Features List Page

A Details Listing Of ProcessDB Features

Construct diagrams of your mechanistic cell biological theories using a beautiful and intuitive graphical editor

Diagram colors can be easily changed

Concentrate on the biology while your diagram is kept visually appealing by ProcessDB's advanced layout tools

Keep track of even complex diagrams using ProcessDB's advanced diagram navigation tools

Share models or keep them private; allow them to be viewed and/or modified even by remote collaborators

Define Molecules, molecular Complexes and physiological Places using your lab's own terminology

Add processes to your model (e.g. chemical reactions, transport, binding) with one simple but powerful tool

Extract, examine, save and analyze subsystems of complex models

Compare or combine models with a single click; automatically resolve any overlap

Enter your experiments and the data you collect via a simple interface including Excel® import

Analyze all kinds of cell biological experiments including:

• agonist or inhibitor addition
• medium changes
• infusions
• perfusions
• radiotracers (bolus, infusion, primed infusion)
• stable isotope tracers (accounting for perturbation of steady state
• photobleaching (FRAP, iFRAP, FLIP)
• photoactivation
• any of these can be superimposed on both steady state and non-steady state systems

Each experiment can have many measurements and multiple data sets

Solve any model with any number of relevant experiments

Using standard biophysical principles, ProcessDB automatically translates your models and their linked experiments to mathematics and exports to a solver

Leverage a complete set of tools for solution, comparison of solutions and data, and parameter optimization in our supported solver (Berkeley Madonna©) or in the SBML-compatible solver of your choice.

Many models can be open at once, each in a separate tab

Automatically builds a personal tabbed searchable database of molecules, molecular complexes, processes and models as you work

Everything in your database is instantly available for re-use

Search your database by name or by unique ProcessDB IDs

Show all models in your database involving a specified molecule

Keeps track of molecular components in a complex even if you rename it

Display all molecules with roles in a given model

Rename or delete a model

Single-click comparison of models showing features unique to each and features present in both - saves modelers valuable time

Specify an experiment based on a given model

Automatic detection of mismatched experiments and models

Prompts user for rate laws when they cannot be determined from the diagram alone

Models can be duplicated in two ways - one that keeps the two models linked so that changes to common processes are always synchronized, and another that separates the two models so they can evolve independently.

Online user guide and modeling textbook

Experimental data can easily be imported from your Excel files or entered manually

Professionally maintained and backed-up on our secure web server directly connected to the Internet backbone

All default rate laws can be displayed and modified if desired