Species Table

Species are used to create variables (molecular species) in reactions and fluxes. Species can exist in both membranes and compartments (volumes) of the cellular structures. Species are unique pools of molecules within a single compartment. If the same species is copied to different compartment, the compartment name is appended to the species name to retain a unique identifier, e.g. species_compartment. Species is shown in Reaction Diagram as a green shape.

For use in rule-based modeling species must have molecular details specified: they are composed of molecules with bonds connecting binding sites. If Molecule has multiple states, each state must be specified - otherwise the species will present a pool of different chemical entities and will not be valid. Species with molecular details can be used as regular species in any reaction network, but they also can serve as seed species in rule-based models: they are either used as starting set of species to generate a network (using BioNetGen software), or used as an initial set of species for stochastic network-free simulations performed by (using NFSim software).

The Species Tab has several columns:

• The species Name. For new species it will be s_number. For imported BNGL this name is autogenerated. The user may change name right in the column.
• the structure that contains a species. For rule-based models, this field is uneditable, as a model may contain only one compartment.
• If the species is linked to a pathway object, a Link to that object will be shown in the Link column. Mousing over a link will open a tooltip box with additional information about the linked object. Double click on that link to navigate to the Pathway Diagram and highlight the object linked to the species.
• Depiction shows the structure of the species. For species without molecular details it will be green shape. For species with moledcular details it will shows connected shapes for every molecule that comprise a species, with sites having states marked by yellow dot. States of sites are omitted for clarity.
• BioNetGen Definition provides BNGL string for species with molecular detail. Ends of the same bonds are show with the same color. This field is uneditable but searchable.

Edit molecular details of species in the Species Properties pane in the lower window.

Filter the list of species using the Search Box to enter a species name or a structure name.

Delete species by highlighting and using the "Delete" button below the table.

If you wish to use Pathways Commons data, select the species and use the Pathway Links button.

Add annotation about the species within the Species Properties pane in the bottom window.