On a sunny August afternoon undergraduates are perusing the tables arranged around the East Campus, learning about clubs and groups to join, while still others are enjoying the warm day reading under the shade of trees. At the same time, 25 Electronic Visualization Laboratory graduate and undergraduate students have gathered in the lab’s Cyber-Commons on the second floor of UIC&rsquo;s Engineering Research Facility to discuss such hard-core geek topics as tele-immersion, autostereoscopic 3-D imaging and large-scale computer display technologies. 
The Cyber-Commons is a 1,000 square-foot, fluorescent- lit conference space within the lab’s warren of cinder- block offices and hallways. Students sit at two long grey tables, focused almost entirely on their laptops. Nine of them busily tweak PowerPoint slides for a presentation to peers on their latest research. Each of their computers also shares a portion of a giant 16-foot-long electronic computer display - made up of eight-tiled flat panel screens - at the front of the room. 
Their computers wirelessly communicate with the wall via a system known as SAGE or Scalable Adaptive Graphics Environment, which was designed at EVL. The software currently runs display walls at more than 70 major institutions around the globe, including
NASA, Argonne National Laboratory, Beijing University, the Russian Academy of Sciences and King Abdullah University of Science and Technology in Saudi Arabia.

Future World

Background: Rule-based modeling (RBM) is a powerful and increasingly popular approach to modeling cell signaling networks. However, novel visual tools are needed in order to make RBM accessible to a broad range of users, to make specification of models less error prone, and to improve workflows. 
Results: We introduce RuleBender, a novel visualization system for the integrated visualization, modeling and simulation of rule-based intracellular biochemistry. We present the user requirements, visual paradigms, algorithms and design decisions behind RuleBender, with emphasis on visual global/local model exploration and integrated execution of simulations. The support of RBM creation, debugging, and interactive visualization expedites the RBM learning process and reduces model construction time; while built-in model simulation and results with multiple linked views streamline the execution and analysis of newly created models and generated networks. 
Conclusion: RuleBender has been adopted as both an educational and a research tool and is available as a free open source tool at http://www.rulebender.org. A development cycle that includes close interaction with expert users allows RuleBender to better serve the needs of the systems biology community

Contact Map with molecule compartment hierarchy (extracellular, cytoplasmic, nucleus etc).

RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry

There is an incoming flood of information to the Astronomy community with the development of new telescopes. Over the next decade the amount of information available to the typical astronomer will grow by two orders of magnitude to the Peta scale, thanks to programs such as Pan-STARRS (Panoramic Survey Telescope and Rapid Response System) and LSST (Large Synoptic Survey Telescope). Moreover, astronomy analyses often require pooling information from multiple data sources, such as a number of measurements from different telescopes at different wavelengths of light. 
However, we lack an easy-to-use and scalable way to analyze anything beyond the most basic data on the thousands to billions of individual events and objects studied. Visually cross-registering astronomy data across multiple sources comes with its own challenges; for example, images may be acquired at different resolutions and may only partially overlap with each other. The
analysis process is further hampered by limited screen space and limited bandwidth (upwards of one minute may be required by large Sloan queries). For example, Fig. 2 shows a typical Google Sky visualization of about 60 annotations (of different types) on objects in a small part of the sky. Even at such low numbers, the glyphs used to represent each piece of data quickly fill the screen space and become difficult to sift through. 
To address the challenges of querying multiple sources, limited screen-space and limited bandwidth, we propose to use a pixel-based overlay approach, computed and implemented through a WebGL client-server architecture; our prototype was developed in close collaboration with astronomy experts. An interactive demo of the prototype is available.

831 points from the Sloan Digital Sky Survey database are visualized efficiently using pixel-based overlays.

Pixel-based Overlays for Navigating a Galaxy of Observations

OmegaDesk is a device that allows for seamless interaction between 2D and 3D content. In order to develop this hybrid device, a new form of Operating System is needed to manage and display heterogeneous content. In this paper we address the hardware and software requirements for such a system, as well as challenges. A set of heterogeneous applications has been successfully developed on OmegaDesk. They allowed us to develop a set of guidelines to drive future investigations into 2D / 3D hybridized viewing and interaction.

