code-of-conduct.html

<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

<meta charset="utf-8">
<meta name="generator" content="quarto-1.3.340">

<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">


<title>ProteomicsML – code_of_conduct</title>
<style>
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
div.columns{display: flex; gap: min(4vw, 1.5em);}
div.column{flex: auto; overflow-x: auto;}
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
ul.task-list{list-style: none;}
ul.task-list li input[type="checkbox"] {
  width: 0.8em;
  margin: 0 0.8em 0.2em -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */ 
  vertical-align: middle;
}
</style>


<script src="site_libs/quarto-nav/quarto-nav.js"></script>
<script src="site_libs/quarto-nav/headroom.min.js"></script>
<script src="site_libs/clipboard/clipboard.min.js"></script>
<script src="site_libs/quarto-search/autocomplete.umd.js"></script>
<script src="site_libs/quarto-search/fuse.min.js"></script>
<script src="site_libs/quarto-search/quarto-search.js"></script>
<meta name="quarto:offset" content="./">
<link href="./static/img/proteomicsml-icon.svg" rel="icon" type="image/svg+xml">
<script src="site_libs/cookie-consent/cookie-consent.js"></script>
<link href="site_libs/cookie-consent/cookie-consent.css" rel="stylesheet">
<script src="site_libs/quarto-html/quarto.js"></script>
<script src="site_libs/quarto-html/popper.min.js"></script>
<script src="site_libs/quarto-html/tippy.umd.min.js"></script>
<script src="site_libs/quarto-html/anchor.min.js"></script>
<link href="site_libs/quarto-html/tippy.css" rel="stylesheet">
<link href="site_libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles">
<script src="site_libs/bootstrap/bootstrap.min.js"></script>
<link href="site_libs/bootstrap/bootstrap-icons.css" rel="stylesheet">
<link href="site_libs/bootstrap/bootstrap.min.css" rel="stylesheet" id="quarto-bootstrap" data-mode="light">
<script id="quarto-search-options" type="application/json">{
  "location": "navbar",
  "copy-button": false,
  "collapse-after": 3,
  "panel-placement": "end",
  "type": "overlay",
  "limit": 20,
  "language": {
    "search-no-results-text": "No results",
    "search-matching-documents-text": "matching documents",
    "search-copy-link-title": "Copy link to search",
    "search-hide-matches-text": "Hide additional matches",
    "search-more-match-text": "more match in this document",
    "search-more-matches-text": "more matches in this document",
    "search-clear-button-title": "Clear",
    "search-detached-cancel-button-title": "Cancel",
    "search-submit-button-title": "Submit"
  }
}</script>
<script async="" src="https://www.googletagmanager.com/gtag/js?id=G-VVRMZHT2W2"></script>

<script type="text/plain" cookie-consent="tracking">

window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'G-VVRMZHT2W2', { 'anonymize_ip': true});
</script>

<script type="text/javascript" charset="UTF-8">
document.addEventListener('DOMContentLoaded', function () {
cookieconsent.run({
  "notice_banner_type":"interstitial",
  "consent_type":"express",
  "palette":"light",
  "language":"en",
  "page_load_consent_levels":["strictly-necessary"],
  "notice_banner_reject_button_hide":false,
  "preferences_center_close_button_hide":false,
  "website_name":""
  });
});
</script> 
  
