VALIS: A Multi-language System for Rapid Prototyping in Computational Biology
Author: Salvatore "Toto" Paxia
Advisor: Bud Mishra


Bioinformatics is a challenging area for computer science, since the underlying computational formalisms span database systems, numerical methods, geometric modeling and visualization, imaging and image analysis, combinatorial algorithms, data analysis and mining, statistical approaches, and reasoning under uncertainty.

This thesis describes the Valis environment for rapid application prototyping in bioinformatics. The core components of the Valis system are the underlying database structure and the algorithmic development platform.

This thesis presents a novel set of data structures that has marked advantages when dealing with unstructured and unbounded data that are common in scientific fields and bioinformatics.

Bioinformatics problems rarely have a one-language, one-platform solution. The Valis environment allows seamless integration between scripts written in different programming languages and includes tools to rapidly prototype graphical user interfaces.

To date the speed of computation of most whole genome analysis tools have stood in the way of developing fast interactive programs that may be used as exploratory tools. This thesis presents the basic algorithms and widgets that permit rapid prototyping of whole genomic scale real-time applications within Valis.