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This session provides attendees with a step-by-step tutorial on using WestGrid resources for the visualization of scientific data. The talk will discuss the visualization software that is available for use on WestGrid computational resources and how to use this software remotely from your desktop. In particular, the presentation will cover the use of the Graphics Processing Units (GPUs) on parallel.westgrid.ca for remote visualization of large data sets.

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Abstract

Modern society demands that people manage, communicate, and interact with digital information at an ever-increasing pace. Even though most people want to be informed, all this information is frequently experienced as stress. It is not the information itself that is the problem, but the manner in which we are bombarded with information in forms that are often hard to interpret. How then can we produce interactive visualizations of digital data in a manner that enhances people's cognitive abilities? Ideally, these visualizations would not only present information visually and aesthetically, but provide people with capabilities for manipulating and exploring this information.

A good visualization provokes interpretation, exploration and appreciation, inviting direct interaction that reveals the data. This sets the stage for my over-arching research goal - to design, develop, and evaluate interactive visualizations so that they support the everyday practices of how people view, represent, manage, and interact with information. To this end, I have followed four intertwined themes: process, presentation, representation, and interaction.

My research process convolves art, science, and design practices, and has become a topic of research in itself. Presentation is the act of displaying visuals, emphasizing and organizing areas of interest. Representation is development of accurate and revealing data-to-visual mappings. And interaction is the key to exploration and manipulation capabilities that can make information comprehension viable. In this talk, I will show how each theme is opening up to indicate exciting new directions and discuss how the currently shifting information climate is opening up new opportunities.


About the speaker:

Sheelagh Carpendale is a Professor in Computer Science at the University of Calgary where she holds a Canada Research Chair in Information Visualization and NSERC/AITF/SMART Technologies Industrial Research Chair in Interactive Technologies. She leads the Innovations in Visualization (InnoVis) Research Group and has initiated the new interdisciplinary graduate- level specialization, Computational Media Design.

Her research on information visualization, large interactive displays, and new media draws on her dual background in Computer Science (BSc. and Ph.D. Simon Fraser University) and Visual Arts (Sheridan College, School of Design and Emily Carr, College of Art). She has just been awarded a NSERC STEACIE Memorial Fellowship in recognition of her outstanding research.

She is an internationally renowned leader in both information visualization and multi-touch tabletop interaction and has recently served in such roles as Papers, Program, or Conference Chair for IEEE InfoVis, and ACM Tabletop and has received both the IEEE and ACM recognition of service awards.

Distributed Research Seminars

Andriy Kovalenko is an Adjunct Professor in the Department of Mechanical Engineering at the University of Alberta and a Senior Research Officer at the National Institute for Nanotechnology. His research focuses on (i) developing fundamental methodology of multiscale theory, modeling and simulation, capable of predicting the behaviour of complex nanomaterials and nanosystems, and (ii) applying this predictive methodology to provide understanding and rational design of realistic systems and processes of crucial importance in nanoscience and nanotechnology.

An essential part of this multiscale methodology is statistical-mechanical, integral equation theory of molecular liquids, in particular, the three-dimensional (3D) molecular theory of solvation, also known as the three-dimensional reference interaction site model with the Kovalenko-Hirata closure relation (3D-RISM-KH). The multiscale methods he developed include the self-consistent field coupling of quantum chemistry methods (ab initio CASSCF, Kohn-Sham DFT, and Orbital-Free Embedded DFT) with 3D-RISM-KH for nanochemistry, photochemistry, electrochemistry, and nanocatalysis in solution, at solid-liquid interfaces, and in nanoporous materials; 3D-RISM-KH based protein-ligand docking algorithms; milti-time-step molecular dynamics (MTS-MD) of biomolecules steered by solvation forces obtained from 3D-RISM-KH for function-related solvation, folding, misfolding, aggregation, interaction, and bioadsorption of proteins and other biomolecular and hybrid nanosystems in solution. In this talk, Dr. Kovalenko will discuss how WestGrid and Compute Canada - Calcul Canada resources support and advance those investigations.

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MATLAB is a general-purpose high-level programming package that is available for use on WestGrid. It is typically used for numerical work such as linear algebra, but, has many add-on toolboxes to extend its capabilities into discipline-specific areas. Although MATLAB is probably used most often on researchers' desktops as an interactive program through its desktop graphical user interface, that is not the primary way it is used in the batch-oriented WestGrid environment.