A user using OmegaDesk to simulate catching a ball as part of physical therapy

The OmegaDesk: Towards A Hybrid 2D &amp; 3D Work Desk

Human Augmentics (HA) refers to technologies for expanding the capabilities, and characteristics of humans. One can think of Human Augmentics as the driving force in the non-biological evolution of humans. HA devices will provide technology to compensate for human biological limitations either natural or acquired. The strengths of HA lie in its applicability to all humans. Its interoperability enables the formation of ecosystems whereby augmented humans can draw from other realms such as &ldquo;the Cloud&rdquo; and other augmented humans for strength. The exponential growth in new technologies portends such a system but must be designed for interaction through the use of open-standards and open-APIs for system development. We discuss the conditions needed for HA to flourish with an emphasis on devices that provide nonbiological rehabilitation.

Human Augmentics: Augmenting Human Evolution

The ENDURANCE autonomous underwater vehicle was developed and deployed to explore and map a unique environment: the waters of Lake Bonney in Taylor Valley, one of the McMurdo Dry Valleys of Antarctica. This permanently ice-covered lake presented several unique challenges and opportunities for exploration and mapping with an AUV. ENDURANCE was successfully deployed in 2008 and 2009, completing the first full synoptic 3-D chemical profile and high-resolution 3-D geometric mapping of such a body of water. Following the 2008 campaign, several upgrades were made to the vehicle to improve its exploration capabilities. The most significant of these was replacement of two battery packs. The improved energy capacity of these batteries coupled with analysis of in-situ transit speed efficiency tests resulted in an almost tripled range of the vehicle. This fact, combined with a longer fiber-optic data tether, enabled vastly more ambitious missions during the 2009 campaign. In addition, operational changes were made in 2009, including a super-ballasted mode to enable the vehicle to operate within the super-saline lower lake layers and investigate previously inaccessible areas of the Taylor Glacier face. 

ENDURANCE successfully navigated in the presence of ice cover and large density gradients, including precise approach and negotiation of narrow passageways and demonstrated autonomous melt hole location, position lock and auto recovery on a routine, daily basis. It performed general automated mapping and profiling surveys, as well as detailed studies of localized phenomena, operating in an extreme, remote, unknown environment. Post-processing of the data gathered on the two campaigns has made available a never-before-seen level of detail greatly enhancing the understanding of the lake biogeochemistry. The ENDURANCE project has demonstrated new underwater mapping capabilities to enhance the understanding of extreme, unique environments. Many of the characteristics and capabilities of ENDURANCE now successfully demonstrated in complex under-ice settings beneath West Lake Bonney are the types of behaviors that will be needed for sub-ice autonomous probes to Europa, Enceladus, and other outer planet watery moons.

Summary view of all 2009 ENDURANCE mission trajectories

SUB-ICE EXPLORATION OF AN ANTARCTIC LAKE: RESULTS FROM THE ENDURANCE PROJECT

In recent years, we have seen a steady increase in the resolution and the amount of collected data that needs to be analyzed or presented. Often, the complexity of the problems that drive this increase requires that multidisciplinary teams work collaboratively towards a solution. Traditional paper-based war rooms have been shown to double the productivity of radically collocated teams when addressing such problems. Large, high-resolution displays have the potential to transform paper-based war rooms into more dynamic digital war rooms by enabling virtual interaction and reconfigurable space. Although of great potential, these affordances alone will not result in increased productivity since our current knowledge of virtual interaction and display space organization is based on contemporary desktop systems with vastly different requirements, necessitating new techniques tailored for wall displays. 

