ProcessDB¶
ProcessDB is a tool for systems biologists who want to state a mechanistic hypothesis precisely and then find out whether it can account for their data.
You draw the mechanism as a diagram: molecules in compartments, and the processes that convert, transport, or regulate them. ProcessDB turns that diagram into a system of differential equations, runs it through a fast numerical solver, and plots the result next to the measurements from your bench experiments. When the two disagree, you have learned something. When they agree, you have a quantitative model you can interrogate.
Nothing in ProcessDB requires you to write code or to write the equations yourself. ProcessDB relies on you for the biology and the data you want to model, and handles the rest — drawing the diagram, deriving and keeping track of the mathematics, running the simulations, plotting the results — so the work stays on the biology.
The shape of the work¶
ProcessDB keeps four things apart, and that separation is what lets you compare alternatives cleanly:
| What it holds | Why it is separate | |
|---|---|---|
| Model | The mechanism: states, processes, and who regulates what | One drawing of the biology, shared by everything below |
| Model Realization | The kinetics: a rate law per process, an initial value per state | Lets you test different kinetics for the same mechanism |
| Experiment | What was done at the bench, and what was measured | Lets one experiment be reused against many models |
| Model of Experiment | A realization simulated under a set of experiments | This is what actually runs and what you fit |
A typical session moves down that table: draw or open a model, create a Model Realization and give the processes rate laws, describe your experiments, create a Model of Experiment that joins the two, then simulate and fit.
Where to start¶
- New to ProcessDB? Read Getting started, then work through Your first model — it takes a small model from a blank diagram to a fitted simulation.
- Coming from an older version of ProcessDB? The vocabulary is unchanged. How ProcessDB is organized is the quickest refresher, The ProcessDB window shows where things moved to, and Arranging the panels covers the panels that now surround the diagram. What's new lists what changed in each release.
- Looking for one specific thing? Use the search box at the top of any page, or start from the Glossary.
Your work is not saved until you commit it
ProcessDB keeps your edits locally until you choose File → Commit. That is deliberate — it lets you experiment freely — but it does mean the Save button in the toolbar matters. See Saving your work.