Dataset Open Access

Supplementary data and scripts for "An Atlas of Human Metabolism"

Robinson, Jonathan L.; Kocabaş, Pınar; Wang, Hao; Cholley, Pierre-Etienne; Cook, Daniel; Nilsson, Avlant; Anton, Mihail; Ferreira, Raphael; Domenzain, Iván; Billa, Virinchi; Limeta, Angelo; Hedin, Alex; Gustafsson, Johan; Kerkhoven, Eduard J.; Svensson, L. Thomas; Palsson, Bernhard O.; Mardinoglu, Adil; Hansson, Lena; Uhlén, Mathias; Nielsen, Jens


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  <identifier identifierType="DOI">10.5281/zenodo.3583004</identifier>
  <creators>
    <creator>
      <creatorName>Robinson, Jonathan L.</creatorName>
      <givenName>Jonathan L.</givenName>
      <familyName>Robinson</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-8567-5960</nameIdentifier>
      <affiliation>Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, Gothenburg, Sweden</affiliation>
    </creator>
    <creator>
      <creatorName>Kocabaş, Pınar</creatorName>
      <givenName>Pınar</givenName>
      <familyName>Kocabaş</familyName>
      <affiliation>Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, Gothenburg, Sweden</affiliation>
    </creator>
    <creator>
      <creatorName>Wang, Hao</creatorName>
      <givenName>Hao</givenName>
      <familyName>Wang</familyName>
      <affiliation>Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, Gothenburg, Sweden</affiliation>
    </creator>
    <creator>
      <creatorName>Cholley, Pierre-Etienne</creatorName>
      <givenName>Pierre-Etienne</givenName>
      <familyName>Cholley</familyName>
      <affiliation>Department of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, Kemivägen 10, Gothenburg, Sweden</affiliation>
    </creator>
    <creator>
      <creatorName>Cook, Daniel</creatorName>
      <givenName>Daniel</givenName>
      <familyName>Cook</familyName>
      <affiliation>Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, Gothenburg, Sweden</affiliation>
    </creator>
    <creator>
      <creatorName>Nilsson, Avlant</creatorName>
      <givenName>Avlant</givenName>
      <familyName>Nilsson</familyName>
      <affiliation>Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, Gothenburg, Sweden</affiliation>
    </creator>
    <creator>
      <creatorName>Anton, Mihail</creatorName>
      <givenName>Mihail</givenName>
      <familyName>Anton</familyName>
      <affiliation>Department of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, Kemivägen 10, Gothenburg, Sweden</affiliation>
    </creator>
    <creator>
      <creatorName>Ferreira, Raphael</creatorName>
      <givenName>Raphael</givenName>
      <familyName>Ferreira</familyName>
      <affiliation>Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, Gothenburg, Sweden</affiliation>
    </creator>
    <creator>
      <creatorName>Domenzain, Iván</creatorName>
      <givenName>Iván</givenName>
      <familyName>Domenzain</familyName>
      <affiliation>Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, Gothenburg, Sweden</affiliation>
    </creator>
    <creator>
      <creatorName>Billa, Virinchi</creatorName>
      <givenName>Virinchi</givenName>
      <familyName>Billa</familyName>
      <affiliation>Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, Gothenburg, Sweden</affiliation>
    </creator>
    <creator>
      <creatorName>Limeta, Angelo</creatorName>
      <givenName>Angelo</givenName>
      <familyName>Limeta</familyName>
      <affiliation>Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, Gothenburg, Sweden</affiliation>
    </creator>
    <creator>
      <creatorName>Hedin, Alex</creatorName>
      <givenName>Alex</givenName>
      <familyName>Hedin</familyName>
      <affiliation>Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, Gothenburg, Sweden</affiliation>
    </creator>
    <creator>
      <creatorName>Gustafsson, Johan</creatorName>
      <givenName>Johan</givenName>
      <familyName>Gustafsson</familyName>
      <affiliation>Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, Gothenburg, Sweden</affiliation>
    </creator>
    <creator>
      <creatorName>Kerkhoven, Eduard J.</creatorName>
      <givenName>Eduard J.</givenName>
      <familyName>Kerkhoven</familyName>
      <affiliation>Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, Gothenburg, Sweden</affiliation>
    </creator>
    <creator>
      <creatorName>Svensson, L. Thomas</creatorName>
      <givenName>L. Thomas</givenName>
      <familyName>Svensson</familyName>
      <affiliation>Department of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, Kemivägen 10, Gothenburg, Sweden</affiliation>
    </creator>
    <creator>
      <creatorName>Palsson, Bernhard O.</creatorName>
      <givenName>Bernhard O.</givenName>
      <familyName>Palsson</familyName>
      <affiliation>Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA</affiliation>
    </creator>
    <creator>
      <creatorName>Mardinoglu, Adil</creatorName>
      <givenName>Adil</givenName>
      <familyName>Mardinoglu</familyName>
      <affiliation>Department of Protein Science, Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden</affiliation>
    </creator>
    <creator>
      <creatorName>Hansson, Lena</creatorName>
      <givenName>Lena</givenName>
      <familyName>Hansson</familyName>
      <affiliation>Novo Nordisk Research Centre Oxford, Oxford, UK</affiliation>
    </creator>
    <creator>
      <creatorName>Uhlén, Mathias</creatorName>
      <givenName>Mathias</givenName>
      <familyName>Uhlén</familyName>
      <affiliation>Department of Protein Science, Science for Life Laboratory, KTH–Royal Institute of Technology, Stockholm, Sweden</affiliation>
    </creator>
    <creator>
      <creatorName>Nielsen, Jens</creatorName>
      <givenName>Jens</givenName>
      <familyName>Nielsen</familyName>
      <affiliation>Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, Gothenburg, Sweden</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Supplementary data and scripts for "An Atlas of Human Metabolism"</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2019</publicationYear>
  <subjects>
    <subject>genome-scale metabolic model</subject>
    <subject>systems biology</subject>
    <subject>human metabolism</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2019-12-16</date>
  </dates>
  <language>en</language>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/3583004</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.3577466</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="http://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;This repository contains the models, data, and scripts associated with the publication &amp;quot;An Atlas of Human Metabolism&amp;quot;.&lt;/p&gt;

&lt;p&gt;The content is divided into three main directories, each containing their own README file containing instructions.&lt;/p&gt;

&lt;ol&gt;
	&lt;li&gt;tINIT_GEMs - Contains the genome-scale metabolic models (GEMs) generated in the study using the tINIT algorithm, as well as many scripts and datasets necessary to reproduce model generation, analyses, and figures.&lt;/li&gt;
	&lt;li&gt;ec_GEMs - Contains the enzyme-constrained models (ecGEMs) generated in the study using the GECKO framework, as well as many scripts and datasets necessary to reproduce model generation, analyses, and figures.&lt;/li&gt;
	&lt;li&gt;GEM_PRO - Contains the GEM-PRO dataframe with the protein structure information associated with the Human1 model.&lt;/li&gt;
&lt;/ol&gt;</description>
  </descriptions>
  <fundingReferences>
    <fundingReference>
      <funderName>National Institutes of Health</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/100000002</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/NIH/NATIONAL+CANCER+INSTITUTE/5F32CA220848-02/">5F32CA220848-02</awardNumber>
      <awardTitle>Deciphering the coupled roles of protein secretion and metabolism in cancer using an integrative omics approach</awardTitle>
    </fundingReference>
  </fundingReferences>
</resource>
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