This dissertation first presents a unique interaction framework that allows multi-user, multi-modal control of wall displays along with scalable, distributed user interface widgets for building novel interfaces for collaborative large, high-resolution environments. The framework enabled subsequent investigations of the user interaction and display space organization issues through numerous real-world usage scenarios. The investigations were aimed at shedding light on two specific questions. First, what is a set of interaction requirements and modalities appropriate for collaborative work across a broad range of wall display use cases? Second, what display space organization techniques and behaviors do users employ in collaboratively managing a large amount of information on wall displays? Based on observations from a number of use cases, a sample set of tools was iteratively developed for addressing the issues of input control and display space organization. Lastly, the developed tools were evaluated in a simulated collaborative analysis task for the purposes of understanding how the developed techniques serve to support traditional war rooms.

Subjects interacting with multi-user interface; physical navigation proved more natural and required minimal window manipulations

Collaborative Interaction And Display Space Organization In Large High-Resolution Environments

Social network analysis is the study of patterns of interaction between social entities. The field is attracting increasing attention from diverse disciplines including sociology, epidemiology, and behavioral ecology. An important sociological phenomenon that draws the attention of analysts is the emergence of communities, which tend to form, evolve, and dissolve gradually over a period of time. Understanding this evolution is crucial to sociologists and domain scientists, and often leads to a better appreciation of the social system under study. Therefore, it is imperative that social network visualization tools support this task. While graph-based representations are well suited for investigating structural properties of networks at a single point in time, they appear to be significantly less useful when used to analyze gradual structural changes over a period of time. In this paper, we present an interactive visualization methodology for dynamic social networks. Our technique focuses on revealing the community structure implied by the evolving interaction patterns between individuals. We apply our visualization to analyze the community structure in the US House of Representatives. We also report on a user study conducted with the participation of behavioral ecologists working with social network datasets that depict interactions between wild animals. Findings from the user study confirm that the visualization was helpful in providing answers to sociological questions as well as eliciting new observations on the social organization of the population under study.

Timeline of of US House of Representatives roll call votes

Visualizing the Evolution of Community Structures in Dynamic Social Networks

In this dissertation I propose the &ldquo;immersive empathic design&rdquo; approach for interdisciplinary collaborations. It is hard to design a useful system and it is even harder to design a system for people who are working in a different knowledge domain. The high domain knowledge barrier can make it difficult for a person who is outside of a given domain to imagine the experience of a user within that domain. This can lead to systems that are designed, implemented, and deployed without sufficient knowledge of the domain they will be used in, leading to a low willingness of users to adopt the new system. Globally distributed collaboration is becoming more common in the modern world, and modern science discovery requires interdisciplinary collaboration. This imposes even more spatial and temporal constraints in designing an interactive system. The goal is to move beyond collaborative technology showcases in the laboratory to workplace deployments that solve real-world problems. 

The proposed &ldquo;immersive empathic design&rdquo; approach attempts to reach across the discipline boundary. In the exploratory case study in geological core drilling, computer scientists were embedded in the core drilling workplace setting. On-site hands-on &ldquo;experiential learning&rdquo; and off-site reflection analysis inspired innovations in the workplace setting while still maintaining their domain-specific perspective. This approach helped to overcome the initial high domain knowledge barrier. It also established trust with domain users and encouraged system adoption. 

The proposed approach helps computer scientists to overcome the initial domain barrier efficiently in interdisciplinary collaborations. The domain knowledge obtained in the immersive experience forms a sustainable common ground between the collaborating parties. It affords authentic user experience and more context-sensitive inquires in later design and development activities. The process encourages computer scientists to design an innovative system that will be used by domain users to solve real-world problems. 

Modern science discovery requires interdisciplinary collaboration. The proposed method suggests system developers to step out of the laboratory environment and be empathic with their new system&rsquo;s potential users through immersive hands-on experience, so the system being designed will better fit the users&rsquo; needs and expectations. The trust established through this process should encourage the users&rsquo; adoption of the new system. It provides a general guideline to &ldquo;co-evolution on a human scale&rdquo; in interdisciplinary collaborations. The method and lessons learned will be beneficial to future human computer interface practitioners when the potential users of the system are within domains sharing similar qualities such as scale, a high knowledge domain barrier, and geographically distributed collaborations.

