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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{
  "inLanguage": {
    "alternateName": "eng", 
    "@type": "Language", 
    "name": "English"
  }, 
  "description": "<p>This repository contains the models, data, and scripts associated with the publication &quot;An Atlas of Human Metabolism&quot;.</p>\n\n<p>The content is divided into three main directories, each containing their own README file containing instructions.</p>\n\n<ol>\n\t<li>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.</li>\n\t<li>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.</li>\n\t<li>GEM_PRO - Contains the GEM-PRO dataframe with the protein structure information associated with the Human1 model.</li>\n</ol>", 
  "license": "http://creativecommons.org/licenses/by/4.0/legalcode", 
  "creator": [
    {
      "affiliation": "Department of Biology and Biological Engineering, Chalmers University of Technology, Kemiv\u00e4gen 10, Gothenburg, Sweden", 
      "@id": "https://orcid.org/0000-0001-8567-5960", 
      "@type": "Person", 
      "name": "Robinson, Jonathan L."
    }, 
    {
      "affiliation": "Department of Biology and Biological Engineering, Chalmers University of Technology, Kemiv\u00e4gen 10, Gothenburg, Sweden", 
      "@type": "Person", 
      "name": "Kocaba\u015f, P\u0131nar"
    }, 
    {
      "affiliation": "Department of Biology and Biological Engineering, Chalmers University of Technology, Kemiv\u00e4gen 10, Gothenburg, Sweden", 
      "@type": "Person", 
      "name": "Wang, Hao"
    }, 
    {
      "affiliation": "Department of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, Kemiv\u00e4gen 10, Gothenburg, Sweden", 
      "@type": "Person", 
      "name": "Cholley, Pierre-Etienne"
    }, 
    {
      "affiliation": "Department of Biology and Biological Engineering, Chalmers University of Technology, Kemiv\u00e4gen 10, Gothenburg, Sweden", 
      "@type": "Person", 
      "name": "Cook, Daniel"
    }, 
    {
      "affiliation": "Department of Biology and Biological Engineering, Chalmers University of Technology, Kemiv\u00e4gen 10, Gothenburg, Sweden", 
      "@type": "Person", 
      "name": "Nilsson, Avlant"
    }, 
    {
      "affiliation": "Department of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, Kemiv\u00e4gen 10, Gothenburg, Sweden", 
      "@type": "Person", 
      "name": "Anton, Mihail"
    }, 
    {
      "affiliation": "Department of Biology and Biological Engineering, Chalmers University of Technology, Kemiv\u00e4gen 10, Gothenburg, Sweden", 
      "@type": "Person", 
      "name": "Ferreira, Raphael"
    }, 
    {
      "affiliation": "Department of Biology and Biological Engineering, Chalmers University of Technology, Kemiv\u00e4gen 10, Gothenburg, Sweden", 
      "@type": "Person", 
      "name": "Domenzain, Iv\u00e1n"
    }, 
    {
      "affiliation": "Department of Biology and Biological Engineering, Chalmers University of Technology, Kemiv\u00e4gen 10, Gothenburg, Sweden", 
      "@type": "Person", 
      "name": "Billa, Virinchi"
    }, 
    {
      "affiliation": "Department of Biology and Biological Engineering, Chalmers University of Technology, Kemiv\u00e4gen 10, Gothenburg, Sweden", 
      "@type": "Person", 
      "name": "Limeta, Angelo"
    }, 
    {
      "affiliation": "Department of Biology and Biological Engineering, Chalmers University of Technology, Kemiv\u00e4gen 10, Gothenburg, Sweden", 
      "@type": "Person", 
      "name": "Hedin, Alex"
    }, 
    {
      "affiliation": "Department of Biology and Biological Engineering, Chalmers University of Technology, Kemiv\u00e4gen 10, Gothenburg, Sweden", 
      "@type": "Person", 
      "name": "Gustafsson, Johan"
    }, 
    {
      "affiliation": "Department of Biology and Biological Engineering, Chalmers University of Technology, Kemiv\u00e4gen 10, Gothenburg, Sweden", 
      "@type": "Person", 
      "name": "Kerkhoven, Eduard J."
    }, 
    {
      "affiliation": "Department of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, Kemiv\u00e4gen 10, Gothenburg, Sweden", 
      "@type": "Person", 
      "name": "Svensson, L. Thomas"
    }, 
    {
      "affiliation": "Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA", 
      "@type": "Person", 
      "name": "Palsson, Bernhard O."
    }, 
    {
      "affiliation": "Department of Protein Science, Science for Life Laboratory, KTH\u2013Royal Institute of Technology, Stockholm, Sweden", 
      "@type": "Person", 
      "name": "Mardinoglu, Adil"
    }, 
    {
      "affiliation": "Novo Nordisk Research Centre Oxford, Oxford, UK", 
      "@type": "Person", 
      "name": "Hansson, Lena"
    }, 
    {
      "affiliation": "Department of Protein Science, Science for Life Laboratory, KTH\u2013Royal Institute of Technology, Stockholm, Sweden", 
      "@type": "Person", 
      "name": "Uhl\u00e9n, Mathias"
    }, 
    {
      "affiliation": "Department of Biology and Biological Engineering, Chalmers University of Technology, Kemiv\u00e4gen 10, Gothenburg, Sweden", 
      "@type": "Person", 
      "name": "Nielsen, Jens"
    }
  ], 
  "url": "https://zenodo.org/record/3583004", 
  "datePublished": "2019-12-16", 
  "keywords": [
    "genome-scale metabolic model", 
    "systems biology", 
    "human metabolism"
  ], 
  "@context": "https://schema.org/", 
  "distribution": [
    {
      "contentUrl": "https://zenodo.org/api/files/4eb3906c-9c0b-4d35-9497-c8aa6d7f19c2/Human1_Publication_Data_Scripts.zip", 
      "encodingFormat": "zip", 
      "@type": "DataDownload"
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  ], 
  "identifier": "https://doi.org/10.5281/zenodo.3583004", 
  "@id": "https://doi.org/10.5281/zenodo.3583004", 
  "@type": "Dataset", 
  "name": "Supplementary data and scripts for \"An Atlas of Human Metabolism\""
}
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