Collaborative discovery through biological language modeling interface

Madhavi Ganapathiraju

Vijayalaxmi Manoharan

Raj Reddy

Judith Klein-Seetharaman

pp. 300-321

in: Yang Cai, Julio Abascal (eds), Ambient intelligence in everyday life, Berlin, Springer, 2006

Abstract

Scientific progress is exponentially increasing, and a typical example is the progress in the area of computational biology. Here, problems pertaining to biology and biochemistry are being solved by way of analogy through the application of computational theories from physics, mathematics, statistical mechanics, material science and computer science. More recently, theories from language processing have been applied to the mapping of protein sequences to their structure, dynamics and function under the Biological Language Modeling project. Scientists from diverse computational and linguistics backgrounds collaborate with experimental biologists and have made significant scientific contributions. The essential component of this collaborative discovery is the web server of the biological language modeling toolkit that enables the computational and non-computational scientists to interface and collaborate with each other. The web server acts as the computational laboratory to which researchers from a variety of scientific disciplines and geographical locations come to characterize specific attributes pertaining to their protein or groups of proteins of interest using the available tools. They then combine the results with their domain expertise to arrive at conclusions. The web server is also useful for education of students entering into the research field in computational biology in general. In this paper, we describe this web server and the results that were arrived at through local and global collaboration and education.