CoreWall user interface screenshot

Immersive Empathic Design for Interdisciplinary Collaborations

Virtual reality systems are an excellent environment for stereo panorama displays. The acquisition and display methods described here combine high-resolution photography with surround vision and full stereo view in an immersive environment. This combination provides photographic stereo-panoramas for a variety of VR displays, including the StarCAVE, NexCAVE, and CORNEA. The zero parallax point used in conventional panorama photography is also the center of horizontal and vertical rotation when creating photographs for stereo panoramas. The two photographically created images are displayed on a cylinder or a sphere. The radius from the viewer to the image is set at approximately 20 feet, or at the object of major interest. A full stereo view is presented in all directions. The interocular distance, as seen from the viewer&rsquo;s perspective, displaces the two spherical images horizontally. This presents correct stereo separation in whatever direction the viewer is looking, even up and down. Objects at infinity will move with the viewer, contributing to an immersive experience. Stereo panoramas created with this acquisition and display technique can be applied without modification to a large array of VR devices having different screen arrangements and different VR libraries. 

<a href="http://dx.doi.org/10.1117/12.872521">doi:10.1117/12.872521</a>

Calit2 UCSD&rsquo;s StarCAVE - Inside the Wisconsin State Capitol - panoramic photography by R. Ainsworth displayed in full stereo

Acquisition of stereo panoramas for display in VR environments

This paper describes case studies and lessons learned from cross-cultural collaborations. A computer scientist was embedded within domain settings to design and develop systems for geological core drilling and medical hand-off. While these domains seem diverge and have different purposes and workflows, one common theme emerged from reflection analysis. They all heavily depends on &ldquo;observable artifacts&rdquo; in early if not all iterations of design and development cycles. Utilizing the common and different signature characteristics would help identifying and taking the proper strategies for different phases of future scientific collaboration projects.

Hundreds of hand-drawn notes lying across the office. (Inset) Scientist switched to use the CoreWall system to assist initial core description

Cross-Cultural Scientific Collaboration Case Studies

The Academy of Motion Picture Arts and Sciences (AMPAS) report &ldquo;The Digital Dilemma&rdquo; describes the issues caused by the rapid increase of storage requirements for long-term preservation and access of high quality digital media content. As one of the research communities focusing on very high quality digital content, CineGrid addresses these issues by building a global-scale distributed storage platform suitable for handling high quality digital media, which we call CineGrid Exchange (CX). Today, the CX connects seven universities and research laboratories in five countries, managing 400TB of storage, of which 250TB are dedicated to CineGrid. All of these sites are interconnected through a 10 Gbps dedicated optical network. The CX distributed repository holds digital motion pictures at HD, 2K and 4K resolutions, digital still images and digital audio in various formats. The goals of the CX are: (1) providing a 10 Gbps interconnected distributed platform for the CineGrid community to study digital content related issues, e.g., digital archiving, the movie production process, and network transfer / streaming protocols; (2) building a tool with which people can securely store, easily share and transfer very high definition digital content worldwide for exhibition and real-time collaboration; (3) automating digital policies through middleware and metadata management. In this publication, we introduce the architecture of the CX, resources managed by the CX and the implementation of the first series of CX management policies using the iRODS programmable middleware. We evaluate the first phase of CX platform implementation. We show that the CX has the potential to be a reliable and scalable digital management system. 

Keywords: CineGrid Exhchange, digital archive, 4k digital media repository, distributed storage, iRODS 

Highlights: 10 Gbps interconnected distributed platform for the CineGrid community. A tool for securely store, easily share and transfer very high definition digital content. Automate digital transfer and archiving policies through middleware.

Publications - 2011

Future World

RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry

Pixel-based Overlays for Navigating a Galaxy of Observations

The OmegaDesk: Towards A Hybrid 2D & 3D Work Desk

Human Augmentics: Augmenting Human Evolution

SUB-ICE EXPLORATION OF AN ANTARCTIC LAKE: RESULTS FROM THE ENDURANCE PROJECT

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