This talk will cover the various ways in which MATLAB can be run on WestGrid systems, as determined by the restrictions imposed by licensing considerations. In particular, the use of the MATLAB compiler to create standalone applications will be illustrated. The compiled applications can then be run in normal WestGrid batch jobs.

Note that the talk will not cover MATLAB programming. Instead, it is intended for researchers who would like to run their own MATLAB code on WestGrid, but, are unsure of how to get started with doing so. Most of the material for the talk is drawn from the MATLAB pages on the WestGrid web site at http://www.westgrid.ca/support/software/matlab.

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Interested in expanding HPC use within your research? Not sure where to begin? This introductory session will provide an overview of the WestGrid and Compute Canada resource structures, as well as walk through the basics of getting started with an account.

Any faculty members and graduate students interested in or curious about using HPC are invited to attend. WestGrid Support Personnel will be on-hand at each site to answer any specific introductory questions attendees may have.

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In this session, Falk Herwig, Associate Professor, Astronomy and Physics at the University of Victoria, will explain how he is using WestGrid / Compute Canada resources to perform complex 3D simulations to study astrophysical fluid dynamics.

This kind of research requires above average HPC cycles, which Herwig has accessed through WestGrid / Compute Canada's Resource Allocation process. He will provide an overview of his research, explain how he gained access to and used WestGrid machines to support that research, and highlight some of the key outcomes achieved as a result.

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Scientific research is rapidly becoming a global endeavour. Today's complex computational problems not only require a wide range of technologies to solve them, but they also require a wide range of expertise which often means distributed research teams, sometimes spread around the world. This session will provide a comprehensive overview of WestGrid's advanced collaboration facilities, which are located at 15 partner institutions across Western Canada and can be used to connect with colleagues across the province, country and overseas. WestGrid Collaboration Staff will showcase recent upgrades, discuss room capabilities, and demonstrate applications within a research environment.

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This introductory seminar will provide an overview of the most commonly used computational tools for studying biomolecules, mainly focusing on potential energy function and its evaluation, general molecular dynamic simulation algorithm, and current methods for free energy calculations implemented in molecular simulation package GROMACS. From the early use of computers to study various aspects of liquids and gases by modeling them as hard spheres, computer simulations now days are routinely used to study dynamics of complex molecules such as proteins, carbohydrates, nucleic acids, and lipid membranes.

Computer simulations have became a useful tool in understanding the dynamics and mechanism of function of these molecules with atomistic details. New sampling methods coupled with increased computational resources have made it possible to simulate the folding of small peptides and proteins. The underlying parameters or force-fields used in atomistic representation have matured to the point that free energies calculated using computer simulations methods are in quantitative agreements with experiments.

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By exploiting our visual abilities, traditional scientific visualization aims at offering engineers and scientists various ways to assist them at exploring complex phenomenon. What Virtual Reality (VR) technologies has to offer is to put an expert user at the center of the exploration process that utilise not only his visual abilities but also his multi-sensory senses such as touch and sound.

To improve the effectiveness of the traditional data exploration process, many researchers has focused on the development of more intuitive interaction techniques that exploits the sensory-motor capacity of humans to deal with complex environments. To achieve this goal two conditions need to be respected. First, exploitation of different modalities must not oppose one another, and each sensory channel must be rendered in a way that fits with human abilities.

During this talk, I will explore how VR can create a true multi-sensory interface by using high-resolution displays, haptics, and sound. We will explore the current state of the art and discuss our implementation for a virtual wind tunnel application and the exploration of medical data.

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This session will host Dr. Ryan D'Arcy, Professor with Simon Fraser University's School of Computing Science, for a presentation that explores the opportunities around embedding new computational tools into front-line clinical environments.

Functional brain imaging enables non-invasive windows into how, when, and where the brain is actively processing information. This technology advances not only create the ability to improve diagnosis and treatment in people immediately, but also generate incredibly rich and complex data. Data we are just now beginning to unlock the potential around in terms of real world applications in the clinical environment.

This talk will review some core functional imaging technologies (functional MRI, electro- and magneto- encephalography) and highlight applications in presurgical mapping for brain tumours/epilepsy, diagnostic evaluation in brain injury, and rehabilitative monitoring during neuroplastic recovery.

 

Distributed Research Seminars

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