion prediction. This work can further help us to understand the underlying dynamic process of large-scale online interactions and make more reasonable decisions regarding emergency situations, epidemic diseases, and political campaigns in cyberspace.     

Cell assembly dynamics in detailed and abstract attractor models of cortical associative memory

Summary During the last few decades we have seen a convergence among ideas and hypotheses regarding functional principles underlying human memory. Hebb’s now more than fifty years old conjecture concerning synaptic plasticity and cell assemblies, formalized mathematically as attractor neural networks, has remained among the most viable and productive theoretical frameworks. It suggests plausible explanations for Gestalt aspects of active memory like perceptual completion, reconstruction and rivalry. We review the biological plausibility of these theories and discuss some critical issues concerning their associative memory functionality in the light of simulation studies of models with palimpsest memory properties. The focus is on memory properties and dynamics of networks modularized in terms of cortical minicolumns and hypercolumns. Biophysical compartmental models demonstrate attractor dynamics that support cell assembly operations with fast convergence and low firing rates. Using a scaling model we obtain reasonable relative connection densities and amplitudes. An abstract attractor network model reproduces systems level psychological phenomena seen in human memory experiments as the Sternberg and von Restorff effects. We conclude that there is today considerable substance in Hebb’s theory of cell assemblies and its attractor network formulations, and that they have contributed to increasing our understanding of cortical associative memory function. The criticism raised with regard to biological and psychological plausibility as well as low storage capacity, slow retrieval etc has largely been disproved. Rather, this paradigm has gained further support from new experimental data as well as computational modeling.     

Integrating Human Health and Environmental Health into the DPSIR Framework: A Tool to Identify Research Opportunities for Sustainable and Healthy Communities

The U.S. Environmental Protection Agency has recently realigned its research enterprise around the concept of sustainability. Scientists from across multiple disciplines have a role to play in contributing the information, methods, and tools needed to more fully understand the long-term impacts of decisions on the social and economic sustainability of communities. Success will depend on a shift in thinking to integrate, organize, and prioritize research within a systems context. We used the Driving forces–Pressures–State–Impact–Response (DPSIR) framework as a basis for integrating social, cultural, and economic aspects of environmental and human health into a single framework. To make the framework broadly applicable to sustainability research planning, we provide a hierarchical system of DPSIR keywords and guidelines for use as a communication tool. The applicability of the integrated framework was first tested on a public health issue (asthma disparities) for purposes of discussion. We then applied the framework at a science planning meeting to identify opportunities for sustainable and healthy communities research. We conclude that an integrated systems framework has many potential roles in science planning, including identifying key issues, visualizing interactions within the system, identifying research gaps, organizing information, developing computational models, and identifying indicators.     

From social network (centralized vs. decentralized) to collective decision-making (unshared vs. shared consensus)

Relationships we have with our friends, family, or colleagues influence our personal decisions, as well as decisions we make together with others. As in human beings, despotism and egalitarian societies seem to also exist in animals. While studies have shown that social networks constrain many phenomena from amoebae to primates, we still do not know how consensus emerges from the properties of social networks in many biological systems. We created artificial social networks that represent the continuum from centralized to decentralized organization and used an agent-based model to make predictions about the patterns of consensus and collective movements we observed according to the social network. These theoretical results showed that different social networks and especially contrasted ones--star network vs. equal network--led to totally different patterns. Our model showed that, by moving from a centralized network to a decentralized one, the central individual seemed to lose its leadership in the collective movement's decisions. We, therefore, showed a link between the type of social network and the resulting consensus. By comparing our theoretical data with data on five groups of primates, we confirmed that this relationship between social network and consensus also appears to exist in animal societies.     

A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks

Background  

The study of biological networks has led to the development of increasingly large and detailed models. Computer tools are essential for the simulation of the dynamical behavior of the networks from the model. However, as the size of the models grows, it becomes infeasible to manually verify the predictions against experimental data or identify interesting features in a large number of simulation traces. Formal verification based on temporal logic and model checking provides promising methods to automate and scale the analysis of the models. However, a framework that tightly integrates modeling and simulation tools with model checkers is currently missing, on both the conceptual and the implementational level.     

