BioLingua is an interactive, web-based programming environment that enables biologists to analyze biological systems by combining knowledge and data through direct end-user programming. BioLingua embeds a mature symbolic programming language in a frame-based knowledge environment, integrating genomic and pathway knowledge about a class of similar organisms. The BioLingua language provides interfaces to numerous state-of-the-art bioinformatic tools, making these available as an integrated package through the novel use of web-based programmability and an integrated Wiki-based community code and data store. The pilot instantiation of BioLingua, which has been developed in collaboration with several cyanobacteriologists, integrates knowledge about a subset of cyanobacteria with the Gene Ontology, KEGG, and BioCyc knowledge bases. We introduce the BioLingua concept, architecture, and language, and give several examples of its use in complex analyses. Extensive documentation is available online at http://nostoc.stanford.edu/Docs/index.html. In the past forty years, molecular biology has come to permeate every biological discipline. A similar revolution is in progress with regard to the massive amount of information becoming available through genomic sequencing and microarray experiments. While biologists were relatively quick to adopt the tools of molecular biology, the same is not true of the tools of bioinformatics, resulting in a growing distance between biologists and the data from which new insights must be drawn. Although some bioinformatic tools, such as Blast, have gained popularity among biologists, combining tools and data often requires hours of painstaking database search and knowledge manipulation. In many cases biologists resort to programmers to conduct computational analyses on their behalf. Thus, the world of computational biology is accessible  BioLingua: A Biologist's Computational Workbench -2 to biologists primarily through programmers. Whereas in the laboratory biologists can adjust their work dynamically, turning partial results over in their hands and modifying their tools to address problems and new subgoals, this flexibility is significantly reduced when programmers mediate between biologists and biological data. BioLingua seeks to give biologists hands-on capability in computational biology by enabling them to work directly with large data sets in a familiar language, while implementation details are hidden so that programmers are needed less often. The BioLingua programming environment hides the many complexities required to implement complex knowledge-based computations by providing a wide range of databases and analytical tools, integrated with one another, and accessible through a common, simple programming language. In the BioLingua world, biologists become programmers in much the same way as molecular biologists have become enzymologists: few have isolated or characterized enzymes themselves, but they are adept at combining enzymes in novel ways. Similarly, users of BioLingua, regardless of their background, may combine the tools of computational biology, forming them in ways that are
In terms of end-user programming, Massar et al. REF designed BioLingua, an interactive web-based programming environment to give biologists more control and flexibility in carrying out analyses with genomics, metabolic, and experimental data and higher-level representations.
BioLingua: a programmable knowledge environment for biologists
Bioinformatics
Computer Science Medicine