Wednesday, May 25, 2011

Steps toward wet-lab integration

Some plans ahead include integrating wet-lab data. The diagram will be generated using semantics in order to make the integration more structured. Currently, users can draw "experiment" connections and "data" nodes. The RDF files in the TinkerCell home folder /Lab store the ontology for each. The idea is that python plugins will be used to fill in details about the experiment and the data. The long term goal is to make diagrams like these part of exchange and maybe lab automation. TinkerCell's ability to explicitly identify cells, plasmids, fluorescent proteins, and other relevant components can serve as the link between predicted results from models and experimental results.

1 comment:

mgaldzic said...

I think you have pretty good idea with this experiment extension. This is a natural organizing scheme for scientific work. Reflecting this organization in a CAD tool will help deal with the need to reconcile laboratory experimental data and computational simulation of the system. Both are experiments and they both attempt to describe the system being designed using a model. The model of the system is the theory both work to refine. Therefore having a computational representation which helps point at the model from the data can help organize the mess of information about experiments in terms of the model. Very interesting and useful conceptualization.