The initial conditions section is located in the bottom right portion of the model page. This section defines the abundances of the agents and complexes that are present in the system at the beginning of the simulation. The contact map of the model page is also constructed based on the initial conditions. Because the initial conditions define the full state of the system prior to simulation, the agents and complexes initial conditions must be fully defined. That is to say that all sites and states must be explicitly declared on agents, and all bonds must be connected at both ends (no "any" and "wild-card" bonds are allowed).  The initial conditions are defined in number of molecules per reaction volume.

In addition to viewing the initial conditions that comprise the model, the initial conditions section is where the user can add, edit, or remove initial conditions. The search bar can be used to filter the full list of initial conditions. If there are more than 20 initial conditions in the list, they are separated on multiple pages that can be accessed via the "next" and page number buttons at the bottom of the list.

The initial conditions section when no initial conditions are present in the model page

The initial conditions section when initial conditions are present in the model page

Adding or editing initial conditions to the model page
The user can add or edit initial conditions via the initial conditions editor by clicking on the edit button at the top of the initial conditions section. If the model is newly created and does not contain any initial conditions, then initial conditions can be added by clicking on the "Add initial conditions" button under the initial condition section header. The "Add All" button will create an initial condition for each agent in the cBook, and the agents will be present without bonds and with any default states defined on the agent pages.

Removing initial conditions from the model page
There are three ways to remove initial conditions from the model page. The user can hit the (x) next to an initial condition in the list to remove that initial condition, or click on the "Edit" button and remove initial conditions via the initial conditions editor. All initial conditions can be removed from the model page via the "Delete All" button.

Editing the abundance of the initial conditions
The user can change the abundance for any initial condition on the model page by clicking on the abundance value in the initial conditions section. The abundances can also be set in the initial conditions editor.