Simulation modelling and visualisation: toolkits for building artificial worlds

Simulations users at all levels make heavy use of compute resources to drive computational simulations for greatly varying applications areas of research using different simulation paradigms. Simulations are implemented in many software forms, ranging from highly standardised and general models that run in proprietary software packages to ad hoc hand-crafted simulations codes for very specific applications. Visualisation of the workings or results of a simulation is another highly valuable capability for simulation developers and practitioners. There are many different software libraries and methods available for creating a visualisation layer for simulations, and it is often a difficult and time-consuming process to assemble a toolkit of these libraries and other resources that best suits a particular simulation model. We present here a break-down of the main simulation paradigms, and discuss differing toolkits and approaches that different researchers have taken to tackle coupled simulation and visualisation in each paradigm

Assessing the effectiveness of multi-touch interfaces for DP operation

Navigating a vessel using dynamic positioning (DP) systems close to offshore installations is a challenge. The operator's only possibility of manipulating the system is through its interface, which can be categorized as the physical appearance of the equipment and the visualization of the system. Are there possibilities of interaction between the operator and the system that can reduce strain and cognitive load during DP operations? Can parts of the system (e.g. displays) be physically brought closer to the user to enhance the feeling of control when operating the system? Can these changes make DP operations more efficient and safe? These questions inspired this research project, which investigates the use of multi-touch and hand gestures known from consumer products to directly manipulate the visualization of a vessel in the 3D scene of a DP system. Usability methodologies and evaluation techniques that are widely used in consumer market research were used to investigate how these interaction techniques, which are new to the maritime domain, could make interaction with the DP system more efficient and transparent both during standard and safety-critical operations. After investigating which gestures felt natural to use by running user tests with a paper prototype, the gestures were implemented into a Rolls-Royce DP system and tested in a static environment. The results showed that the test participants performed significantly faster using direct gesture manipulation compared to using traditional button/menu interaction. To support the results from these tests, further tests were carried out. The purpose is to investigate how gestures are performed in a moving environment, using a motion platform to simulate rough sea conditions. The key results and lessons learned from a collection of four user experiments, together with a discussion of the choice of evaluation techniques will be discussed in this paper

Simulation of Water Distribution Systems

In this paper a software package offering a means of simulating complex water distribution systems is described. It has been developed in the course of our investigations into the applicability of neural networks and fuzzy systems for the implementation of decision support systems in operational control of industrial processes with case-studies taken from the water industry. Examples of how the simulation package have been used in a design and testing of the algorithms for state estimation, confidence limit analysis and fault detection are presented. Arguments for using a suitable graphical visualization techniques in solving problems like meter placement or leakage diagnosis are also given and supported by a set of examples

Modelling and simulation framework for reactive transport of organic contaminants in bed-sediments using a pure java object - oriented paradigm

Numerical modelling and simulation of organic contaminant reactive transport in the environment is being increasingly relied upon for a wide range of tasks associated with risk-based decision-making, such as prediction of contaminant profiles, optimisation of remediation methods, and monitoring of changes resulting from an implemented remediation scheme. The lack of integration of multiple mechanistic models to a single modelling framework, however, has prevented the field of reactive transport modelling in bed-sediments from developing a cohesive understanding of contaminant fate and behaviour in the aquatic sediment environment. This paper will investigate the problems involved in the model integration process, discuss modelling and software development approaches, and present preliminary results from use of CORETRANS, a predictive modelling framework that simulates 1-dimensional organic contaminant reaction and transport in bed-sediments

