Species Table

Species are used to create variables (molecular species) in reactions and fluxes and can exist in both membranes and volume compartments (volumes). Species are unique pools of molecules within a single structure; if the same species is copied to a different structure, the structure name is appended to the species name to retain a unique identifier, e.g. species_structure. A species is depicted in the Reaction Diagram as a green shape.

In rule-based models, molecular details must be specified for all species. Species are composed of molecules with bonds that connect binding sites. If the molecule has multiple states, each state of the molecule (at each site) must be specified - otherwise the species would represent a pool of different chemical entities and would not be valid. Species with molecular details can be used in any reaction networt. In rule-based models a species serves as a seed species when rule-based models: they are either used as starting set of species to generating a network (using BioNetGen), or is used as part of an initial set of species for stochastic network-free simulations performed using the (using NFSim solver).

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 the species.
• 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. Species without molecular details appear as green shapes. Molecular details of species appear as differently colored shapes, depicting each molecule that comprises the species,connect by bonds. Sites having states marked by yellow dot. States of sites are omitted for clarity.
• BioNetGen Definition provides a BNGL string for species with molecular detail. The two ends of the same bond will have the same color font. This field is cannot be edited but is 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.