- Design patterns,
- Galactose metabolism,
- Object oriented programming,
- Saccharomyces cerevisiae,
- Systems biology,
- Systems theory,
- Transcription networks
Being in the post-genomic era, there is a need for new methodologies from an interdisciplinary perspective, which can complement current genomics research. Bioinformatics and systems biology are rapidly growing research areas that are meeting this need. Operating with the assumption that there is design with a purpose, creationists provide a unique perspective for discovering order in the complexity of genes, regulatory networks, and biochemical reactions.
Since the genome acts as an information storage system, it seems reasonable to apply design concepts, originating from computer and network programming, to make sense of genomic information. One such concept is that of design patterns, which has been formalized by programmers and analysts working with object-oriented programming (OOP). Several patterns are introduced and related to biochemical systems in the cell.
A more detailed analysis of the observer pattern is made in the context of galactose metabolism in Saccharomyces cerevisiae. Since design patterns embody good OOP practice and do not specify a specific implementation, it is possible to explore a variety of implementations that can achieve regulation of galactose metabolism. This methodology can complement current research approaches by clarifying what is meant by system homology at the biochemical level.
Available at: http://works.bepress.com/steven_gollmer/18/