BioVelo, a Language and Web Interface to Query Biological Databases

The BioVelo query language is as flexible as SQL (Structured Query Language for relational databases), but based on a simpler syntax and semantics. Online documentation for the BioVelo language is available at BioVelo language description. An online web interface is available based on BioVelo -- it can be used without knowing its syntax. Here is a snapshot of this web interface (Safari browser).

For more information and do online queries: BioCyc Advanced Query Page.

Display of Gene Regulatory Networks

The following image is an overview of the E. coli transcriptional regulatory network from version 11.5 of Pathway Tools. A subset of the regulatory relations is shown with green arcs. The innermost ellipse is composed of genes that have no regulators. The outermost ellipse has genes that do not regulate any gene. The inner ellipse has genes that regulate and are regulated. On the outer ellipse, genes that are regulated by the same set of genes are combined together and displayed in the form of a triangle. There are over 1800 genes in this overview -- most of them are not transciptional regulators and are therefore on the outermost ellipse.

For more information, see the Pathway Tools software.