Here are some suggestions and resources for learning more advanced
GENESIS programming techniques.
Building large networks
This is covered in BoG Chapter 17, and uses examples from the genesis/Scripts/orient_tut simulation. genesis/Scripts/examples/fileconnect has an example of reading in a network connection matrix from a file with the new GENESIS 2.2 fileconnect command.
The default integration method (exponential Euler) is fine for simple models with just a few compartments. Models with many compartments should use an implicit method (e.g. Crank-Nicholson) with the Hines algorithm in order to avoid numerical instablilities. This is covered in BoG Chapter 20 and the GENESIS documentation for hsolve. Also see genesis/Scripts/examples/hines for examples.
The genesis/Scripts/examples directory has examples of other genesis capabilities such as hebbian and facilitating synapses, markovian channels, Ca diffusion in spines, and various types of device objects for input and output, or for applying stimuli to model neurons. For performing parameter searches to "tune" a model, see genesis/Scripts/param, and the documentation for The GENESIS Parameter Search Library.
A demonstration of the use of GENESIS for modeling biochemical reactions such as occur in biochemical signaling pathways can be found in genesis/Scripts/kinetikit. If you need to create your own new GENESIS objects and commands, see the documentation on Customizing GENESIS.
For a summary of all the objects that are available in GENESIS, see the Objects section in the hypertext documentation. To simply see a list of available objects, type "listobjects" from within GENESIS. To see a list of commands, type "listcommands".