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STEP 5: Run Your Protocols on the Model

ProcessDB allows you to link any experimental protocol recorded (Step 3) to any quantitative model you have created (Step 2). Furthermore, multiple experiments can be linked to any quantitative model (called a Model Realization, or MR, in ProcessDB, as explained in detail, in Step 2).† In ProcessDB, the linking of experimental protocols to a Model Realization, and then the quantifying of this, so that your hypothesis can be quantitatively tested, is called a Model of Experiments.

Often, Model of Experiments is abbreviated to MOE in ProcessDB.

In the Model of Experiments, the user can also create functions that are unique to each experiment. The final stage of creating an MOE is the generating of all the equations that constitute your quantitative model. This includes the equations created in Step 2, or the MR step AND equations that represent your experimental protocols that you have recorded and linked to a given MR. At this step also, lists are created where you can indicate which specific states and processes from your model are being traced.

As in Step 2, ProcessDB does everything it can to automate conversion of your MR and experimental protocol to an accurate computational model. This is an area of active development at IBI and if you encounter something you think we should automate, donít hesitate to contact us by creating a suggestion entry in our online bug/suggestion reporting tool at http://www.integrativebioinformatics.com/processdb.html

Coming Soon: Step by step instructions for creating a Model of Experiments.