Generating data in the field of life science can be a complex task. Putting aside any actual science, dealing with the technological plumbing necessary to communicate with databases, convert files between the different formats used by analytical tools and store results in any sensible fashion can be time consuming enough. Workflow based middleware and the semantic web are making things better, and can by dealing with the issues of finding data, marshalling services and generating results, and by explicitly supporting a scientific process are turning ad-hoc scripting into a more controlled form of in-silico experimentation. UTOPIA is the final part of this experimental process: an attempt to make visualisation and interactive analysis of protein sequence and structure data no harder than it needs to be. Two principles have driven the design:

Visualisation tools that are fast and friendly.

User friendly visualisation tools are hard to come by. They need to be optimized for performance (computer power rarely outstrips a user's expectations), and should be so intuitive to use that you hardly know they are there.

A model that can capture the properties of protein sequence and structure to mediate between data and visualisation.

Life Science data is horribly complicated. There are very few handy axioms or laws that can definitively, without question, relate Thing A to Thing B with 100% certainty. Everyone has their own way of capturing, naming and interpreting data that is meaningful to them. But to avoid building fast and friendly visualisation tools for every possible variation of a protein sequence, need some kind of common model to map between data and representation. Not a common model for the entirety of biology, but a common model that can be used for visualising life science data.