<style>html{ scroll-behavior: smooth; }</style>
<script type="application/ld+json">
  {
    "@context": "https://schema.org/",
    "@type": "LearningResource",
    "@id": "https://proteomicsml.org/",
    "dct:conformsTo": {
      "http://purl.org/dc/terms/conformsTo": {
        "@id": "https://bioschemas.org/profiles/TrainingMaterial/1.0-RELEASE",
        "@type": "CreativeWork"
      }
    },
    "name": "ProteomicsML",
    "description": "ProteomicsML provides ready-made datasets for machine learning models accompanied by tutorials on how to work with even the most complex data types in the field of proteomics. The resource is set up to evolve together with the field, and we welcome everyone to contribute to the project by adding new datasets and accompanying notebooks.",
    "keywords": [
      "machine learning",
      "deep learning",
      "proteomics",
      "educational platform",
      "community platform",
      "bioinformatics",
      "detectability",
      "fragmentation",
      "retention time",
      "ion mobility"
    ],
    "about": [
      {
        "@type": "DefinedTerm",
        "@id": "http://edamontology.org/topic_0091",
        "inDefinedTermSet": "http://edamontology.org",
        "termCode": "topic_0091",
        "name": "bioinformatics",
        "url": "https://bioportal.bioontology.org/ontologies/EDAM/?p=classes&conceptid=http%3A%2F%2Fedamontology.org%2Ftopic_0091"
      },
      {
        "@type": "DefinedTerm",
        "@id": "http://edamontology.org/3474",
        "inDefinedTermSet": "http://edamontology.org",
        "termCode": "topic_3474",
        "name": "machine learning",
        "url": "https://bioportal.bioontology.org/ontologies/EDAM/?p=classes&conceptid=http%3A%2F%2Fedamontology.org%2Ftopic_3474"
      },
      {
        "@type": "DefinedTerm",
        "@id": "http://edamontology.org/0121",
        "inDefinedTermSet": "http://edamontology.org",
        "termCode": "topic_0121",
        "name": "proteomics",
        "url": "https://bioportal.bioontology.org/ontologies/EDAM/?p=classes&conceptid=http%3A%2F%2Fedamontology.org%2Ftopic_0121"
      },
      {
        "@type": "DefinedTerm",
        "@id": "http://edamontology.org/data_3670",
        "inDefinedTermSet": "http://edamontology.org",
        "termCode": "data_3670",
        "name": "Online course",
        "url": "https://bioportal.bioontology.org/ontologies/EDAM/?p=classes&conceptid=http%3A%2F%2Fedamontology.org%2Fdata_3670"
      },
      {
        "@type": "DefinedTerm",
        "@id": "http://edamontology.org/data_2536",
        "inDefinedTermSet": "http://edamontology.org",
        "termCode": "data_2536",
        "name": "Mass spectrometry data",
        "url": "https://bioportal.bioontology.org/ontologies/EDAM/?p=classes&conceptid=http%3A%2F%2Fedamontology.org%2Fdata_2536"
      }
    ],
    "abstract": "Data set acquisition and curation are often the most difficult and time-consuming parts of a machine learning endeavor. This is especially true for proteomics-based liquid chromatography (LC) coupled to mass spectrometry (MS) data sets, due to the high levels of data reduction that occur between raw data and machine learning-ready data. Since predictive proteomics is an emerging field, when predicting peptide behavior in LC-MS setups, each lab often uses unique and complex data processing pipelines in order to maximize performance, at the cost of accessibility and reproducibility. For this reason we introduce ProteomicsML, an online resource for proteomics-based data sets and tutorials across most of the currently explored physicochemical peptide properties. This community-driven resource makes it simple to access data in easy-to-process formats, and contains easy-to-follow tutorials that allow new users to interact with even the most advanced algorithms in the field. ProteomicsML provides data sets that are useful for comparing state-of-the-art machine learning algorithms, as well as providing introductory material for teachers and newcomers to the field alike. The platform is freely available at https://www.proteomicsml.org/, and we welcome the entire proteomics community to contribute to the project at https://github.com/ProteomicsML/ProteomicsML.",
    "audience": [
      {
        "@type": "Audience",
        "audienceType": "Students"
      },
      {
        "@type": "Audience",
        "audienceType": "PhD students"
      },
      {
        "@type": "Audience",
        "audienceType": "Postdoctoral researchers"
      }
    ],
    "competencyRequired": [
      "Basic python programming",
      "Machine learning basics",
      "Basic proteomics and mass spectrometry knowledge"
    ],
    "inLanguage": ["en-US"],
    "learningResourceType": ["tutorials"],
    "license": "https://spdx.org/licenses/CC-BY-4.0.html",
    "url": "https://proteomicsml.org/"
  }
</script>


