INTERNET-BASED SOFTWARE FOR MODELING BIOLOGICAL SYSTEMS
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.

OVERVIEW OF ProcessDB DOCUMENTATION
To find out more about ProcessDB and the modeling of biological systems, the following information is available:  

Getting Started:  this page tells you how to install and quickly get started using the ProcessDB software.  

User Guide:  this is a document that describes in detail the 6-step process for constructing and evaluating a biological hypothesis or theory.  This document includes a number of examples from published models.  

Reference Manual:  You can go directly to detailed information about every screen and diagram page of the ProcessDB software from this reference manual.  

Computational Cell Biology Textbook:  This online textbook can be used by advanced undergraduate and graduate students and professionals in the biomedical sciences or in biomedical engineering who want or need to use modern computer modeling approaches to test theories against experimental data. The textbook is focused on practical application; it is a handbook, a guidebook, and a map for the process of formulating and testing biological models. The reader will learn a step-by-step method, applicable to a wide range of biological problems.