In this section we explain how to create a new metabolic network project. We also have a video on that topic https://youtu.be/bsNXZBmtyWw.
CNApy starts with an empty project. You can directly add new reactions via the reaction mask on the right. by pressing the Add new reaction button.
Then, you can type the reaction formula into the Equation field. For example A + 2 B -> C.
The associated metabolites A, B and C are then automatically added to the model.
Changing metabolite identifiers in the metabolite form instantly rewrites the reaction equation of the associated reactions.
Since creating big models by adding single reactions is very cumbersome, CNApy also allows you to create a new project from a pre-existing SBML file. You find the action New project from SBML in the Project menu.
After importing an SBML model, the reaction list is populated with all the reactions from the model.
You can add a map to the project by going to the Map menu and clicking add new map.
From the Map menu we can also change the background image of our map. Any SVG image can be used as a background.
You can add multiple maps that highlight different aspects of your model.
Reaction boxes can be put on the map by dragging over them from the reactions list.
You can adjust the box size with the keyboard shortcuts Ctrl{.grey} + +{.grey} and Ctrl{.grey} + -{.grey}.
You can move the reaction box to the desired position by dragging them on their handles.
If you want to move all reaction boxes together, press Ctrl{.grey} while dragging.
You can also set a specific (pixel-wise) position by right-clicking on a reaction box and selecting "set box position...".
Positioning a big number of reaction boxes can be tiresome. Therefore, CNApy allows you to load and save reaction box positions via the Map menu. This facilitates reuse among similar projects.
The size of the background image can be adjusted with the shortcuts Ctrl{.grey} + Shift{.grey} + +{.grey} and Ctrl{.grey} + Shift{.grey} + -{.grey}.
To save a project click Save Project as in the Project menu.
It is important to add the .cna extension to the file name.
This way your files can be directly found by CNApy. .cna files both include the metabolic model as well as its associated maps.