Summary of ProcessDB features and philosophy

Diagrams

ProcessDB modeling always starts with a diagram. This was a conscious choice based on decades of experience in modeling and experimental biology. Again and again we have found that a mechanistic diagram is the common ground between modeling teams and an experimental teams. ProcessDB diagrams are beautiful because we used state-of-the-art diagram layout tools that are simple to use. ProcessDB diagrams are active, not passive; every element of the diagram has its own context menu so that you can quickly find out what you want to know and do what you want to do.

Diagrams are also active in the sense that you construct your model directly on the diagram screen using a simple and efficient set of drawing tools.

The Database

The "DB" in ProcessDB stands for "database." But the ProcessDB database is no mere repository of experimental data. Instead, it brings the awesome power of a relational database to the every aspect of model building and testing. Within the ProcessDB database there are more than 30,000 lines of PL SQL code and all of them were written to make your modeling and hypothesis testing work faster and easier.

A Model is a Collection of Processes

Our bedrock organizational principle is that every model is a collection of Processes. This core idea allows you to compare models with a single click. You can extract subsystems from complex models and work on them independently. You can combine models with a single click. A searchable model tree structure is always immediately available to allow you to drill down quickly to the details of every element of your diagram.

Hypothesis Testing

We think of all models as hypotheses and ProcessDB is specifically designed to test those hypotheses against experimental data.

Biology Separate from Experiments

As much as possible, ProcessDB separates your biological theory or model from the experiments to be performed on that model. Some modeling philosophies assert that there is no such thing as a model separate from an experiment, but biologists rarely think this way. ProcessDB supports the testing of models, simultaneously, against as many different experimental protocols and data sets as you like.