Preprint Open Access

Exploring the Dynamics of Nonlinear Biochemical Systems using Control-Based Continuation

Gomes, Brandon; de Cesare, Irene; Guarino, Agostino; di Bernardo, Mario; Renson, Ludovic; Marucci, Lucia


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/4837515">
    <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/4837515</dct:identifier>
    <foaf:page rdf:resource="https://zenodo.org/record/4837515"/>
    <dct:creator>
      <rdf:Description>
        <rdf:type rdf:resource="http://xmlns.com/foaf/0.1/Agent"/>
        <foaf:name>Gomes, Brandon</foaf:name>
        <foaf:givenName>Brandon</foaf:givenName>
        <foaf:familyName>Gomes</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>Engineering Mathematics Department, University of Bristol, Bristol BS8 1UB, 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>de Cesare, Irene</foaf:name>
        <foaf:givenName>Irene</foaf:givenName>
        <foaf:familyName>de Cesare</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>Department of Electrical Engineering and Information Technology, University of Naples, Naples 80125 Naples, Italy</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>Guarino, Agostino</foaf:name>
        <foaf:givenName>Agostino</foaf:givenName>
        <foaf:familyName>Guarino</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>Department of Electrical Engineering and Information Technology, University of Naples, Naples 80125 Naples, Italy</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>di Bernardo, Mario</foaf:name>
        <foaf:givenName>Mario</foaf:givenName>
        <foaf:familyName>di Bernardo</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>Engineering Mathematics Department, University of Bristol, Bristol BS8 1UB, UK - Department of Electrical Engineering and Information Technology, University of Naples, Naples 80125 Naples, Italy - Bristol Centre for Synthetic Biology, University of Bristol, Life Sciences Building Tyndall Avenue, Bristol, BS8 1TQ, 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>Renson, Ludovic</foaf:name>
        <foaf:givenName>Ludovic</foaf:givenName>
        <foaf:familyName>Renson</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>Engineering Mathematics Department, University of Bristol, Bristol BS8 1UB, 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>Marucci, Lucia</foaf:name>
        <foaf:givenName>Lucia</foaf:givenName>
        <foaf:familyName>Marucci</foaf:familyName>
        <org:memberOf>
          <foaf:Organization>
            <foaf:name>Engineering Mathematics Department, University of Bristol, Bristol BS8 1UB, UK - Bristol Centre for Synthetic Biology, University of Bristol, Life Sciences Building Tyndall Avenue, Bristol, BS8 1TQ, UK</foaf:name>
          </foaf:Organization>
        </org:memberOf>
      </rdf:Description>
    </dct:creator>
    <dct:title>Exploring the Dynamics of Nonlinear Biochemical Systems using Control-Based Continuation</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">2019</dct:issued>
    <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">2019-11-18</dct:issued>
    <owl:sameAs rdf:resource="https://zenodo.org/record/4837515"/>
    <adms:identifier>
      <adms:Identifier>
        <skos:notation rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://zenodo.org/record/4837515</skos:notation>
        <adms:schemeAgency>url</adms:schemeAgency>
      </adms:Identifier>
    </adms:identifier>
    <owl:sameAs rdf:resource="https://doi.org/10.1101/695866"/>
    <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;Mathematical modelling is routinely used in Systems Biology to understand the mechanisms causing nonlinear phenomena in gene expression, such as switch-like behaviours and temporal oscillations. The reliability of model predictions and bifurcation analysis depend on modelling assumptions and specific choices of model parameters; however, the identification of models is highly challenging due to the complexity of biochemical interactions and noise in experimental data.&lt;/p&gt; &lt;p&gt;This paper numerically investigates the use of control-based continuation (CBC) for tracking dynamical features of biochemical systems and, in particular, the bistable dynamics of a gene regulating pluripotency in embryonic stem cells.&lt;/p&gt; &lt;p&gt;CBC is a method that exploits feedback control and path following algorithms to explore the dynamic features of a nonlinear physical system directly during experimental tests. CBC applications have so far been limited to non-living (i.e. electro-mechanical) systems. Our numerical simulations show that, in principle, CBC could also be applied to biological experiments to characterise the switch-like dynamics of genes that are important for cell decision making.&lt;/p&gt;</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/4837515"/>
      </dcat:Distribution>
    </dcat:distribution>
    <dcat:distribution>
      <dcat:Distribution>
        <dcat:accessURL>https://doi.org/10.1101/695866</dcat:accessURL>
        <dcat:byteSize>265585</dcat:byteSize>
        <dcat:downloadURL rdf:resource="https://zenodo.org/record/4837515/files/Gomes et al 2018 biorxiv.pdf">https://zenodo.org/record/4837515/files/Gomes et al 2018 biorxiv.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>
2
3
views
downloads
Views 2
Downloads 3
Data volume 796.8 kB
Unique views 2
Unique downloads 3

Share

Cite as