Features List Page

A Detailed Listing Of ProcessDB Features

Construct diagrams of your mechanistic biochemical, molecular cell biological, and physiological theories using a beautiful and intuitive graphical editor

Automatic translation of diagrams to quantitative models based on standard biophysical principles (This is the Run Initial Simulation tool.)

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

Ground these molecules to the corresponding entries in international databases such as ChEBI and UniProt

Private free text notes can be attached to molecules, processes and models

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 models with a single click; ProcessDB highlights those states and processes unique to each model.

Combine models with a single click; ProcessDB automatically resolves any overlap.

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

Analyze all kinds of biological experiments including:

• agonist addition
• inhibitor addition
• bolus injections (e.g. glucose tolerance test)
• medium changes
• infusions
• perfusions
• radiotracers (bolus, infusion, primed infusion)
• stable isotope tracers
• photobleaching (FRAP, iFRAP, FLIP)
• photoactivation
• using measured data as forcing functions to open loops and simplify analysis (can use forcing functions for tracer data or chemical system ("tracee") data or both)
• any of these can be superimposed on both steady state and non-steady state systems
• experimentally initiated changes in conditions can be implemented at any time using a very general "events" tool

Each experiment can have many measurements and multiple data sets

Any experimental data set can be used as a forcing function to drive the model at its boundary or to decouple the model at points of high complexity

Simulate any model with any number of relevant experiments

ProcessDB is one of the only tools available that was specifically designed to support the analysis of non-steady state tracer kinetic models.

Experimental protocols automatically imposed on models

Using standard biophysical principles, ProcessDB can automatically translate your models and their linked experiments to mathematics, ready to be simulated

To speed the transition from your model diagram to your first simulation, use the Run Initial Simulation tool.

Leverage a complete set of tools for solution (CVODE), comparison of solutions and data, gradient parameter optimization (ODRPACK95), and global parameter optimization (Particle Swarm).

Optimize over many experiments, each with many data sets, simultaneously

Reports detailed parameter statistics including fractional standard deviations (FSDs) and 95% confidence intervals

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

Flexible graphing for model output and comparison to data

• User-specified graph titles and axis labels
• Unlimited user-defined graphs of any model variable
• Expand any graph to full screen
• Automatic pairing of graphs for experimental data and associated model solutions
• Flexible control of Y-axis range for both linear and semi-log graphs
• Optional reference graphs for your current best parameter set
• User-control of solution and data point colors
• Display all graphs or a selected subset of graphs
• Import graph definitions from other models
• Visual parameter sensitivity tool
• Load saved parameter sets into reference solution for comparison
• Temporarily hide any plot in a graph by clicking its legend
• Copy any graph to the clipboard for pasting into reports
• Automatically plot precursors for any plotted state
• Apply user-defined tags to subsets of graphs so they can be displayed as a related group

Automatically builds a personal and 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 chosen molecule or molecular complex

Show all models in your database involving a chosen process

Show all models in your database involving a chosen physiological Place

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

Display all molecules with roles in a given model

Diagram colors can be easily changed

Rename or delete a model

Specify an experiment based on a given model

Automatic detection of mismatched experiments and models

From a model diagram, select a State and display a list of all models that include that molecule in that place

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, reference manual, and modeling textbook

More than 100 sample models in ProcessDB's Public Models database. Public models may be copied to your own database for study, practice or re-use.

Experimental data can easily be imported from Excel files (that have no formulas) or entered manually

Any data set can be used as a forcing function to implement open-loop analysis or to define boundary conditions.

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

Simulate models with the fast integrated Simulator based on CVODE and a custom interpreter that has proven faster than other solvers/simulators.