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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.

WestGrid Seminar Series

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.

WestGrid Seminar Series

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.

WestGrid Seminar Series

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.

WestGrid Seminar Series

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.

WestGrid Seminar Series

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.

WestGrid Seminar Series

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.

 

Coast to Coast Seminar Series

Abstract: 

In this talk, we will review some of the recent applied text mining work at Dalhousie. We will argue the need for a text representation that would be more linguistically informed than the standard vector model. We will present one such proposal, in which a co-occurrence model takes into account the distribution of words throughout the corpus. We will then show how this representation is successfully applied in the task of categorizing dream descriptions by their emotional valuation (joint work with J. De Koninck and A. Razavi, Ottawa). We will round up the talk with our experience with some of the other text mining techniques used in the analysis of the twitter traffic in the 2012 presidential elections in France and in the US (joint work with LIRMM, France).

About the Speaker: 

Stan Matwin is a Professor and Canada Research Chair at Dalhousie University, and a Distinguished Professor at the University of Ottawa (on leave). Fellow of ECCAI and CAIAC and an Ontario Champion of Innovation. Internationally recognized for his work in text mining and in applications of Machine Learning, member of Editorial Boards of the leading journals in Machine Learning and Data Mining. Stan Matwin is one of the founders of Distil Interactive Inc. and Devera Logic Inc., and has significant experience and interest in innovation and technology transfer.

Coast to Coast Seminar Series

Abstract:

This talk explores the larger implications of visual analytics-- "the science of analytical reasoning facilitated by interactive visual interfaces"-- for cognitive science and informatics. I will argue that the methods that will advance this new science go beyond those of natural science and engineering, and will require researchers to create a new translational cognitive science of analytic systems. We will begin by building field study methods that characterize human and computational cognitive capabilities as they are used for decision-making in a range of situations. Because findings from field methods do not generalize well, we must then investigate these proposed capabilities in the laboratory.

Finally, we must build mathematical and computational theories that predict the impact of changes in technology on cognitive processes in technology-rich environments. These methods will only suffice until processing capacity reduces the lag between an analyst's query and a graphical response to a certain level. When the response is generated at the same pace as the sequence of cognitive operations that the analyst performs, human and computational processes become "close coupled". At this point the distinction between processes originating from the mind of the analyst (i.e. a mental representation) versus the computer (i.e. a visualization) become impossible to determine, and the subsystems we will study will seamlessly incorporate natural and artificial processes.

About the Speaker:

I have built upon my early training in the experimental investigation of human cognitive processes to develop a program of translational research bridging cognitive science and the design of interactive visualization systems. My goal is to advance new theories and research methods for understanding how highly interactive visual information systems can support “close-coupling” of human and computational processes for improved performance in cognitive tasks such as situation analysis, decision-making, creativity, and collaboration in situations ranging from emergency management to aircraft safety, computer-aided design, security administration, and computer-supported learning.

Central to all of these projects is the emerging cognitive systems science that advances current research on cognitive style, expert cognition and skilled perceptuomotor performance to adapt information technology to individual capabilities. Together with field research and “pair analytics” translational methods, this core of laboratory research provides a knowledge-based approach to the design and customization of information systems and their integration in organizational processes.

Coast to Coast Seminar Series

The combined effects of habitat loss and proliferation of introduced species present serious conservation challenges. These aspects of global change have created a black hole for species in Canada and globally, pulling many toward extinction. Human activities have added climate change to this dangerous mix. Recent research improves capacity to predict species impacts of such effects. Species losses can erode the robust provision of economically and ecologically indispensable ecosystem services, like pollination. In the past 25 years, several wild pollinator species have nearly totally collapsed in North America.

Although habitat loss, introduced diseases, and pesticide use have not helped, we present new evidence that climate change alone could explain some bumblebee losses. Massive increases in weather extremes can precipitate species collapses, even among widespread, abundant insect pollinators. These effects, known from the paleoecological record, have not previously been linked to a modern extinction. Further losses of species and ecosystem service degradation are not inevitable. Informed by concerted scientific action and an involved public, elected leaders sometimes take landmark steps to conserve wilderness areas and strengthen legal frameworks protecting species at risk.

Coast to Coast Seminar Series

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