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Introduction

IBI's product offering, ProcessDB, helps molecular cell biologists, biochemists and physiologists 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 simulation and testing against experimental data or they can be simulated using our integrated Simulator.

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 simulate models without leaving the ProcessDB environment. We have implemented an extremely fast Simulator based on the famous CVODE ordinary differential equation solver, which benchmarks have shown averages sixteen times faster than the same problem simulated in the Berkeley Madonna environment. Simulator 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 simulator 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 accessible 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.

Features List

Summary of ProcessDB features and philosophy

Glossary of ProcessDB terminology

To see a detailed list of all ProcessDB features, view the Features List Page.

Logging In To ProcessDB

To log in to ProcessDB, you must first have a user name and password. If you don't have an assigned user name, click on the Contact Us link to request one. ProcessDB can be found by selecting the ProcessDB link. Enter your user name and password and click the Launch button.

Getting Started with a Sample Model

Once you have a username and password, you will be able to see all models that have been tagged as "public" in the ProcessDB database. Here is a step-by-step guide to running one of those public models in ProcessDB: Step-By-Step You can use this model to verify that your installation of ProcessDB is running correctly or you can use it to learn some of the basics of ProcessDB workflow.

ProcessDB User Guide

An important role of computational modeling at all levels from molecular cell biology to human 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. If you are NEW TO ProcessDB, start here.

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

ProcessDB Reference Manual

ProcessDB Reference Manual
This is the place to look for detailed information on all ProcessDB tools and features. The ProcessDB Reference Manual is organized alphabetically by the name of the tool or feature as displayed in ProcessDB itself. Currently this is the least developed portion of our documentation, but it's on our list.