Comparing chemical reaction networks: a categorical and algorithmic perspective
We study chemical reaction networks (CRNs) as a kernel language for concurrency models with semantics based on ordinary differential equations. We investigate the problem of comparing two CRNs, i.e., to decide whether the trajectories of a source CRN can be matched by a target CRN under an appropria...
| Hoofdauteurs: | , , , |
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| Formaat: | Conference item |
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Association for Computing Machinery
2016
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| _version_ | 1826267011389325312 |
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| author | Cardelli, L Tribastone, M Tschaikowski, M Vandin, A |
| author_facet | Cardelli, L Tribastone, M Tschaikowski, M Vandin, A |
| author_sort | Cardelli, L |
| collection | OXFORD |
| description | We study chemical reaction networks (CRNs) as a kernel language for concurrency models with semantics based on ordinary differential equations. We investigate the problem of comparing two CRNs, i.e., to decide whether the trajectories of a source CRN can be matched by a target CRN under an appropriate choice of initial conditions. Using a categorical framework, we extend and relate model-comparison approaches based on structural (syntactic) and on dynamical (semantic) properties of a CRN, proving their equivalence. Then, we provide an algorithm to compare CRNs, running linearly in time with respect to the cardinality of all possible comparisons. Finally, we apply our results to biological models from the literature. |
| first_indexed | 2024-03-06T20:47:39Z |
| format | Conference item |
| id | oxford-uuid:36759081-e922-4e31-96f5-427da579bd1a |
| institution | University of Oxford |
| last_indexed | 2024-03-06T20:47:39Z |
| publishDate | 2016 |
| publisher | Association for Computing Machinery |
| record_format | dspace |
| spelling | oxford-uuid:36759081-e922-4e31-96f5-427da579bd1a2022-03-26T13:38:05ZComparing chemical reaction networks: a categorical and algorithmic perspectiveConference itemhttp://purl.org/coar/resource_type/c_5794uuid:36759081-e922-4e31-96f5-427da579bd1aSymplectic Elements at OxfordAssociation for Computing Machinery2016Cardelli, LTribastone, MTschaikowski, MVandin, AWe study chemical reaction networks (CRNs) as a kernel language for concurrency models with semantics based on ordinary differential equations. We investigate the problem of comparing two CRNs, i.e., to decide whether the trajectories of a source CRN can be matched by a target CRN under an appropriate choice of initial conditions. Using a categorical framework, we extend and relate model-comparison approaches based on structural (syntactic) and on dynamical (semantic) properties of a CRN, proving their equivalence. Then, we provide an algorithm to compare CRNs, running linearly in time with respect to the cardinality of all possible comparisons. Finally, we apply our results to biological models from the literature. |
| spellingShingle | Cardelli, L Tribastone, M Tschaikowski, M Vandin, A Comparing chemical reaction networks: a categorical and algorithmic perspective |
| title | Comparing chemical reaction networks: a categorical and algorithmic perspective |
| title_full | Comparing chemical reaction networks: a categorical and algorithmic perspective |
| title_fullStr | Comparing chemical reaction networks: a categorical and algorithmic perspective |
| title_full_unstemmed | Comparing chemical reaction networks: a categorical and algorithmic perspective |
| title_short | Comparing chemical reaction networks: a categorical and algorithmic perspective |
| title_sort | comparing chemical reaction networks a categorical and algorithmic perspective |
| work_keys_str_mv | AT cardellil comparingchemicalreactionnetworksacategoricalandalgorithmicperspective AT tribastonem comparingchemicalreactionnetworksacategoricalandalgorithmicperspective AT tschaikowskim comparingchemicalreactionnetworksacategoricalandalgorithmicperspective AT vandina comparingchemicalreactionnetworksacategoricalandalgorithmicperspective |