I am a computer scientist working on a general problem in multi-agent (using the word agent loosely) simulation, and I wanted to see if modeling some processes that are similar to cell signaling and such is a good target. Due to the nature of what we are trying to contribute, it is not necessary that we literally capture the exact interactions that bioinformatics have revealed, but rather that we can model processes similar in nature to what would occur in the real world.
Unfortunately, I know virtually nothing about biology, so I don't even know where to start. Is there a typology or classification system for biological reactions and processes? What sorts of events occur in intercellular/molecular processes, and what sorts of conditions have to be upheld for them to occur? I know this is incredibly vague (because I don't know enough to be more specific), so any pointers to introductory material would be appreciated as well.