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IBI's product offering, ProcessDB, helps molecular cell biologists manage and test their increasingly complex mechanistic hypotheses. ProcessDB does this with a bio-savvy graphical user interface that helps users formulate, visualize, compare, modify, manage and test their own mechanistic theories of cellular function. All models in ProcessDB can be automatically combined with user-specified experimental protocols. The models can be exported to the Berkeley Madonna solver for testing against experimental data or they can be solved using our new integrated solver.
ProcessDB version 4.0, released in 2012, is a major upgrade from version 3. Among the most significant changes is that it is now possible to solve models without leaving the ProcessDB environment. We have recently implemented an extremely fast version of the famous CVODE ordinary differential equation solver, which benchmarks have shown averages sixteen times faster than the same problem solved in the Berkeley Madonna environment. Solver output is displayed in a flexible graphing interface that allows any model variable to be plotted and compared to experimental data. Modelers will be happy to learn that we have also implemented the new and already popular "particle swarm" algorithm for searching parameter space during least squares parameter optimization. Particle swarm searching was designed to find global minima in least squares space. It is resistant to being trapped in a local minimum and thus finds better solutions to complex multiparameter optimization problems. We will continue to support the Berkeley Madonna software, but we think you will find that an integrated solver and optimizer greatly speeds your work.
ProcessDB allows investigators to know with precision what their theories predict, and speeds discovery of mechanisms that account for all of the available data. ProcessDB, which is accessable from any Internet-connected computer, offers a highly secure and professionally maintained tool that supports mechanistic knowledge management for research laboratories working on complex biological or biomedical problems.
ProcessDB User Guide
An important role of computational modeling in cell physiology is quantitative hypothesis testing. This role can be seen as having 6 steps which are supported by ProcessDB. The following pages document each of the steps and show how ProcessDB can be used to assist your work.
Overview Familiarize Yourself With ProcessDB
Step 1 Start With A Diagram of Your Hypothesis
Step 2 Quantify Your Hypothesis
Step 3 Record Your Experimental Protocols
Step 4 Collect Your Experimental Data
Step 5 Run Your Protocols on the Model
Step 6 Test Your Hypothesis Against Your Data