A Scalable Computational Framework for Establishing Long-Term Behavior of Stochastic Reaction Networks

Reaction networks are systems in which the populations of a finite number of species evolve through predefined interactions. Such networks are found as modeling tools in many biological disciplines such as biochemistry, ecology, epidemiology, immunology, systems biology and synthetic biology. It is now well-established that, for small population sizes, stochastic models for biochemical reaction networks are necessary to capture randomness in the interactions. The tools for analyzing such models, however, still lag far behind their deterministic counterparts. In this paper, we bridge this gap by developing a constructive framework for examining the long-term behavior and stability properties of the reaction dynamics in a stochastic setting. In particular, we address the problems of determining ergodicity of the reaction dynamics, which is analogous to having a globally attracting fixed point for deterministic dynamics. We also examine when the statistical moments of the underlying process remain bounded with time and when they converge to their steady state values. The framework we develop relies on a blend of ideas from probability theory, linear algebra and optimization theory. We demonstrate that the stability properties of a wide class of biological networks can be assessed from our sufficient theoretical conditions that can be recast as efficient and scalable linear programs, well-known for their tractability. It is notably shown that the computational complexity is often linear in the number of species. We illustrate the validity, the efficiency and the wide applicability of our results on several reaction networks arising in biochemistry, systems biology, epidemiology and ecology. The biological implications of the results as well as an example of a non-ergodic biological network are also discussed.     

Manipulating animal social interactions to enhance translocation impact

Species’ ecological interactions, evolutionary trajectories, and survival strategies are intertwined with their social relationships. Conservation translocations can disrupt social systems, interrupting the mechanisms driving population and ecosystem trends. We outline a research framework to provide targeted tools for translocation practitioners, where appropriate, while advancing the theoretical understanding of social resiliency.     

Comparative studies of de novo assembly tools for next-generation sequencing technologies

MOTIVATION: Several new de novo assembly tools have been developed recently to assemble short sequencing reads generated by next-generation sequencing platforms. However, the performance of these tools under various conditions has not been fully investigated, and sufficient information is not currently available for informed decisions to be made regarding the tool that would be most likely to produce the best performance under a specific set of conditions. RESULTS: We studied and compared the performance of commonly used de novo assembly tools specifically designed for next-generation sequencing data, including SSAKE, VCAKE, Euler-sr, Edena, Velvet, ABySS and SOAPdenovo. Tools were compared using several performance criteria, including N50 length, sequence coverage and assembly accuracy. Various properties of read data, including single-end/paired-end, sequence GC content, depth of coverage and base calling error rates, were investigated for their effects on the performance of different assembly tools. We also compared the computation time and memory usage of these seven tools. Based on the results of our comparison, the relative performance of individual tools are summarized and tentative guidelines for optimal selection of different assembly tools, under different conditions, are provided.     

Effects of scale on interpreting life-history characteristics of ungulates and carnivores

Many life-history characteristics of large mammals are scale sensitive. We provide examples where varying temporal and spatial scales can affect interpretation of data concerning life-history characteristics in large herbivores and carnivores and offer recommendations for selecting the most appropriate sampling scale or scales. We also document that some animals make decisions concerning their spatial distribution at scales well beyond the size of the home range. Conversely, other decisions involving sexual segregation of sexes, or where to give birth, may be made at scales below the level of the habitat patch. Such differences in behaviour affect our understanding of habitat selection in large herbivores, and interpreting tradeoffs between acquiring essential resources and avoiding predators. Moreover, some landscape attributes may be selected at one scale, whereas other characteristics of the environment may be selected at another. We argue that even sophisticated models for explaining the ecology and behaviour of mammals benefit from framing specific hypotheses that are related to the to the life-history characteristics of those animals. We also believe that the failure to consider and select the most appropriate scale, or suite of scales, may lead to the mismanagement of critical natural resources. We forge relationships among scale, life-history characteristics of mammals, and biodiversity. Finally, we synthesize the literature on scale for large mammals and make recommendations for future research.     

