COEL: A Web-based Chemistry Simulation Framework

The chemical reaction network (CRN) is a widely used formalism to describe macroscopic behavior of chemical systems. Available tools for CRN modelling and simulation require local access, installation, and often involve local file storage, which is susceptible to loss, lacks searchable structure, and does not support concurrency. Furthermore, simulations are often single-threaded, and user interfaces are non-trivial to use. Therefore there are significant hurdles to conducting efficient and collaborative chemical research. In this paper, we introduce a new enterprise chemistry simulation framework, COEL, which addresses these issues. COEL is the first web-based framework of its kind. A visually pleasing and intuitive user interface, simulations that run on a large computational grid, reliable database storage, and transactional services make COEL ideal for collaborative research and education. COEL's most prominent features include ODE-based simulations of chemical reaction networks and multicompartment reaction networks, with rich options for user interactions with those networks. COEL provides DNA-strand displacement transformations and visualization (and is to our knowledge the first CRN framework to do so), GA optimization of rate constants, expression validation, an application-wide plotting engine, and SBML/Octave/Matlab export. We also present an overview of the underlying software and technologies employed and describe the main architectural decisions driving our development. COEL is available at http://coel-sim.org for selected research teams only. We plan to provide a part of COEL's functionality to the general public in the near future.Comment: 23 pages, 12 figures, 1 tabl

Architecture of Environmental Risk Modelling: for a faster and more robust response to natural disasters

Demands on the disaster response capacity of the European Union are likely to increase, as the impacts of disasters continue to grow both in size and frequency. This has resulted in intensive research on issues concerning spatially-explicit information and modelling and their multiple sources of uncertainty. Geospatial support is one of the forms of assistance frequently required by emergency response centres along with hazard forecast and event management assessment. Robust modelling of natural hazards requires dynamic simulations under an array of multiple inputs from different sources. Uncertainty is associated with meteorological forecast and calibration of the model parameters. Software uncertainty also derives from the data transformation models (D-TM) needed for predicting hazard behaviour and its consequences. On the other hand, social contributions have recently been recognized as valuable in raw-data collection and mapping efforts traditionally dominated by professional organizations. Here an architecture overview is proposed for adaptive and robust modelling of natural hazards, following the Semantic Array Programming paradigm to also include the distributed array of social contributors called Citizen Sensor in a semantically-enhanced strategy for D-TM modelling. The modelling architecture proposes a multicriteria approach for assessing the array of potential impacts with qualitative rapid assessment methods based on a Partial Open Loop Feedback Control (POLFC) schema and complementing more traditional and accurate a-posteriori assessment. We discuss the computational aspect of environmental risk modelling using array-based parallel paradigms on High Performance Computing (HPC) platforms, in order for the implications of urgency to be introduced into the systems (Urgent-HPC).Comment: 12 pages, 1 figure, 1 text box, presented at the 3rd Conference of Computational Interdisciplinary Sciences (CCIS 2014), Asuncion, Paragua

Platform-independent Dynamic Reconfiguration of Distributed Applications

The aim of dynamic reconfiguration is to allow a system to evolve incrementally from one configuration to another at run-time, without restarting it or taking it offline. In recent years, support for transparent dynamic reconfiguration has been added to middleware platforms, shifting the complexity required to enable dynamic reconfiguration to the supporting infrastructure. These approaches to dynamic reconfiguration are mostly platform-specific and depend on particular implementation approaches suitable for particular platforms. In this paper, we propose an approach to dynamic reconfiguration of distributed applications that is suitable for application implemented on top of different platforms. This approach supports a platform-independent view of an application that profits from reconfiguration transparency. In this view, requirements on the ability to reconfigure components are expressed in an abstract manner. These requirements are then satisfied by platform-specific realizations

Developing a distributed electronic health-record store for India

The DIGHT project is addressing the problem of building a scalable and highly available information store for the Electronic Health Records (EHRs) of the over one billion citizens of India

Safe, Remote-Access Swarm Robotics Research on the Robotarium

This paper describes the development of the Robotarium -- a remotely accessible, multi-robot research facility. The impetus behind the Robotarium is that multi-robot testbeds constitute an integral and essential part of the multi-agent research cycle, yet they are expensive, complex, and time-consuming to develop, operate, and maintain. These resource constraints, in turn, limit access for large groups of researchers and students, which is what the Robotarium is remedying by providing users with remote access to a state-of-the-art multi-robot test facility. This paper details the design and operation of the Robotarium as well as connects these to the particular considerations one must take when making complex hardware remotely accessible. In particular, safety must be built in already at the design phase without overly constraining which coordinated control programs the users can upload and execute, which calls for minimally invasive safety routines with provable performance guarantees.Comment: 13 pages, 7 figures, 3 code samples, 72 reference

Modeling the Internet of Things: a simulation perspective

This paper deals with the problem of properly simulating the Internet of Things (IoT). Simulating an IoT allows evaluating strategies that can be employed to deploy smart services over different kinds of territories. However, the heterogeneity of scenarios seriously complicates this task. This imposes the use of sophisticated modeling and simulation techniques. We discuss novel approaches for the provision of scalable simulation scenarios, that enable the real-time execution of massively populated IoT environments. Attention is given to novel hybrid and multi-level simulation techniques that, when combined with agent-based, adaptive Parallel and Distributed Simulation (PADS) approaches, can provide means to perform highly detailed simulations on demand. To support this claim, we detail a use case concerned with the simulation of vehicular transportation systems.Comment: Proceedings of the IEEE 2017 International Conference on High Performance Computing and Simulation (HPCS 2017

Integrating public datasets using linked data: challenges and design principles

The world is moving from a state where there is paucity of data to one of surfeit. These data, and datasets, are normally in different datastores and of different formats. Connecting these datasets together will increase their value and help discover interesting relationships amongst them. This paper describes our experience of using Linked Data to inter-operate these different datasets, the challenges we faced, and the solutions we devised. The paper concludes with apposite design principles for using linked data to inter-operate disparate datasets