Add New Reaction

Important

It is recommended to understand the notations of nodes and edges to proceed further with the documentation. Check out the Notations

Note

When a model is uploaded, the server automatically detects whether the model is from KEGG or BiGG. Based on the database, corresponding reactions will be fetched for the selected metabolite

About

The Add New Reaction feature allows you to expand your uploaded model dynamically.
When you select a metabolite from the graph, the system queries the detected database (KEGG or BiGG) and retrieves all reactions in which that metabolite is consumed or produced.

From the suggested list, you can add one or more reactions to your model. This makes it easy to:

• Explore alternative metabolic routes.
• Extend incomplete pathways.

By iteratively adding reactions, you can refine your network and tailor it to the biological system you are modeling.

Result Table

Note

Once results are fetched for potential reactions where the selected metabolite is consumed or produced, you will be redirected to a table below the canvas.

Each row in the table corresponds to a potential reaction that can be added to the model.

Column	Description
Reaction	Identifier for the reaction (e.g., PPC, ICL)
Description	Full name of the reaction (e.g., Phosphoenolpyruvate carboxylase)
Reaction string	Stoichiometric equation showing substrates and products (e.g., PEP + CO₂ → OAA)
Lower bound	Minimum allowable flux value (e.g., 0 for irreversible reactions). Default -1000
Upper bound	Maximum allowable flux value (e.g., 1000 for unconstrained forward flux). Default 1000
Subsystem	Pathway the reaction should belong to (chosse from existing subsystems). Default: Reaction assigned to the subsystem, the metabolite was part of

Recommendation

It is recommended to understand the definitions of lower bound and upper bound to effectively apply them to the potential new reactions.