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MUFINS : multi-formalism interaction network simulator
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(2016) MUFINS : multi-formalism interaction network simulator. npj Systems Biology and Applications, 2 . 16032. doi:10.1038/npjsba.2016.32
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WRAP-MUFINS-multi-formalism-interaction-simulator-Mannan-2016.pdf - Published Version - Requires a PDF viewer. Available under License Creative Commons Attribution 4.0. Download (3984Kb) | Preview |
Official URL: http://doi.org/10.1038/npjsba.2016.32
Abstract
Systems Biology has established numerous approaches for mechanistic modeling of molecular networks in the cell and a legacy ofmodels. The current frontier is the integration of models expressed in different formalisms to address the multi-scale biologicalsystem organization challenge. We present MUFINS (MUlti-Formalism Interaction Network Simulator) software, implementing aunique set of approaches for multi-formalism simulation of interaction networks. We extend the constraint-based modeling (CBM)framework by incorporation of linear inhibition constraints, enabling for thefirst time linear modeling of networks simultaneouslydescribing gene regulation, signaling and whole-cell metabolism at steady state. We present a use case where a logical hypergraphmodel of a regulatory network is expressed by linear constraints and integrated with a Genome-Scale Metabolic Network (GSMN) ofmouse macrophage. We experimentally validate predictions, demonstrating application of our software in an iterative cycle ofhypothesis generation, validation and model refinement. MUFINS incorporates an extended version of our Quasi-Steady State PetriNet approach to integrate dynamic models with CBM, which we demonstrate through a dynamic model of cortisol signalingintegrated with the human Recon2 GSMN and a model of nutrient dynamics in physiological compartments. Finally, we implementa number of methods for deriving metabolic states from ~ omics data, including our new variant of the iMAT congruency approach.We compare our approach with iMAT through the analysis of 262 individual tumor transcriptomes, recovering features of metabolicreprogramming in cancer. The software provides graphics user interface with network visualization, which facilitates use byresearchers who are not experienced in coding and mathematical modeling environments.
| Item Type: | Journal Article | ||||||||||||||||||
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| Subjects: | Q Science > QA Mathematics Q Science > QH Natural history > QH301 Biology Q Science > QR Microbiology |
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| Divisions: | Faculty of Science, Engineering and Medicine > Engineering > Engineering | ||||||||||||||||||
| Library of Congress Subject Headings (LCSH): | Genetic regulation -- Software, Cells -- Metabolism -- Software, Genomes -- Software, Hypergraphs, Petri nets | ||||||||||||||||||
| Journal or Publication Title: | npj Systems Biology and Applications | ||||||||||||||||||
| Publisher: | Nature Partner Journals | ||||||||||||||||||
| ISSN: | 2056-7189 | ||||||||||||||||||
| Official Date: | 17 November 2016 | ||||||||||||||||||
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| Volume: | 2 | ||||||||||||||||||
| Article Number: | 16032 | ||||||||||||||||||
| DOI: | 10.1038/npjsba.2016.32 | ||||||||||||||||||
| Status: | Peer Reviewed | ||||||||||||||||||
| Publication Status: | Published | ||||||||||||||||||
| Access rights to Published version: | Open Access | ||||||||||||||||||
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