Model

Within the framework of the Simmune Modeler a model refers to a set of specifications describing molecules, molecule components, binding sites, complex species, complexes, complex association, complex dissociation, and complex transformations.

Model file

The file saved by Simmune Modeler, which contains the complete specification of a model.

Molecule

A molecule refers to a biological molecule, and is composed of molecule component(s).

Molecule component and molecule component state

A molecule component can carry any (in principle) number of named states. Such states could, for instance stand for particular phosphorylation states of the molecule component.

A molecule component can have any (in principle) number of binding sites, but the molecule components of a molecule must have at least one binding site in total.

A molecule component can have zero or multiple states assigned to it. Each state is tagged with a unique name, called "state tag". A molecule component state can have one of the following values: "on", "off" or "don't care". The purpose of these state tags is to encode modifications the molecule components experience in the course of reactions. The transition from unphosphorylated to phosphorylated of a molecule component as part of a complex of an Enzyme and a Substrate complex, for instance, could be encoded with a state tag with name "phosphorylated" that would switch from "off" to "on" as the result of a transformation of the Enzyme:Substrate complex.

Binding site and binding site status

Binding sites can be connected through bonds thereby linking the molecules within multi-molecular complexes. These bonds are the results of complex associations.

A binding site can have one of the following states: "bound", "unbound", or "don't care". Binding sites that are involved in the binding between two molecules of a complex are automatically in the state bound. For binding sites that are not involved in bonds with explicitly specified binding partners (other binding sites of other molecules) the user can specify a binding state to restrict the allowed states for the specification of reactions. The user could, for example, specify that a certain transformation of a complex can only take place if a particular binding site in the complex is "unbound". On the other hand, if the state of this binding site does not affect the transformation the user would specify its state as "don't care".

Complex species

A complex species refers to a set of complexes composed of the same set of molecule(s) and binding site interaction(s) within the complex.

Complex

A complex is a particular instance of a complex species. It shares the binding structure of all complexes belonging to the same species but can have unique states of its molecule components and binding status of those binding sites not used for explicit bonds (e.g. with explicitly specified binding partners within the complex species).

Complex transformation

A complex transformation is a reaction rule in a model. It describes how a complex "source" undergoes a transformation into another complex "result" with a given transformation rate. The complex species of the "source" and "result" complexes must be the same, or equivalent. "Equivalent" complex species may differ only with regard to intra-complex bonds. For instance, the breaking of one bond may transform a "closed ring structure" complex into an "open ring structure" complex.

Complex association

A complex association is a reaction rule in a model. It describes how a complex interacts with another complex to generate a result complex through the formation of a bond between the two, mediated by a binding site interaction and proceeding with a given association rate. Associations can involve state changes.

Complex dissociation

A complex dissociation is a reaction rule in a model. It describes how a complex splits into 2 fragment complexes with a given dissociation rate. Dissociations can involve state changes.

Complex species node

A complex species node corresponds to a unique complex species in the model.

Complex species nodes are visualized using the same iconographical representation as in the Simmune Modeler.

Intermediate node

An intermediate node corresponds to a unique reaction specification in the model.

Intermediate nodes are visualized as arrows showing the direction of the incident edges.

Edge

An edge connects a complex species node and an intermediate node if that complex species contains a complex which is involved in the reaction specification. An edge's direction depends on whether that complex is a reactant (i.e. on the 'left-hand side' of the reaction), in which case the edge goes from complex species node to intermediate node. Otherwise (i.e. the involved complex is the result of the reaction), the edge goes from intermediate node to complex species node. Edge color indicates the type of reaction corresponding to the intermediate node. It also provides hint on the edge direction -- if the involved complex is a reactant the color is less saturated.

For instance, a complex dissociation rule involves three complexes -- the source complex and the two fragment complexes. Each complex belongs to a complex species corresponding to a complex species node. Three edges, along with the intermediate node and complex species nodes, describe the reaction: One edge from the source complex species to the intermediate node, and two edges from the intermediate node to the two fragment complex species.

Network

Formally speaking, a network is a directed bipartite graph generated from the model. A network contains two node sets, complex species nodes and intermediate nodes, and a set of directed edges.

Network panel

The network panel shows the iconographical representation of the network and provides, interactively, various features for visual exploration of the model.

Tree panel

The tree panel shows the complex species-complex hierarchy as a two-level tree. Each complex is a child of the complex species it belongs.

Rule panel

The rule panel shows the rules categorized by their types (i.e. transformation, association, and dissociation).

Filter panel

The filter panel allows the user to filter items in tree panel.