NetBuilder is a tool for modeling genetic regulatory networks (GRNs). A GRN can be seen as a signalling network: a network in which the components send, receive, and respond to signals. A gene responds to the binding of transcription factors (the input signals) by modulating its transcription rate (the output signal). Cell surface receptors respond to agonists by activating intracellular pathways. Thus, a signal can be many things: molecules, rates, interactions. In NetBuilder, the transformation of input into output signals is done by the network nodes, and the signals are transferred between these nodes through links, mostly without further transformation. The calculations that underlie the transformations are based on highly simplified and abstracted descriptions of biophysical and biochemical processes, such as ligand binding and enzyme activation (see the theory page).
To install NetBuilder, follow the instructions on the Installation page.
Run NetBuilder from the Windows Start menu. NetBuilder appears on the screen. A new empty document is opened automatically.
In this tutorial, you will find general information about NetBuilder, and instructions on how to build a small multi-cellular example network. Whenever you are required to add to or do something with your existing diagram, the text colour changes from normal to red. It is recommended to read the whole text, not just the red sentences, since only some of the available features are used in the example, and many more are mentioned in the normal text.