Base model recommendation for XomicsToModel

[Dana Luong]

Hi Ronan and COBRA team,

We are currently still optimizing our protocols for running XomicsToModel. One of the outstanding issues with our output models generated from the base Recon3D reconstruction is that they retain metabolite leaks, which contaminate downstream analyses. We have considered beginning with Recon3DModel (fully leakless), but the concern is that there are reactions/metabolites/genes missing from the model that are present in the reconstruction.

To ameliorate this, we have attempted to (1) remove leaks from our contextualized model post-hoc and (2) add back reactions to Recon3DModel while avoiding re-introducing leaks.

What is the recommended starting point for XomicsToModel? If the full Recon3D reconstruction the recommended starting point, do you have suggestions on how to handle metabolite leaks in the Xomics output models? Do you have additional context on the content diff between the full Recon3D reconstruction and the Recon3DModel?

Thank you in advance for your time and guidance!

Best,

Dana

[Ines Thiele]

Hi Dana

Pls use Recon3DModel which has been designed to be a starting point for cell-type and tissue-specific metabolic models.

best ines

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Ines Thiele, PhD
Professor in Systems Biomedicine
Director, Digital Metabolic Twin Centre

Principal Investigator, APC Microbiome Ireland 

Principal Investigator, Ryan Institute

Principal Investigator, Galway Neuroscience Centre

University of Galway
School of Medicine
School of Biological and Chemical Sciences | Microbiology, 

Orbsen Building | Galway, Ireland

thielelab.eu,
GoogleScholarProfile,
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[Dana Luong]

Hi Ines,

Understood, thanks very much!

Best,

Dana