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
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
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
Solve 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 automatically translates your models and their linked experiments to mathematics and exports to a solver
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
Many models can be open at once, each in a separate tab
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 specified molecule
Show all models in your database involving a specified process
Show all models in your database involving a specified state
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
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 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 your Excel files 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