MMINT: a Metabolic Model Interactive Network Tool for the exploration and comparative visualisation of metabolic networks Article Swipe
Juan Pablo Molina Ortiz
,
Matthew J. Morgan
,
Amy M. Paten
,
Andrew C. Warden
,
Philip Kilby
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1101/2024.08.06.606923
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1101/2024.08.06.606923
Genome-scale metabolic models (GEMs) are essential tools in systems and synthetic biology, enabling the mathematical simulation of metabolic pathways encoded in genomes to predict phenotypes. The complexity of GEMs, however, can often limit the interpretation and comparison of their outputs. Here, we present MMINT (Metabolic Modelling Interactive Network Tool), designed to facilitate the exploration and comparison of metabolic networks. MMINT employs GEM networks and flux solutions derived from Constraint Based Analysis (e.g. Flux Balance Analysis) to create interactive visualizations. This tool allows for seamless toggling of source and target metabolites, network decluttering, enabling exploration and comparison of flux solutions by highlighting similarities and differences between metabolic states, which enhances the identification of mechanistic drivers of phenotypes. We demonstrate MMINT’s capabilities using the Pyrococcus furiosus GEM, showcasing its application in distinguishing the metabolic drivers of acetate- and ethanol-producing phenotypes. By providing an intuitive and responsive model-exploration experience, MMINT addresses the need for a tool that simplifies the interpretation of GEM outputs and supports the discovery of novel metabolic engineering strategies. MMINT is available at https://doi.org/10.6084/m9.figshare.26409328 Graphical abstract MMINT functionalities provide an intuitive and responsive model-exploration experience, enabling flux solution comparison and the identification of metabolic drivers of phenotypes
Related Topics
Concepts
Metabolic network
Flux balance analysis
Computer science
Flux (metallurgy)
Metabolic engineering
Identification (biology)
Visualization
Constraint (computer-aided design)
Interactive visualization
Computational biology
Systems biology
Adaptation (eye)
Metabolic pathway
Metabolic flux analysis
Data mining
Biology
Chemistry
Engineering
Ecology
Gene
Genetics
Neuroscience
Metabolism
Mechanical engineering
Organic chemistry
Endocrinology
Metadata
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2024.08.06.606923
- https://www.biorxiv.org/content/biorxiv/early/2024/08/07/2024.08.06.606923.full.pdf
- OA Status
- green
- References
- 39
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4401436005
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4401436005Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1101/2024.08.06.606923Digital Object Identifier
- Title
-
MMINT: a Metabolic Model Interactive Network Tool for the exploration and comparative visualisation of metabolic networksWork title
- Type
-
preprintOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2024Year of publication
- Publication date
-
2024-08-07Full publication date if available
- Authors
-
Juan Pablo Molina Ortiz, Matthew J. Morgan, Amy M. Paten, Andrew C. Warden, Philip KilbyList of authors in order
- Landing page
-
https://doi.org/10.1101/2024.08.06.606923Publisher landing page
- PDF URL
-
https://www.biorxiv.org/content/biorxiv/early/2024/08/07/2024.08.06.606923.full.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
greenOpen access status per OpenAlex
- OA URL
-
https://www.biorxiv.org/content/biorxiv/early/2024/08/07/2024.08.06.606923.full.pdfDirect OA link when available
- Concepts
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Metabolic network, Flux balance analysis, Computer science, Flux (metallurgy), Metabolic engineering, Identification (biology), Visualization, Constraint (computer-aided design), Interactive visualization, Computational biology, Systems biology, Adaptation (eye), Metabolic pathway, Metabolic flux analysis, Data mining, Biology, Chemistry, Engineering, Ecology, Gene, Genetics, Neuroscience, Metabolism, Mechanical engineering, Organic chemistry, EndocrinologyTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
0Total citation count in OpenAlex
- References (count)
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39Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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