Journal article Open Access

On-Line Optimal Input Design Increases the Efficiency and Accuracy of the Modelling of an Inducible Synthetic Promoter

Bandiera, Lucia; Hou, Zhaozheng; Kothamachu, Varun B.; Balsa-Canto, Eva; Swain, Peter S.; Menolascina, Filippo


DCAT Export

<?xml version='1.0' encoding='utf-8'?>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:adms="http://www.w3.org/ns/adms#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dct="http://purl.org/dc/terms/" xmlns:dctype="http://purl.org/dc/dcmitype/" xmlns:dcat="http://www.w3.org/ns/dcat#" xmlns:duv="http://www.w3.org/ns/duv#" xmlns:foaf="http://xmlns.com/foaf/0.1/" xmlns:frapo="http://purl.org/cerif/frapo/" xmlns:geo="http://www.w3.org/2003/01/geo/wgs84_pos#" xmlns:gsp="http://www.opengis.net/ont/geosparql#" xmlns:locn="http://www.w3.org/ns/locn#" xmlns:org="http://www.w3.org/ns/org#" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:prov="http://www.w3.org/ns/prov#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:schema="http://schema.org/" xmlns:skos="http://www.w3.org/2004/02/skos/core#" xmlns:vcard="http://www.w3.org/2006/vcard/ns#" xmlns:wdrs="http://www.w3.org/2007/05/powder-s#">
  <rdf:Description rdf:about="https://zenodo.org/record/2668525">
    <rdf:type rdf:resource="http://www.w3.org/ns/dcat#Dataset"/>
    <dct:type rdf:resource="http://purl.org/dc/dcmitype/Text"/>
    <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://zenodo.org/record/2668525</dct:identifier>
    <foaf:page rdf:resource="https://zenodo.org/record/2668525"/>
    <dct:creator>
      <rdf:Description>
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Bandiera, Lucia</foaf:name>
        <foaf:givenName>Lucia</foaf:givenName>
        <foaf:familyName>Bandiera</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>1. School of Engineering, Institute for Bioengineering, The University of Edinburgh, Edinburgh EG9 3DW, UK; 2. Synthsys—Centre for Synthetic and Systems Biology, The University of Edinburgh, Edinburgh EH9 3BF, UK</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description>
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Hou, Zhaozheng</foaf:name>
        <foaf:givenName>Zhaozheng</foaf:givenName>
        <foaf:familyName>Hou</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>School of Engineering, Institute for Bioengineering, The University of Edinburgh, Edinburgh EG9 3DW, UK</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description>
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Kothamachu, Varun B.</foaf:name>
        <foaf:givenName>Varun B.</foaf:givenName>
        <foaf:familyName>Kothamachu</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>School of Engineering, Institute for Bioengineering, The University of Edinburgh, Edinburgh EG9 3DW, UK</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description>
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Balsa-Canto, Eva</foaf:name>
        <foaf:givenName>Eva</foaf:givenName>
        <foaf:familyName>Balsa-Canto</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>(Bio)Process Engineering Group, IIM-CSIC Spanish Reasearch Council, 36208 Vigo, Spain</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description>
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Swain, Peter S.</foaf:name>
        <foaf:givenName>Peter S.</foaf:givenName>
        <foaf:familyName>Swain</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>Synthsys—Centre for Synthetic and Systems Biology, The University of Edinburgh, Edinburgh EH9 3BF, UK</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:creator>
      <rdf:Description>
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Menolascina, Filippo</foaf:name>
        <foaf:givenName>Filippo</foaf:givenName>
        <foaf:familyName>Menolascina</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>1. School of Engineering, Institute for Bioengineering, The University of Edinburgh, Edinburgh EG9 3DW, UK; 2. Synthsys—Centre for Synthetic and Systems Biology, The University of Edinburgh, Edinburgh EH9 3BF, UK</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:title>On-Line Optimal Input Design Increases the Efficiency and Accuracy of the Modelling of an Inducible Synthetic Promoter</dct:title>
    <dct:publisher>
      <foaf:Agent>
        <foaf:name>Zenodo</foaf:name>
      </foaf:Agent>
    </dct:publisher>
    <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#gYear">2018</dct:issued>
