Quick Start: CS329e Elements of Biological Data Models

This is a UML class diagram, it is a logical data model of gene sequences

The diagram means,

• I want to make a database with a collection of gene sequences
• I want my database to contain tables that correctly represent (model) that genes are comprised of at least 1 exon and any number of introns

By focusing on the logic of the problem and capturing it in drawings like these, one can consider the properties of the problem being solved without getting distracted by details like, do I use a : or ;, or -where do the parenthesis go- . Of course this is easier, faster and likely to be a better result than if you simply started by writing computer code.

The course is not just about how diagrams like these are defined. Through an application example you will see how, when addressing a new informatics problem in a laboratory, how a person may organize the process, and by documenting explanations of the problem at hand, one may go from explanation to diagram.

Diagrams, such as this one above can be drawn using UML tools, such as Rational Rose. Then literally at the click of a mouse button the tool will generate a bunch of SQL code that will set up a database just as you intended it, per the logic of the diagram. In practice you may never see the SQL code. I show it below, just to make clear that this method of developing applications really is about be able to take simple parts of a problem and getting them done simply; leaving the messy stuff for the computers to deal with on their own.

The National Cancer Institute really is demanding that cancer laboratories incorporate this design and implementation methodology into software development. DoD (department of defense) demanded this of their contractors in the 1990s. Many major companies, including IBM use these methods. You are probably wondering,; all companies should be doing this. There is no good answer why many companies do not. Eventually they will.