Adding Ultra-Structure to Systems Biology

We’ve heard about data deluges for years, but we don’t usually hear much about interesting approaches to solving the problem. Today’s biologists expect data issues to grow, especially as scientists work harder to make comparisons between various data sets. Still, most solutions seem to revolve around faster computers with more memory. Nonetheless, Christopher Maier and his colleagues put an existing solution to work in systems biology—as described in Ultra-Structure database design methodology for managing systems biology data and analyses, which appeared in BMC Bioinformatics. The existing solution is called ultra-structure, which is a way to represent and work with complex rules that change.

The ultra-structure approach provides a range of benefits to biologists. For one thing, the file format can change, and ultra-structure can handle that without the need for new computer code. The kind of data—say, from a new device—can also change without the need for rewriting code. As Maier and his colleagues write:

End users themselves can change the system’s capabilities without programmer intervention, simply by altering database contents; no computer code or schemas need be modiﬁed.

Nonetheless, going to ultra-structure is not necessarily an easy switch. As Maier and his colleagues note: