T-Profiler Development Issues

From Informatics

These are notes taken by John Watkinson during the integration of T-Profiler in to geWorkbench by Bussemaker's lab.

• T-Profiler consists of an analysis step (where the actual T tests are run) and a visualization step (where the results are viewed in tabular format). There was some initial difficulty establishing how this should be done in geWorkbench. This confusion was probably due to the ad hoc nature of the existing components in the application. Some are separated in to an analysis step and a visualization step, while others are combined in to one component. Eventually, the two-component model was established.
• The component that takes the intial parameters and runs the T tests was not integrated in to the Analysis Panel, as it probably should have been. This was due to the added difficulty of integrating a component int to the Analysis Panel. The analysis itself must be a single method that takes an Object as a parameter and returns an Object. A parameter panel is required, and it must properly serialize and deserialize in order to work with the Analysis Panel. This requires some complicated serialization tricks.
• The developers had a difficult time with Bison. They needed a lot of example code and guidance to manipulate even simple types, such as DSMicroarraySet. In particular, instantiation of Bison types was confusing, as was ascertaining which arrays and markers were in actively selected sets.
• The developers were dismayed with the confusing interfaces of the Marker Panel and Array/Phenotype Panel. The need for checkboxes and for case/control assignments led to confusion.
• The developers required annotations data and found this to be lacking. Some chip types did not properly load annotations data, and the GO terms were not available in a form that they could use. Additional, custom code was required to make GO terms work with their components.
• The developers had trouble understanding the publish/subscribe model. It seems that the model is not easily grasped by those who are not at an expert level in Java. Eventually, the publish/subscribe code was provided for them for their components.