Date of Award

Spring 2008

Project Type


Program or Major


Degree Name

Doctor of Philosophy

First Advisor

Thomas M Lane


In order to accelerate the development of knowledge about protein associations, further improvements to acquisition, sharing, and analysis of Analytical Ultracentrifugation (AU) data must be made. XML data formats have been defined to allow complete exchange of the information associated with an AU experiment. Extensible formats to record solution identity, instrument setup parameters, acquired data, and analysis of that data have been developed. A normalized relational database to allow storage and searching of this data has also been created. A computer program called PANDaS (Protein Association Network Data Server) was built to interact with any software conforming to the data exchange standard. Conforming software will be able to access centrifuge data with the complete context required for analysis. It is also possible to import existing data files to the database and convert them to the exchange format using the import tool described in this dissertation. Aggregation of multiple analysis results through PANDaS allows for machine-assisted interpretation of results from heterogeneous analysis techniques and multiple experiments. This common data exchange format and attendant software are necessary underpinnings that enable the diverse developers of AU analysis software to collaborate more effectively. Such collaboration facilitates the construction of a system of interacting software tools that will improve our understanding of molecular associations as the effectors of interesting biology.