<link rel="stylesheet" href="static/css/custom-styles.css">
</head>

<body class="nav-sidebar floating nav-fixed">

<div id="quarto-search-results"></div>
  <header id="quarto-header" class="headroom fixed-top">
    <nav class="navbar navbar-expand-lg navbar-dark ">
      <div class="navbar-container container-fluid">
      <div class="navbar-brand-container">
    <a href="./index.html" class="navbar-brand navbar-brand-logo">
    <img src="./static/img/proteomicsml-logo-inverse.svg" alt="ProteomicsML logo" class="navbar-logo">
    </a>
  </div>
            <div id="quarto-search" class="" title="Search"></div>
          <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarCollapse" aria-controls="navbarCollapse" aria-expanded="false" aria-label="Toggle navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
  <span class="navbar-toggler-icon"></span>
</button>
          <div class="collapse navbar-collapse" id="navbarCollapse">
            <ul class="navbar-nav navbar-nav-scroll me-auto">
  <li class="nav-item">
    <a class="nav-link active" href="./index.html" rel="" target="" aria-current="page">
 <span class="menu-text">Home</span></a>
  </li>  
  <li class="nav-item">
    <a class="nav-link" href="./publication.html" rel="" target="">
 <span class="menu-text">Publication</span></a>
  </li>  
  <li class="nav-item">
    <a class="nav-link" href="./tutorials/index.html" rel="" target="">
 <span class="menu-text">Tutorials</span></a>
  </li>  
  <li class="nav-item">
    <a class="nav-link" href="./datasets/index.html" rel="" target="">
 <span class="menu-text">Datasets</span></a>
  </li>  
</ul>
            <ul class="navbar-nav navbar-nav-scroll ms-auto">
  <li class="nav-item">
    <a class="nav-link" href="./contributing.html" rel="" target="">
 <span class="menu-text">Contributing</span></a>
  </li>  
  <li class="nav-item">
    <a class="nav-link" href="./code-of-conduct.html" rel="" target="">
 <span class="menu-text">Code of Conduct</span></a>
  </li>  
  <li class="nav-item compact">
    <a class="nav-link" href="https://github.com/ProteomicsML" rel="" target=""><i class="bi bi-github" role="img" aria-label="GitHub">
</i> 
 <span class="menu-text"></span></a>
  </li>  
  <li class="nav-item compact">
    <a class="nav-link" href="https://twitter.com/ProteomicsML" rel="" target=""><i class="bi bi-twitter" role="img" aria-label="Twitter">
</i> 
 <span class="menu-text"></span></a>
  </li>  
</ul>
            <div class="quarto-navbar-tools">
</div>
          </div> <!-- /navcollapse -->
      </div> <!-- /container-fluid -->
    </nav>
  <nav class="quarto-secondary-nav">
    <div class="container-fluid d-flex">
      <button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
        <i class="bi bi-layout-text-sidebar-reverse"></i>
      </button>
      <nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./code-of-conduct.html">Code of Conduct</a></li></ol></nav>
      <a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">      
      </a>
    </div>
  </nav>
</header>
<!-- content -->
<div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article page-navbar">
<!-- sidebar -->
  <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation floating overflow-auto">
    <div class="sidebar-menu-container"> 
    <ul class="list-unstyled mt-1">
        <li class="sidebar-item">
  <div class="sidebar-item-container"> 
  <a href="./index.html" class="sidebar-item-text sidebar-link">
 <span class="menu-text">Home</span></a>
  </div>
</li>
        <li class="sidebar-item">
  <div class="sidebar-item-container"> 
  <a href="./publication.html" class="sidebar-item-text sidebar-link">
 <span class="menu-text">Publication</span></a>
  </div>
</li>
        <li class="sidebar-item sidebar-item-section">
      <div class="sidebar-item-container"> 
            <a href="./tutorials/index.html" class="sidebar-item-text sidebar-link">
 <span class="menu-text">Tutorials</span></a>
          <a class="sidebar-item-toggle text-start collapsed" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-1" aria-expanded="false" aria-label="Toggle section">
            <i class="bi bi-chevron-right ms-2"></i>
          </a> 
      </div>
      <ul id="quarto-sidebar-section-1" class="collapse list-unstyled sidebar-section depth1 ">  
          <li class="sidebar-item sidebar-item-section">
      <div class="sidebar-item-container"> 
            <a href="./tutorials/ionmobility/index.html" class="sidebar-item-text sidebar-link">
 <span class="menu-text">Ion mobility</span></a>
          <a class="sidebar-item-toggle text-start collapsed" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-2" aria-expanded="false" aria-label="Toggle section">
            <i class="bi bi-chevron-right ms-2"></i>
          </a> 
      </div>
      <ul id="quarto-sidebar-section-2" class="collapse list-unstyled sidebar-section depth2 ">  
