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

Big data analytics:Computational intelligence techniques and application areas

Big Data has significant impact in developing functional smart cities and supporting modern societies. In this paper, we investigate the importance of Big Data in modern life and economy, and discuss challenges arising from Big Data utilization. Different computational intelligence techniques have been considered as tools for Big Data analytics. We also explore the powerful combination of Big Data and Computational Intelligence (CI) and identify a number of areas, where novel applications in real world smart city problems can be developed by utilizing these powerful tools and techniques. We present a case study for intelligent transportation in the context of a smart city, and a novel data modelling methodology based on a biologically inspired universal generative modelling approach called Hierarchical Spatial-Temporal State Machine (HSTSM). We further discuss various implications of policy, protection, valuation and commercialization related to Big Data, its applications and deployment

Visual analytics for supply network management: system design and evaluation

We propose a visual analytic system to augment and enhance decision-making processes of supply chain managers. Several design requirements drive the development of our integrated architecture and lead to three primary capabilities of our system prototype. First, a visual analytic system must integrate various relevant views and perspectives that highlight different structural aspects of a supply network. Second, the system must deliver required information on-demand and update the visual representation via user-initiated interactions. Third, the system must provide both descriptive and predictive analytic functions for managers to gain contingency intelligence. Based on these capabilities we implement an interactive web-based visual analytic system. Our system enables managers to interactively apply visual encodings based on different node and edge attributes to facilitate mental map matching between abstract attributes and visual elements. Grounded in cognitive fit theory, we demonstrate that an interactive visual system that dynamically adjusts visual representations to the decision environment can significantly enhance decision-making processes in a supply network setting. We conduct multi-stage evaluation sessions with prototypical users that collectively confirm the value of our system. Our results indicate a positive reaction to our system. We conclude with implications and future research opportunities.The authors would like to thank the participants of the 2015 Businessvis Workshop at IEEE VIS, Prof. Benoit Montreuil, and Dr. Driss Hakimi for their valuable feedback on an earlier version of the software; Prof. Manpreet Hora for assisting with and Georgia Tech graduate students for participating in the evaluation sessions; and the two anonymous reviewers for their detailed comments and suggestions. The study was in part supported by the Tennenbaum Institute at Georgia Tech Award # K9305. (K9305 - Tennenbaum Institute at Georgia Tech Award)Accepted manuscrip

Designing Improved Sediment Transport Visualizations

Monitoring, or more commonly, modeling of sediment transport in the coastal environment is a critical task with relevance to coastline stability, beach erosion, tracking environmental contaminants, and safety of navigation. Increased intensity and regularity of storms such as Superstorm Sandy heighten the importance of our understanding of sediment transport processes. A weakness of current modeling capabilities is the ability to easily visualize the result in an intuitive manner. Many of the available visualization software packages display only a single variable at once, usually as a two-dimensional, plan-view cross-section. With such limited display capabilities, sophisticated 3D models are undermined in both the interpretation of results and dissemination of information to the public. Here we explore a subset of existing modeling capabilities (specifically, modeling scour around man-made structures) and visualization solutions, examine their shortcomings and present a design for a 4D visualization for sediment transport studies that is based on perceptually-focused data visualization research and recent and ongoing developments in multivariate displays. Vector and scalar fields are co-displayed, yet kept independently identifiable utilizing human perception\u27s separation of color, texture, and motion. Bathymetry, sediment grain-size distribution, and forcing hydrodynamics are a subset of the variables investigated for simultaneous representation. Direct interaction with field data is tested to support rapid validation of sediment transport model results. Our goal is a tight integration of both simulated data and real world observations to support analysis and simulation of the impact of major sediment transport events such as hurricanes. We unite modeled results and field observations within a geodatabase designed as an application schema of the Arc Marine Data Model. Our real-world focus is on the Redbird Artificial Reef Site, roughly 18 nautical miles offshor- Delaware Bay, Delaware, where repeated surveys have identified active scour and bedform migration in 27 m water depth amongst the more than 900 deliberately sunken subway cars and vessels. Coincidently collected high-resolution multibeam bathymetry, backscatter, and side-scan sonar data from surface and autonomous underwater vehicle (AUV) systems along with complementary sub-bottom, grab sample, bottom imagery, and wave and current (via ADCP) datasets provide the basis for analysis. This site is particularly attractive due to overlap with the Delaware Bay Operational Forecast System (DBOFS), a model that provides historical and forecast oceanographic data that can be tested in hindcast against significant changes observed at the site during Superstorm Sandy and in predicting future changes through small-scale modeling around the individual reef objects

The THREAT-ARREST Cyber-Security Training Platform

Cyber security is always a main concern for critical infrastructures and nation-wide safety and sustainability. Thus, advanced cyber ranges and security training is becoming imperative for the involved organizations. This paper presets a cyber security training platform, called THREAT-ARREST. The various platform modules can analyze an organization’s system, identify the most critical threats, and tailor a training program to its personnel needs. Then, different training programmes are created based on the trainee types (i.e. administrator, simple operator, etc.), providing several teaching procedures and accomplishing diverse learning goals. One of the main novelties of THREAT-ARREST is the modelling of these programmes along with the runtime monitoring, management, and evaluation operations. The platform is generic. Nevertheless, its applicability in a smart energy case study is detailed

An Assessment of PIER Electric Grid Research 2003-2014 White Paper

This white paper describes the circumstances in California around the turn of the 21st century that led the California Energy Commission (CEC) to direct additional Public Interest Energy Research funds to address critical electric grid issues, especially those arising from integrating high penetrations of variable renewable generation with the electric grid. It contains an assessment of the beneficial science and technology advances of the resultant portfolio of electric grid research projects administered under the direction of the CEC by a competitively selected contractor, the University of California’s California Institute for Energy and the Environment, from 2003-2014

Training of Crisis Mappers and Map Production from Multi-sensor Data: Vernazza Case Study (Cinque Terre National Park, Italy)

This aim of paper is to presents the development of a multidisciplinary project carried out by the cooperation between Politecnico di Torino and ITHACA (Information Technology for Humanitarian Assistance, Cooperation and Action). The goal of the project was the training in geospatial data acquiring and processing for students attending Architecture and Engineering Courses, in order to start up a team of "volunteer mappers". Indeed, the project is aimed to document the environmental and built heritage subject to disaster; the purpose is to improve the capabilities of the actors involved in the activities connected in geospatial data collection, integration and sharing. The proposed area for testing the training activities is the Cinque Terre National Park, registered in the World Heritage List since 1997. The area was affected by flood on the 25th of October 2011. According to other international experiences, the group is expected to be active after emergencies in order to upgrade maps, using data acquired by typical geomatic methods and techniques such as terrestrial and aerial Lidar, close-range and aerial photogrammetry, topographic and GNSS instruments etc.; or by non conventional systems and instruments such us UAV, mobile mapping etc. The ultimate goal is to implement a WebGIS platform to share all the data collected with local authorities and the Civil Protectio