John L. Moreland

The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications

BackgroundThe large amount of data that are currently produced in the biological sciences can no longer be explored and visualized efficiently with traditional, specialized software. Instead, new capabilities are needed that offer flexibility, rapid application development and deployment as standalone applications or available through the Web.ResultsWe describe a new software toolkit – the Molecular Biology Toolkit (MBT; http://mbt.sdsc.edu) – that enables fast development of applications for protein analysis and visualization. The toolkit is written in Java, thus offering platform-independence and Internet delivery capabilities. Several applications of the toolkit are introduced to illustrate the functionality that can be achieved.ConclusionsThe MBT provides a well-organized assortment of core classes that provide a uniform data model for the description of biological structures and automate most common tasks associated with the development of applications in the molecular sciences (data loading, derivation of typical structural information, visualization of sequence and standard structural entities).

The Virtual Reality Behavior System (VRBS): a behavior language protocol for VRML

YRML [I] provides constructs for controlling the shape, appearance, position. size, and orientation of 3D objects. It does not include constructs to change these features in response to user interaction or automated actions. Such behaviors are clearly needed. To provide the flexibility and power needed for complex behaviors. a scripting language is necessary. Several possible languages have been proposed by the VRML community. A common denominator, however. is the need for an interprocess communications protocol that links an executing behavior script to a VRML browser. This paper discusses the prototype Virtual Reality Behavior System (VRBS) behavior communications protocol and system structure in development at SDSC.