Engineering simulations for cancer systems biology

Computer simulation can be used to inform in vivo and in vitro experimentation, enabling rapid, low-cost hypothesis generation and directing experimental design in order to test those hypotheses. In this way, in silico models become a scientific instrument for investigation, and so should be developed to high standards, be carefully calibrated and their findings presented in such that they may be reproduced. Here, we outline a framework that supports developing simulations as scientific instruments, and we select cancer systems biology as an exemplar domain, with a particular focus on cellular signalling models. We consider the challenges of lack of data, incomplete knowledge and modelling in the context of a rapidly changing knowledge base. Our framework comprises a process to clearly separate scientific and engineering concerns in model and simulation development, and an argumentation approach to documenting models for rigorous way of recording assumptions and knowledge gaps. We propose interactive, dynamic visualisation tools to enable the biological community to interact with cellular signalling models directly for experimental design. There is a mismatch in scale between these cellular models and tissue structures that are affected by tumours, and bridging this gap requires substantial computational resource. We present concurrent programming as a technology to link scales without losing important details through model simplification. We discuss the value of combining this technology, interactive visualisation, argumentation and model separation to support development of multi-scale models that represent biologically plausible cells arranged in biologically plausible structures that model cell behaviour, interactions and response to therapeutic interventions

ROOT - A C++ Framework for Petabyte Data Storage, Statistical Analysis and Visualization

ROOT is an object-oriented C++ framework conceived in the high-energy physics (HEP) community, designed for storing and analyzing petabytes of data in an efficient way. Any instance of a C++ class can be stored into a ROOT file in a machine-independent compressed binary format. In ROOT the TTree object container is optimized for statistical data analysis over very large data sets by using vertical data storage techniques. These containers can span a large number of files on local disks, the web, or a number of different shared file systems. In order to analyze this data, the user can chose out of a wide set of mathematical and statistical functions, including linear algebra classes, numerical algorithms such as integration and minimization, and various methods for performing regression analysis (fitting). In particular, ROOT offers packages for complex data modeling and fitting, as well as multivariate classification based on machine learning techniques. A central piece in these analysis tools are the histogram classes which provide binning of one- and multi-dimensional data. Results can be saved in high-quality graphical formats like Postscript and PDF or in bitmap formats like JPG or GIF. The result can also be stored into ROOT macros that allow a full recreation and rework of the graphics. Users typically create their analysis macros step by step, making use of the interactive C++ interpreter CINT, while running over small data samples. Once the development is finished, they can run these macros at full compiled speed over large data sets, using on-the-fly compilation, or by creating a stand-alone batch program. Finally, if processing farms are available, the user can reduce the execution time of intrinsically parallel tasks - e.g. data mining in HEP - by using PROOF, which will take care of optimally distributing the work over the available resources in a transparent way

Towards a Holistic CAD Platform for Nanotechnologies

Silicon-based CMOS technologies are predicted to reach their ultimate limits by the middle of the next decade. Research on nanotechnologies is actively conducted, in a world-wide effort to develop new technologies able to maintain the Moore's law. They promise revolutionizing the computing systems by integrating tremendous numbers of devices at low cost. These trends will have a profound impact on the architectures of computing systems and will require a new paradigm of CAD. The paper presents a work in progress on this direction. It is aimed at fitting requirements and constraints of nanotechnologies, in an effort to achieve efficient use of the huge computing power promised by them. To achieve this goal we are developing CAD tools able to exploit efficiently these huge computing capabilities promised by nanotechnologies in the domain of simulation of complex systems composed by huge numbers of relatively simple elements.Comment: Submitted on behalf of TIMA Editions (http://irevues.inist.fr/tima-editions

Computational Simulation and 3D Virtual Reality Engineering Tools for Dynamical Modeling and Imaging of Composite Nanomaterials

An adventure at engineering design and modeling is possible with a Virtual Reality Environment (VRE) that uses multiple computer-generated media to let a user experience situations that are temporally and spatially prohibiting. In this paper, an approach to developing some advanced architecture and modeling tools is presented to allow multiple frameworks work together while being shielded from the application program. This architecture is being developed in a framework of workbench interactive tools for next generation nanoparticle-reinforced damping/dynamic systems. Through the use of system, an engineer/programmer can respectively concentrate on tailoring an engineering design concept of novel system and the application software design while using existing databases/software outputs.Comment: Submitted on behalf of TIMA Editions (http://irevues.inist.fr/tima-editions