Senior Project - GeneJACKET

The object of this project was to create a graphical platform for constructing, annotating, and testing models of biological regulatory pathways. After biologists perform experiments and collect data, an essential next step involves drawing a regulatory pathway that summarizes the biologist's hypotheses about the results observed. Scientists still do this with pen and paper because the prior volume of experimental data has been small.

With the availability of completely sequenced genomes, large-scale experiments are being performed; thus, the data interpretation problem became equally larger and more difficult. To handle this increase in modeling complexity, a tool was developed that can help a biologist to filter large-scale experimental data and visually develop regulatory pathway models. In addition, a well-formulated computational tool makes these models more than just static representations of the scientist's hypotheses.

Because regulatory pathway models frequently suggest new experiments, the computational tool allows the models to be annotated with additional experimental data that support or refute the model. Finally, because these models implicitly predict biological behavior, this tool can be used to perform and display simulations of biological behavior given a model and some input experimental conditions. The system was implemented in Java.