    <dcat:keyword>Model-based optimal experimental design</dcat:keyword>
    <dcat:keyword>Syntethic biology</dcat:keyword>
    <dcat:keyword>Model calibration</dcat:keyword>
    <dcat:keyword>Optimal inputs</dcat:keyword>
    <dcat:keyword>System identification</dcat:keyword>
    <frapo:isFundedBy rdf:resource="info:eu-repo/grantAgreement/EC/H2020/766840/"/>
    <schema:funder>
      <foaf:Organization>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10.13039/501100000780</dct:identifier>
        <foaf:name>European Commission</foaf:name>
      </foaf:Organization>
    </schema:funder>
    <dct:issued rdf:datatype="http://www.w3.org/2001/XMLSchema#date">2018-09-01</dct:issued>
    <owl:sameAs rdf:resource="https://zenodo.org/record/2668525"/>
    <adms:identifier>
      <adms:Identifier>
        <skos:notation rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://zenodo.org/record/2668525</skos:notation>
        <adms:schemeAgency>url</adms:schemeAgency>
      </adms:Identifier>
    </adms:identifier>
    <owl:sameAs rdf:resource="https://doi.org/10.3390/pr6090148"/>
    <dct:isPartOf rdf:resource="https://zenodo.org/communities/cosy-bio"/>
    <dct:description>&lt;p&gt;&lt;strong&gt;Abstract&lt;/strong&gt;&lt;/p&gt; &lt;p&gt;Synthetic biology seeks to design biological parts and circuits that implement new functions in cells. Major accomplishments have been reported in this field, yet predicting a priori the in vivo behaviour of synthetic gene circuits is major a challenge. Mathematical models offer a means to address this bottleneck. However, in biology, modelling is perceived as an expensive, time-consuming task. Indeed, the quality of predictions depends on the accuracy of parameters, which are traditionally inferred from&amp;nbsp;poorly informative&amp;nbsp;data. How much can parameter accuracy be improved by using model-based optimal experimental design (MBOED)? To tackle this question, we considered an inducible promoter in the yeast&amp;nbsp;S. cerevisiae. Using in vivo data, we re-fit a dynamic model for this component and then compared the performance of standard (e.g., step inputs) and optimally designed experiments for parameter inference. We found that MBOED improves the quality of model calibration by &amp;sim;60%. Results further improve up to&amp;nbsp;84%&amp;nbsp;when considering on-line optimal experimental design (OED). Our in silico results suggest that MBOED provides a significant advantage in the identification of models of biological parts and should thus be integrated into their characterisation.&lt;/p&gt;</dct:description>
    <dct:description>This paper is an extended version of our paper published in 57th IEEE Conference on Decision and Control, Miami Beach, FL, USA, 17–19 December 2018.</dct:description>
    <dct:accessRights rdf:resource="http://publications.europa.eu/resource/authority/access-right/PUBLIC"/>
    <dct:accessRights>
      <dct:RightsStatement rdf:about="info:eu-repo/semantics/openAccess">
        <rdfs:label>Open Access</rdfs:label>
      </dct:RightsStatement>
    </dct:accessRights>
    <dcat:distribution>
      <dcat:Distribution>
        <dct:license rdf:resource="https://creativecommons.org/licenses/by/4.0/legalcode"/>
        <dcat:accessURL rdf:resource="https://zenodo.org/record/2668525"/>
      </dcat:Distribution>
    </dcat:distribution>
    <dcat:distribution>
      <dcat:Distribution>
        <dcat:accessURL>https://doi.org/10.3390/pr6090148</dcat:accessURL>
        <dcat:byteSize>2021304</dcat:byteSize>
        <dcat:downloadURL>https://zenodo.org/record/2668525/files/Bandiera et al Processes 2018.pdf</dcat:downloadURL>
        <dcat:mediaType>application/pdf</dcat:mediaType>
      </dcat:Distribution>
    </dcat:distribution>
  </rdf:Description>
  <foaf:Project rdf:about="info:eu-repo/grantAgreement/EC/H2020/766840/">
    <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">766840</dct:identifier>
    <dct:title>Control Engineering of Biological Systems for Reliable Synthetic Biology Applications</dct:title>
    <frapo:isAwardedBy>
      <foaf:Organization>
        <dct:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#string">10.13039/501100000780</dct:identifier>
        <foaf:name>European Commission</foaf:name>
      </foaf:Organization>
    </frapo:isAwardedBy>
  </foaf:Project>
</rdf:RDF>
18
28
views
downloads
Views 18
Downloads 28
Data volume 56.6 MB
Unique views 16
Unique downloads 27

Share

Cite as