Solid Model Experiments in Force Feedback for Molecular Docking

系统发育分析是一种强大的方法，具有广泛的解释力，因为它能够预测进化过程。然而，达到分类的过程涉及到如何协调多个树解，如何可视化系统发育树拓扑结构上的数据变化，如何表示基于不同数据集的解决方案之间的冲突，最后，以可发布的形式呈现这些结果的方法。科学可视化领域专注于可视化显示技术的发展，以揭示(1)数据集内的模式和结构，以及(2)数据集之间的模式和结构。系统发育树或进化图是类型(1)可视化的一个例子，因为它揭示了单个数据集中各分类群之间的关系。相反，类型(2)可视化侧重于同时呈现多个数据集或同一数据集的多个表示。在本提案中，我们概述了一系列高度可视化的数据驱动方法，用于数据检查，同时多树可视化，对分析假设的评估（例如，根分类单元的选择），分层数据的表示技术以及通过万维网（WWW）将系统发育树链接到生成结果的数据的方法。这些技术很少或根本没有在系统学中使用，事实上，它们代表了计算机科学中最近的研究。我们相信，系统发育分析的丰富性和复杂性需要新的方法来可视化分析过程。MacClade Maddison92是一个用于在单个树上可视化数据变化的Macintosh程序，它增强了我们对单个树拓扑中字符变化如何发生的理解。我们将扩展这种类型的分析，包括更丰富的视觉隐喻，以查看系统发育途径的数据矩阵。我们提出的研究是探索性的，根据设计，我们将调查可能无法证明对所有数据集都有效的方法。然而，这些方法对其他形式的分层数据的适用性使得一些甚至大多数可视化工具将在比较生物学的所有领域帮助研究人员的可能性很高。在解决可视化问题时，必须重新审视当前树木可视化技术中隐含的假设——二维、静态介质、欧几里得绘图空间、单独的图形、数据和解释以及单个插图中的均匀细节水平。我们设想，随着电子期刊在所有科学领域变得越来越突出，将存在对在线观看优化的显示技术的需求。这项研究应该为在这种新媒体中显示分类和系统分析的方法提供重要的见解。尽管这项研究的大量具体交付成果将是用于创建可视化的“后端”程序。以及用于存储树和数据的数据库架构，我们将通过WWW浏览器提供对整套技术的访问（到1996年年中，所有主要工作站和个人电脑平台的浏览器都应包含查看这些结果的功能）。用户将能够在浏览器中输入和存储树和NEXUS（系统发育数据的标准文件格式）数据矩阵，以供后续分析。

Phylogenetic analysis is a powerful methodology with broad explanatory power derived from its ability to make predictions about evolutionary process. However, the process of arriving at a classification involves decisions about how to reconcile multiple tree solutions, how to visualize data changes on phylogenetic tree topologies, how to represent conflicts among solutions based on different data sets and finally, methods for presenting these results in publishable form. The field of scientific visualization specializes in the development of visual display techniques to reveal (1) patterns and structure within a data set, and (2) patterns and structure between data sets. The phylogenetic tree, or cladogram, is an example of type (1) visualization because it reveals the relationships among taxa within a single data set. Type (2) visualizations instead focus upon the simultaneous presentation of multiple data sets or multiple representations of the same data set. Within this proposal we outline a series of highly visual, data driven methods for data inspection, simultaneous multiple tree visualization, evaluation of assumptions about the analysis (e.g., choice of root taxon), presentation techniques for hierarchical data and methods for linking, through the World Wide Web (WWW), phylogenetic trees to the data that generated the result(s). Few or none of these techniques are in current use in systematics, in fact, they represent very recent research within computer science. We -believe that the richness and complexity of phylogenetic analysis invites new methods for visualizing the analytical process. MacClade Maddison92 , a Macintosh program for visualizing data change on a single tree, enhanced our understanding of the how character changes occurred on single tree topologies. We will expand that type of analysis to include far richer visual metaphors for viewing the da ta matrix to phylogeny pathway. The research we are proposing is exploratory and by design we will investigate methods that may not prove fruitful for all data sets. However, the applicability of these methods for other forms of hierarchical data makes the likelihood high that some or even most of the visualization tools will assist researchers in all areas of comparative biology. In addressing the visualization problem, the assumptions--a 2D, static medium, Euclidean drawing space, separate figures, data and explanations and homogeneous levels of detail in single illustrations--implicit in current tree visualization techniques must be re-examined. We envision that as electronic journals become ever more prominent in all-areas of science the need will exist for display techniques optimized to on-line viewing. This research should provide significant insight into means for displaying classifications and systematic analyses within this new medium. Although a large number of the specific deliverables for this research will be "backend" programs for creating the visualizations .and database architectures for storing trees and data, we will provide access to the entire suite of technologies through WWW browsers (by mid-1996, browsers for all major workstation and PC platforms should incorporate the capability for viewing these results). Users will be able to input and store trees and NEXUS (a standard file format for phylogenetic data) data matrices for subsequent analysis, all within their browser.