GDSCalc: A Web-Based Application for Evaluating Discrete Graph Dynamical Systems

Discrete dynamical systems are used to model various realistic systems in network science, from social unrest in human populations to regulation in biological networks. A common approach is to model the agents of a system as vertices of a graph, and the pairwise interactions between agents as edges. Agents are in one of a finite set of states at each discrete time step and are assigned functions that describe how their states change based on neighborhood relations. Full characterization of state transitions of one system can give insights into fundamental behaviors of other dynamical systems. In this paper, we describe a discrete graph dynamical systems (GDSs) application called GDSCalc for computing and characterizing system dynamics. It is an open access system that is used through a web interface. We provide an overview of GDS theory. This theory is the basis of the web application; i.e., an understanding of GDS provides an understanding of the software features, while abstracting away implementation details. We present a set of illustrative examples to demonstrate its use in education and research. Finally, we compare GDSCalc with other discrete dynamical system software tools. Our perspective is that no single software tool will perform all computations that may be required by all users; tools typically have particular features that are more suitable for some tasks. We situate GDSCalc within this space of software tools.     

Using multilayer network analysis to explore the temporal dynamics of collective behavior

Social organisms often show collective behaviors such as group foraging or movement.Collective behaviors can emerge from interactions between group members and may depend on the behavior of key individuals.When social interactions change over time,collective behaviors may change because these behaviors emerge from interactions among individuals.Despite the importance of,and growing interest in,the temporal dynamics of social interactions,it is not clear how to quantify changes in interactions over time or measure their stability.Furthermore,the temporal scale at which we should observe changes in social networks to detect biologically meaningful changes is not always apparent.Here we use multilayer network analysis to quantify temporal dynamics of social networks of the social spider Stegodyphus dumicola and determine how these dynamics relate to individual and group behaviors.We found that social interactions changed over time at a constant rate.Variation in both network structure and the identity of a keystone individual was not related to the mean or variance of the collective prey attack speed.Individuals that maintained a large and stable number of connections,despite changes in network structure,were the boldest individuals in the group.Therefore,social interactions and boldness are linked across time,but group collective behavior is not influenced by the stability of the social network.Our work demonstrates that dynamic social networks can be modeled in a multilayer framework.This approach may reveal biologically important temporal changes to social structure in other systems.     

Trade-offs in covariate selection for species distribution models: a methodological comparison

Species distribution models (SDMs) are a common approach to describing species’ space-use and spatially-explicit abundance. With a myriad of model types, methods and parameterization options available, it is challenging to make informed decisions about how to build robust SDMs appropriate for a given purpose. One key component of SDM development is the appropriate parameterization of covariates, such as the inclusion of covariates that reflect underlying processes (e.g. abiotic and biotic covariates) and covariates that act as proxies for unobserved processes (e.g. space and time covariates). It is unclear how different SDMs apportion variance among a suite of covariates, and how parameterization decisions influence model accuracy and performance. To examine trade-offs in covariation parameterization in SDMs, we explore the attribution of spatiotemporal and environmental variation across a suite of SDMs. We first used simulated species distributions with known environmental preferences to compare three types of SDM: a machine learning model (boosted regression tree), a semi-parametric model (generalized additive model) and a spatiotemporal mixed-effects model (vector autoregressive spatiotemporal model, VAST). We then applied the same comparative framework to a case study with three fish species (arrowtooth flounder, pacific cod and walleye pollock) in the eastern Bering Sea, USA. Model type and covariate parameterization both had significant effects on model accuracy and performance. We found that including either spatiotemporal or environmental covariates typically reproduced patterns of species distribution and abundance across the three models tested, but model accuracy and performance was maximized when including both spatiotemporal and environmental covariates in the same model framework. Our results reveal trade-offs in the current generation of SDM tools between accurately estimating species abundance, accurately estimating spatial patterns, and accurately quantifying underlying species–environment relationships. These comparisons between model types and parameterization options can help SDM users better understand sources of model bias and estimate error.     

