Koeppl, H. ; Hafner, M. ; Lu, J. (2013)
Mapping behavioral specifications to model parameters in synthetic biology.
In: BMC Bioinformatics, 14 (S10)
doi: 10.1186/1471-2105-14-S10-S9
Artikel, Bibliographie
Dies ist die neueste Version dieses Eintrags.
Kurzbeschreibung (Abstract)
With recent improvements of protocols for the assembly of transcriptional parts, synthetic biological devices can now more reliably be assembled according to a given design. The standardization of parts open up the way for in silico design tools that improve the construct and optimize devices with respect to given formal design specifications. The simplest such optimization is the selection of kinetic parameters and protein abundances such that the specified design constraints are robustly satisfied. In this work we address the problem of determining parameter values that fulfill specifications expressed in terms of a functional on the trajectories of a dynamical model. We solve this inverse problem by linearizing the forward operator that maps parameter sets to specifications, and then inverting it locally. This approach has two advantages over brute-force random sampling. First, the linearization approach allows us to map back intervals instead of points and second, every obtained value in the parameter region is satisfying the specifications by construction. The method is general and can hence be incorporated in a pipeline for the rational forward design of arbitrary devices in synthetic biology.
| Typ des Eintrags: | Artikel |
|---|---|
| Erschienen: | 2013 |
| Autor(en): | Koeppl, H. ; Hafner, M. ; Lu, J. |
| Art des Eintrags: | Bibliographie |
| Titel: | Mapping behavioral specifications to model parameters in synthetic biology |
| Sprache: | Englisch |
| Publikationsjahr: | 2013 |
| Verlag: | BioMed Central |
| Titel der Zeitschrift, Zeitung oder Schriftenreihe: | BMC Bioinformatics |
| Jahrgang/Volume einer Zeitschrift: | 14 |
| (Heft-)Nummer: | S10 |
| DOI: | 10.1186/1471-2105-14-S10-S9 |
| URL / URN: | http://www.biomedcentral.com/1471-2105/14/S10/S9 |
| Zugehörige Links: | |
| Kurzbeschreibung (Abstract): | With recent improvements of protocols for the assembly of transcriptional parts, synthetic biological devices can now more reliably be assembled according to a given design. The standardization of parts open up the way for in silico design tools that improve the construct and optimize devices with respect to given formal design specifications. The simplest such optimization is the selection of kinetic parameters and protein abundances such that the specified design constraints are robustly satisfied. In this work we address the problem of determining parameter values that fulfill specifications expressed in terms of a functional on the trajectories of a dynamical model. We solve this inverse problem by linearizing the forward operator that maps parameter sets to specifications, and then inverting it locally. This approach has two advantages over brute-force random sampling. First, the linearization approach allows us to map back intervals instead of points and second, every obtained value in the parameter region is satisfying the specifications by construction. The method is general and can hence be incorporated in a pipeline for the rational forward design of arbitrary devices in synthetic biology. |
| ID-Nummer: | Artikel-ID: S9 |
| Fachbereich(e)/-gebiet(e): | 18 Fachbereich Elektrotechnik und Informationstechnik 18 Fachbereich Elektrotechnik und Informationstechnik > Institut für Nachrichtentechnik > Bioinspirierte Kommunikationssysteme 18 Fachbereich Elektrotechnik und Informationstechnik > Institut für Nachrichtentechnik |
| Hinterlegungsdatum: | 04 Apr 2014 12:27 |
| Letzte Änderung: | 13 Mai 2024 09:57 |
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| Suche nach Titel in: | TUfind oder in Google |
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Mapping behavioral specifications to model parameters in synthetic biology. (deposited 30 Apr 2024 09:09)
- Mapping behavioral specifications to model parameters in synthetic biology. (deposited 04 Apr 2014 12:27) [Gegenwärtig angezeigt]
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