Curtis Lisle

Networked virtual environments

The problem of resource bottlenecks is encountered in almost any distributed virtual environment or networked game. Whenever the demand for resources – such as network bandwidth, the graphics pipeline, or processing power – exceeds their availability, the resulting competition for the resources leads to a degradation of the system’s performance. In a typical client-server setup, for example, where the virtual world is managed by a server and replicated by connected clients which visualize the scene, the server must repeatedly transmit update messages to the clients. The computational power needed to select the messages to transmit to each client, or the network bandwidth limitations often allow only a subset of the update messages to be transmitted to the clients; this leads to a performance degradation and an accumulation of errors, e.g. a visual error based on the positional displacement of the moving objects. This thesis presents a scheduling algorithm, developed to manage the objects competing for system resources, that is able to achieve a graceful degradation of the system’s performance, while retaining an output sensitive behavior and being immune to starvation. This algorithm, called Priority Round-Robin (PRR) scheduling, enforces priorities based on a freely definable error metric, trying to minimize the overall error. The output sensitivity is a crucial requirement for the construction of scalable systems, and the freely definable error metric makes it suitable to be employed whenever objects compete for system resources, in client-server and peer-to-peer architectures as well. Therefore Priority Round-Robin scheduling is a substantial contribution to the development of distributed virtual environments and networked online-games.

Best Practices for Data Sharing in Phylogenetic Research

As phylogenetic data becomes increasingly available, along with associated data on species’ genomes, traits, and geographic distributions, the need to ensure data availability and reuse become more and more acute. In this paper, we provide ten “simple rules” that we view as best practices for data sharing in phylogenetic research. These rules will help lead towards a future phylogenetics where data can easily be archived, shared, reused, and repurposed across a wide variety of projects.

Arbor: comparative analysis workflows for the tree of life.

We describe our efforts to develop a software package, Arbor, that will enable scientific research in all aspects of comparative biology. This software will enable developmental biologists, geneticists, ecologists, geographers, paleobiologists, educators, and students to analyze diverse types of comparative data at multiple phylogenetic and spatiotemporal scales using an intuitive visual interface. Arbor’s user-defined workflows will be exported and shared so that entire analyses can be quickly replicated with new or updated data. Arbor will also be designed to easily and seamlessly expand to include novel analytical tools as they are developed. Here we describe the core components of Arbor, as well as provide details of one proposed test case to illustrate the software’s key functionality.

Research in virtual environments and simulation at the institute for simulation and training of the university of central florida

The Institute for Simulation and Training (IST) was created in 1984 by the University of Central Florida to provide research support to the U.S. Department of Defense in the area of simulation-based training. In 1989, ISTs Visual Systems Laboratory (VSL) was inaugurated. Focal areas of research at VSL include distributed realtime physical simulation, interoperability among networked simulators, the application of virtual environments to education, training, and design, and head-mounted display technology. Section 1 describes the history of IST and VSL, and VSLs early projects. Section 2 surveys current research projects in three main areas: dynamic environments, interoperability, and virtual environments. Section 3 describes service and educational activities, and Section 4 provides insight into future research plans.

PhyloPen: Phylogenetic Tree Browsing Using a Pen and Touch Interface.

Phylogenetic trees are used by researchers across multiple fields of study to display historical relationships between organisms or genes. Trees are used to examine the speciation process in evolutionary biology, to classify families of viruses in epidemiology, to demonstrate co-speciation in host and pathogen studies, and to explore genetic changes occurring during the disease process in cancer, among other applications. Due to their complexity and the amount of data they present in visual form, phylogenetic trees have generally been difficult to render for publication and challenging to directly interact with in digital form. To address these limitations, we developed PhyloPen, an experimental novel multi-touch and pen application that renders a phylogenetic tree and allows users to interactively navigate within the tree, examining nodes, branches, and auxiliary information, and annotate the tree for note-taking and collaboration. We present a discussion of the interactions implemented in PhyloPen and the results of a formative study that examines how the application was received after use by practicing biologists -- faculty members and graduate students in the discipline. These results are to be later used for a fully supported implementation of the software where the community will be welcomed to participate in its development.

The design and applications of a recursive molecular modeling framework

In this paper, we present a recursive molecular model that is suitable for multi-resolution analysis in a variety of application areas. Our approach allows ease of use by computer scientists and biologists by proposing a software interface for molecular analysis that hides programming details. We demonstrate that our design is flexible enough for use in desktop analytical applications, in large-scale parallel simulations, and as a server for remote molecular analysis across wide-area networks.

Recursive, object-oriented structures for molecular modeling

In this paper, we present a molecular modeling approach based on recursive object-oriented class instances. Our approach allows ease of use by the scientist and includes a heuristic for evaluating molecular interaction and rendering at multiple levels of detail. Our implementation in C++ employs abstractions to encapsulate the implementation and details of the computations. Visualization is accomplished with OpenGL or the Visualization Toolkit (VTK), an application-independent scientific visualization library.

Virtual Reality: Its Potential Impact on Embedded Training

Virtual Reality (VR) denotes a multi-sensory realtime simulation that immerses the user in 3d graphical space, allows freedom of movement within the space, and supports complex interactions including the modification of most features of the space itself.