Toward a Nanobioinformatics Infrastructure for Nanotechnology-based Prostate Cancer Therapeutic Response Tracking

Nanobioinformatics is an emerging field of study born out of a necessity of nanotechnology researchers in the life sciences whose work is dependent on timely access to an emerging wealth of data. It brings together the three very diverse fields of nanotechnology, molecular biology and biomedical informatics that until now have had little overlap and where major cultural gaps exist. It is critical that nanobioinformatics be embraced as an extension of biomedical informatics and not be orphaned prematurely. Because of the combinatorial nature of nanoparticle composition (core + surface modifier + payload) and the enthusiasm for this area in general, nanotechnology in biomedicine will see a rapid exponential increase in the data produced, thus making it critical to develop robust infrastructure to support data standardization and storage, modeling and simulation, symbolic reasoning and information retrieval. The goal of the multi-institutional Center for Cancer Nanotechnology Excellence focused on therapy response (CCNE-TR) at Stanford University is to develop a combined ex vivo nanosensor and in vivo molecular imaging approach toward highly sensitive tracking of prostate cancer response to therapy. As a part of this effort, we are developing an informatics platform to serve the diverse needs of this group. In particular, our data portal is designed to support electronic communication and data sharing within the center as well as data and knowledge sharing with the greater scientific community. We are developing this platform to be caBIG compatible integrating a number of different caBIG components that are each the best of breed solution for their particular area. While our approach is designed to meet the needs of our specific center, the methods and infrastructure developed should prove useful for other similar informatics efforts as well.