Can collective memories shape fish distributions? A test,linking space‐time occurrence models and population demographics

Social learning can be fundamental to cohesive group living, and schooling fishes have proven ideal test subjects for recent work in this field. For many species, both demographic factors, and inter‐ (and intra‐) generational information exchange are considered vital ingredients in how movement decisions are reached. Yet key information is often missing on the spatial outcomes of such decisions, and questions concerning how migratory traditions are influenced by collective memory, density‐dependent and density‐independent processes remain open. To explore these issues, we focused on Atlantic herring Clupea harengus, a long‐lived, dense‐schooling species of high commercial importance, noted for its unpredictable shifts in winter distribution, and developed a series of Bayesian space‐time occurrence models to investigate wintering dynamics over 23 yr, using point‐referenced fishery and survey records from Icelandic waters. We included covariates reflecting local‐scale environmental factors, temporally‐lagged prey biomass and recent fishing activity, and through an index capturing distributional persistence over time, derived two proxies for spatial memory of past wintering sites. The previous winter's occurrence pattern was a strong predictor of the present pattern, its influence increasing with adult population size. Although the mechanistic underpinnings of this result remain uncertain, we suggest that a ‘wisdom of the crowd’ dynamic may be at play, by which navigational accuracy towards traditional wintering sites improves in larger and/or denser, better synchronized schools. Wintering herring also preferred warmer, fresher, moderately stratified waters of lower velocity, close to hotspots of summer zooplankton biomass, our results indicative of heightened environmental sensitivity in younger cohorts. Incorporating spatiotemporal correlation structure and time‐varying regression coefficients improved model performance, and validation tests on independent observations one‐year ahead illustrate the potential of uniting demographic information and non‐stationary models to quantify both the strength of collective memory in animal groups and its relevance for the spatial management of populations.     

Environmental Impact Assessment of the Heterogeneity in Consumers’ Usage Behavior: An Agent‐Based Modeling Approach

The aim of this study is to develop a framework for understanding the heterogeneity and uncertainties present in the usage phase of the product life cycle through utilizing the capabilities of an agent‐based modeling (ABM) technique. An ABM framework is presented to model consumers’ daily product usage decisions and to assess the corresponding electricity consumption patterns. The theory of planned behavior (TPB), with the addition of the habit construct, is used to model agents’ decision‐making criteria. A case study is presented on the power management behavior of personal computer users and the possible benefits of using smart metering and feedback systems. The results of the simulation demonstrate that the utilization of smart metering and feedback systems can promote the energy conservation behaviors and reduce the total PC electricity consumption of households by 20%.     

Guaranteeing the quality of multidimensional analysis in data warehouses of simulation results: Application to pesticide transfer data produced by the MACRO model

Currently, the vital impact of environmental pollution on economic, social and health dimensions has been recognized. The need for theoretical and implementation frameworks for the acquisition, modeling and analysis of environmental data as well as tools to conceive and validate scenarios is becoming increasingly important. For these reasons, different environmental simulation models have been developed. Researchers and stakeholders need efficient tools to store, display, compare and analyze data that are produced by simulation models. One common way to manage simulation results is to use text files; however, text files make it difficult to explore the data. Spreadsheet tools (e.g., OpenOffice, MS Excel) can help to display and analyze model results, but they are not suitable for very large volumes of information. Recently, some studies have shown the feasibility of using Data Warehouse (DW) and On-Line Analytical Processing (OLAP) technologies to store model results and to facilitate model visualization, analysis and comparisons. These technologies allow model users to easily produce graphical reports and charts. In this paper, we address the analysis of pesticide transfer simulation results by warehousing and OLAPing data, for which the data results from the MACRO simulation model. This model simulates hydrological transfers of pesticides at the plot scale. We demonstrate how the simulation results can be managed using DW technologies. We also demonstrate how the use of integrity constraints can improve OLAP analysis. These constraints are used to maintain the quality of the warehoused data as well as to maintain the aggregations and queries, which will lead to better analysis, conclusions and decisions.