The Reaction Equations Plug-In
allows to load metabolic networks from reaction equations as frequently used in scientific publications.
Using the Plug-In
After installation, you can find the entry "Load Reaction Equations" in the File -> New menu.
File menu containing access to the Reaction Equations Plug-In
After choosing this option, the following dialog appears where you can enter reaction equations:
Screenshot of the reaction equation input dialog
Basically, reaction equations have the form:
list of educts
- list of educts <=> list of products for reversible reactions and
- list of educts -> list of products for irreversible reactions.
and list of products
one or more reactants (metabolites) separated by '+':
ATP + GLU <=> ADP + G6P
Optionally, a reaction name can be specified:
g6pt: ATP + GLU <=> ADP + G6P
Furthermore, it is possible to specify stoichiometric coefficients:
g6pt: 2 ATP + GLU <=> 2 ADP + G6P
It is additionally possible to specify the compartments of the metabolites and the pathway, a reaction belongs to. Therfore, the compartment/pathway name is to be declared in brackets behind the metaolite/reaction name:
g6pt[Glycolysis]: ATP[Cytosol] + GLU[Cytosol] <=> ADP[Cytosol] + G6P[Cytosol]
transport: G6P[Cytosol] <=> G6P[Mitochondria]
The names of reactions and metabolites can only contain letters and numbers. If other characters shall be used, the name can be embedded in quotations:
"D-glucose 6-phosphotransferase": ATP + "D-Glucose" <=> ADP + "D-Glucose 6-phosphate"
The dialog editor continuously checks your input and warns if you make mistakes.
After loading the network from the entered reaction equations all reactions and metabolites are not drawn on the drawing area but listed in the component view (highlighted red) because, no positioning information is available for the components. You can place the individual items on the drawing area by drag and drop, you can use the layout pattern and motif stamp feature of Omix (see User Manual
) and/or you can use the AutoLayout Plug-In
in order to arrange the network on the drawing area.
Non-positioned network nodes available in the component view
Importing into other Documents
Instead of loading reaction equations into new Omix documents as described, you can also choose to import reaction equations into existing documents. Therefore, choose the menu entry File -> Import... -> Import Reaction Equations.
Adding Single Reaction Equation to Network
You can also insert individual reaction equations one by one. Therefore, choose the button "Insert Reaction" -> "Insert Reaction Equation". Subsequently, you have to specify one single reaction equation according to the rules introduced above. After pressing OK, you have to click on the desired position for the new reaction in the diagram. Finally, the reaction and it's educts and products are inserted there.
Adding reaction by equation