Add Full Reaction
The Add Full Reaction is a feature that helps you add an entire reaction based on a query search
Information
This feature is similar to Add New Reaction, with the only difference that this feature allows you to search a reaction by their abbreviation, name or its reaction string
Steps to Add Reaction
- Click the Add Full Reaction button to start adding a new reaction
- In doing so, you will be prompted with a text box to search a reaction by name, abbreviation or its reaction string
- Based on the query, you will be provided a resulting table for potential reactions based on your query
Result Table
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 |
Recommendation
It is recommended to understand the definitions of lower bound and upper bound to effectively apply them to the potential new reactions.
Assigning Subsystem
For each row in the result table, you are required to assign a subsystem to that reaction. You are provided with the following two options
graph TD
A[Subsystem Assignment] ---> B[Existing Subsystem]
A[Subsystem Assignment] ---> C[New custom Subsystem]Existing Subsystem
If the model already contains reactions with subsystems assigned, you can potentially assign it based on the existing subsystems
Custom Subsystem
Alternatively, you also provided with a textbox to enter the name of a new subsystem.
Point to be noted
The custom subsystem will appear as existing subsystem when you use the Add Full Reaction feature again.