Call for Papers

Tools for Visualization and Interaction

Pacific Symposium on Biocomputing
(http://psb.stanford.edu)
Sheraton Waikiki, Honolulu, Hawaii
January 5-9, 2000

Session Co-chairs:

Eileen Kraemer, The University of Georgia
Thomas Ferrin, University of California, San Francisco

Data continues to flood in from large-scale sequencing projects as well as from such methods as X-ray crystallography, NMR spectroscopy, electron microscopy and scanning probe microscopy. The vast volume of sequence, structural, and functional data, the wide variety of analyses and annotations to be performed, and the variety of organisms and projects represented in this deluge of information combine to present the bioinformatics community with unprecedented challenges.

This session deals with one particular challenge of enormous importance to the molecular biology and structural biology communities: tools and techniques to assist scientists in evaluating, absorbing, navigating, and correlating this sea of information, through visualization and user interaction. We are seeking novel contributions from groups working in a wide range of computational biology and bioinformatics areas, including:

• Interactive Molecular Visualization
  With novel techniques for functional molecular analysis such as fast surface generation, property mapping, information filtering, and volume rendering, a new age of molecular visualization and a new role for the supporting hardware architectures is emerging. Recent hardware development trends indicate the emergence of two distinct strategies with separate but related tasks. On the high-end, increased throughput and functionality is the goal, allowing for larger molecular systems or longer molecular dynamics simulations. At the low-end, the main focus is to compare, communicate, educate, and review results obtained by others. Information resources such as the World-Wide Web provide a fruitful environment for chemical and biological information sharing. Example relevant topics include:
  • Representations of Structure
  • Supramolecular Modeling
  • Comparative Structure Analysis
  • Molecular Properties
  • Surface Geometry
  • Volumetric Information
  • Analysis of Molecular Dynamics
  • Multi-Media
  • 3-D on the Web
  • Rendering Toolkits
  • Molecular Primitives

• Interactive Visualization of Sequence Data
  Graphical displays of sequence maps, alignments, and genetic relationships, and graphical descriptions of metabolic pathways aid the viewer in acquiring additional domain knowledge. Such visualizations can assist the viewer in developing intuition about the relationships that exist in the system under study, in detecting patterns in the data displayed, and in spotting anomalies in those patterns. Example relevant topics include:
  • Tools and techniques for representing DNA, RNA, and protein sequences
  • Tools and techniques for the graphical depiction of metabolic pathways
  • Tools and techniques to support gene-finding and annotation

• Interactive Visualization of Databases
  Interactive graphical displays serve as much needed navigational aids to accessing large databases and in correlating information across interrelated databases, and especially in describing how this large volume of data interrelates in the sequence-structure-function triad. Example relevant topics include:
  • Tools and techniques for the display, retrieval, navigation, and correlation of data residing in biological databases.

• Interactive Steering
  Visualization and interactive steering of computations can serve as an aid to understanding the behavior and tuning the parameters of computationally intensive programs. Example relevant topics include:
  • Tools and techniques for depicting and controlling the behavior of computationally intensive applications in an on-line interactive fashion.

• Standardization Efforts
  The construction of "standard" visualization components, widget libraries, and component toolkits can serve to promote the interoperability of analysis software, and to reduce the duplication of effort across projects. Example relevant topics include:
  • Discussions of proposed, in progress, and de facto standards, toolkit and library development efforts, and new techniques and technologies.
  • Discussion of WWW chemical published standards such as the Chemical Markup Language (CML), chemical MIME, and the Chemical Information Exchange.

During the conference, we plan to have both low- and high-end workstations available for live demonstrations during talks. In addition, the demo room will be equipped with systems to load software for interactive discussion during the poster sessions and open free time.

The ultimate goal of this session is to provide a forum for presentation of recent results and discussion among tool developers, researchers, and practitioners in visualization, user interaction, computational biology, and bioinformatics.