What are Agents?

The agents are the "players" in the model, representing the functional components of a system. Conceptually, an agent is simply a named entity that has sites; these sites can have states designated by labels and they can also be bound to sites on other agents. Given this extremely flexible definition, agents can be used to represent virtually any functional component of a cell from a single atom of calcium up to the largest macromolecular assembly such as a ribosome or even a whole cell itself.

Example of an agent (RTK) with sites (ligand and tyrosine) and state (unphospho)

Cellucidate provides the user with the ability to either define the agent using the intuitive graphical interface provided or through the textual kappa language. It also offers tools for annotating agents and for linking them to other biological resources online, in the case where the agent represents a known biological entity (such as a protein or gene). Learn more about the Agent Page. In addition, Cellucidate displays a contact map of the interactions between agents. 

Agent Creation:

1. Add a new agent to a cBook via the Book Toolbar.
2. Name the agent in the title field. The agent name has to be alphanumeric and can only be edited in the title field. Agent names must be unique within a cBook. Thus, two agents cannot have the same name.
3. Add a short textual description of the agent. This is optional.
4. Add sites and states to the agent via the graphical interface. Site names must be unique to an agent. The user can also use the kappa string to edit the agent by inputting kappa descriptions e.g. RTK(ligand,tyrosine~unphospho). Learn more about Kappa.
   
5. Annotate the agent. The user can add any associated synonyms to the agent as well as any annotations relating to the agent. This too, is optional.