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Collaborating Amidst the Molecules

Arthur Olson, Director, Molecular Graphics Laboratory, Professor, Molecular Biology, The Scripps Research Institute; Interaction Environments thrust area leader, NPACI

The 3-D structures of proteins and other biological molecules are helping to unlock the secrets of how living systems work. Protein structures hold significant promise for pharmaceutical and biotechnology companies in the search for new drugs with few side effects and the effort to understand human disease. Medical researchers also envision gaining new insights into the causes, effects, and treatment of diseases by understanding the structure and function of biological molecules, which is needed to unlock their disease-fighting potential. To allow researchers scattered across the nation to explore the complex structures of such molecules, a team of NPACI researchers is building tools for on-line collaboration.

To combine the expertise of researchers in all areas of molecular science, molecular biologist Arthur Olson is prototyping 3-D collaborative environments for molecular science. Based on general-purpose collaborative visualization systems developed at the University of Houston and SDSC, NPACI researchers are developing interactive, extensible environments that allow scientists and researchers to engage in complex data analysis and visualization, to share, view, and modify 3-D information, and to use virtual reality, "virtual whiteboards," sound, gestures, and other modes of communication in conducting joint research efforts.

The Collaborative Environments project, part of the Interaction Environments thrust area, is evaluating existing tools to combine the best into a multipurpose, extensible system that allows multiple users to share information and interact in a simulated 3-D world. A closely related project, the Molecular Science Prototype, is investigating how the environments meet the requirements of a particular field. (Another project is developing a similar prototype in collaboration with the Earth Systems Science thrust area.)

"The goal is to integrate standard computational and visualization capabilities into an environment shared by two or more groups in different locations," said Olson, leader of the thrust area. "My own work on the Molecular Science Prototype project will test collaborative environment concepts and technologies with applications from structural molecular biology."

User interacting with DNA in PaulingWorldFigure 1. PaulingWorld

Molecular Science and Interaction Environments partners are developing a prototype system to enable molecular biologists to collaborate over long distances. PaulingWorld, a project from the University of Houston, is one technology being explored for the prototype. Here, a PaulingWorld user interacts with a small strand of DNA.



As various collaborative environments come online, researchers will implement the molecular science application in these environments and test their relative performance for modeling tasks. "For example, we will explore the utility of Bowen Loftin's PaulingWorld as an immersive collaborative environment," Olson said.

PaulingWorld's collaborative features were demonstrated at SC97 in November 1997, when R. Bowen Loftin, director of the University of Houston's Virtual Environment Technology Laboratory, and SDSC's Allan Snavely jointly interacted with molecular models in a colorful but completely virtual 3-D workspace (Figure 1). Using stereo glasses and a six-degrees-of-freedom tracking device in Houston, Loftin was able to collaborate with Snavely in San Jose to share views of molecular structures as conference attendees viewed their interaction on color monitors. Snavely used a Fakespace Boom virtual reality viewer to view and wander around in the virtual environment.

"Over the past year, NPACI researchers have improved PaulingWorld's performance and explored mechanisms to exchange control of objects in a shared virtual environment," Olson said. "We also have increased the number of molecular structure data formats that can be read by PaulingWorld."

In the year since SC97, NPACI researchers have continued to work on developing an environment for analyzing and manipulating structural information on biological macromolecules, modeling molecules, and visualizing molecular surfaces. A component-based viewer being developed in the Olson lab is written in the Python language, and is made up of 40 or so classes that describe various geometries, objects such as cameras, and event handlers. The system's features include control of visualization through the use of simulated cameras, light sources, arbitrary clipping planes, and textures, and a virtual trackball to transform objects in the virtual world. A graphical user interface provides visual feedback and control of rendering parameters to define and alter virtual objects.

Collaborative AVS screenFigure 2: Module to Module

In Collaborative AVS, data moves from one module to another in the same AVS processing network or to a module in an AVS network on a different computer through a collaboration (or "share") module. Adding a collaboration server allows data to pass from one AVS system to multiple AVS networks on different computers.



Meanwhile, other researchers have been active in the Interaction Environments thrust area in ways that complement the molecular science developments. In particular, SDSC's Greg Johnson has developed a system called Collaborative AVS, which consists of custom add-on modules that augment the capabilities of the Application Visualization System (AVS) commercial product to support collaborative visualization.

"Extending the capabilities of a popular visualization system gives us the opportunity to readily explore the role of computer supported cooperative work in the science and research community," Johnson said. "Blending collaborative tools into visualization software already in use also makes it relatively easy for researchers to adopt collaborative work habits." AVS was chosen because of its widespread use, high level of functionality, and general extensibility. "The extensibility was key," he said. "By adding seven small software modules, we turned AVS from a single-user tool into a system that supports collaboration."

AVS is a data flow visualization system, in which data moves from module to module in a processing-flow structure. Modules are "wired" together into "networks", and these connections define how data will move and be operated on. Johnson extended this concept so that data may move from one module to another in the same AVS network or to a module in an AVS network on a different computer by means of a collaboration module. "The design allows users to access a central data set or multiple local copies, and for multiple users to interactively share any visualization parameters," Johnson said (Figure 2).

Collaborative AVS has been tested between SDSC, UC San Diego, The Scripps Research Institute in La Jolla, the Baylor College of Medicine in Houston, the University of Sydney's Visualization Laboratory, and the U.S. Naval Oceanographic Office in Stennis, Mississippi. These tests have demonstrated that complex data analysis and visualization tasks can be shared effectively among geographically distributed individuals using commonly available computer hardware and networking infrastructure.

"For our molecular prototype, we initially intend to use the AVS-based environment developed by Johnson, integrated with the Python tools," Olson said. "Of the ones we've seen, Collaborative AVS is the environment closest to being ready for integration with our molecular applications."


In addition to PaulingWorld and Collaborative AVS, NPACI researchers also intend to investigate the MICE system and several other collaborative environments for their potential. Other molecular science applications are being considered, including UC San Diego and SDSC biochemist Lynn Ten Eyck's Java3D-based Prototype Molecular Viewer and the DOT program for docking macromolecules to other molecules.

"We're going to try several different systems and interaction paradigms," Olson said. "The most critical function of a prototype is to see what works and what doesn't."--MG END