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How is it possible to add or remove reactions and metabolites within a metabolic model?

MB
Maëva Beugin
Feb 22, 2024

Co-authors : 
TE
Thibault ETIENNE
1

Introduction


If you're looking to adjust reactions or metabolites within a metabolic network using Constellab,


you are in the right place! 



The objective of this story is to outline various straightforward tasks for altering a metabolic network, with the goal of enhancing its functionality or streamlining its structure. These tasks can be seamlessly integrated and executed in any preferred order.



Prerequesites


To make modifications to a metabolic network, you require the specific metabolic network you wish to alter.


For this purpose, this story uses  the E. coli core model. All essential files for this model are attached to this story.


Steps to follow


  1. Import your metabolic network in Constellab
    1. Link it to the Task "Reaction Adder".
      1. Import a Entity ID table and link it to the Task "Reaction Adder".
        1. Link the output the Task "Reaction Remover".
          1. You can also link a Entity ID table to the Task "Reaction Remover". Here we linked the same.
            1. Link the output to the Task "Orphan Remover"
              1. Get a better network every step of the way!




                Results


                Once the “Reaction Adder” task was completed, the reaction was successfully integrated into the metabolic network, along with its corresponding metabolites.





                After running the “Reaction Remover” task, it becomes clear that the reaction has been successfully removed. Nonetheless, the metabolites added in the previous step remain present within the network.



                To remove these metabolites as well, you'll need to use the 'Orphan Remover' task. Upon completion of this task,


                the metabolites will no longer be present in the metabolic network.


                Conclusion


                In summary, Constellab offers a straightforward method for modifying a metabolic network by either incorporating or eliminating reactions. Additionally, the platform enables the cleanup of metabolic networks by removing orphan compounds.



                These tasks prove highly beneficial and versatile, serving various purposes across different applications.