          <li class="sidebar-item">
  <div class="sidebar-item-container"> 
  <a href="./tutorials/ionmobility/meier-tims-ccs.html" class="sidebar-item-text sidebar-link">
 <span class="menu-text">Predicting CCS values for TIMS data</span></a>
  </div>
</li>
      </ul>
  </li>
          <li class="sidebar-item sidebar-item-section">
      <div class="sidebar-item-container"> 
            <a href="./tutorials/fragmentation/index.html" class="sidebar-item-text sidebar-link">
 <span class="menu-text">Fragmentation</span></a>
          <a class="sidebar-item-toggle text-start collapsed" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-3" aria-expanded="false" aria-label="Toggle section">
            <i class="bi bi-chevron-right ms-2"></i>
          </a> 
      </div>
      <ul id="quarto-sidebar-section-3" class="collapse list-unstyled sidebar-section depth2 ">  
          <li class="sidebar-item">
  <div class="sidebar-item-container"> 
  <a href="./tutorials/fragmentation/nist-1-parsing-spectral-library.html" class="sidebar-item-text sidebar-link">
 <span class="menu-text">NIST (part 1): Preparing a spectral library for ML</span></a>
  </div>
</li>
          <li class="sidebar-item">
  <div class="sidebar-item-container"> 
  <a href="./tutorials/fragmentation/nist-2-traditional-ml-gradient-boosting.html" class="sidebar-item-text sidebar-link">
 <span class="menu-text">NIST (part 2): Traditional ML: Gradient boosting</span></a>
  </div>
</li>
          <li class="sidebar-item">
  <div class="sidebar-item-container"> 
  <a href="./tutorials/fragmentation/preannotated-prosit.html" class="sidebar-item-text sidebar-link">
 <span class="menu-text">Prosit-style GRU with pre-annotated ProteomeTools data</span></a>
  </div>
</li>
          <li class="sidebar-item">
  <div class="sidebar-item-container"> 
  <a href="./tutorials/fragmentation/raw-to-prosit.html" class="sidebar-item-text sidebar-link">
 <span class="menu-text">Raw file processing with PROSIT style annotation</span></a>
  </div>
</li>
      </ul>
  </li>
          <li class="sidebar-item sidebar-item-section">
      <div class="sidebar-item-container"> 
            <a href="./tutorials/detectability/index.html" class="sidebar-item-text sidebar-link">
 <span class="menu-text">Detectability</span></a>
          <a class="sidebar-item-toggle text-start collapsed" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-4" aria-expanded="false" aria-label="Toggle section">
            <i class="bi bi-chevron-right ms-2"></i>
          </a> 
      </div>
      <ul id="quarto-sidebar-section-4" class="collapse list-unstyled sidebar-section depth2 ">  
          <li class="sidebar-item">
  <div class="sidebar-item-container"> 
  <a href="./tutorials/detectability/modeling-protein-detectability.html" class="sidebar-item-text sidebar-link">
 <span class="menu-text">Modelling protein detectability with an MLP</span></a>
  </div>
</li>
      </ul>
  </li>
          <li class="sidebar-item sidebar-item-section">
      <div class="sidebar-item-container"> 
            <a href="./tutorials/retentiontime/index.html" class="sidebar-item-text sidebar-link">
 <span class="menu-text">Retention time</span></a>
          <a class="sidebar-item-toggle text-start collapsed" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-5" aria-expanded="false" aria-label="Toggle section">
            <i class="bi bi-chevron-right ms-2"></i>
          </a> 
      </div>
      <ul id="quarto-sidebar-section-5" class="collapse list-unstyled sidebar-section depth2 ">  
          <li class="sidebar-item">
  <div class="sidebar-item-container"> 
  <a href="./tutorials/retentiontime/deeplc-transfer-learning.html" class="sidebar-item-text sidebar-link">
 <span class="menu-text">Transfer learning with DeepLC</span></a>
  </div>
</li>
          <li class="sidebar-item">
  <div class="sidebar-item-container"> 
  <a href="./tutorials/retentiontime/dlomix-prosit-rt.html" class="sidebar-item-text sidebar-link">
 <span class="menu-text">DLOmix embedding of Prosit model on ProteomeTools data</span></a>
  </div>
</li>
          <li class="sidebar-item">
  <div class="sidebar-item-container"> 
  <a href="./tutorials/retentiontime/manual-prosit-rt.html" class="sidebar-item-text sidebar-link">
 <span class="menu-text">Manual embedding of Bi-LSTM model on ProteomeTools data</span></a>
  </div>
</li>
          <li class="sidebar-item">
  <div class="sidebar-item-container"> 
  <a href="./tutorials/retentiontime/mq-evidence-to-ml.html" class="sidebar-item-text sidebar-link">
 <span class="menu-text">Preparing a retention time data set for machine learning</span></a>
  </div>
</li>
      </ul>
  </li>
      </ul>
  </li>
        <li class="sidebar-item sidebar-item-section">
      <div class="sidebar-item-container"> 
            <a href="./datasets/index.html" class="sidebar-item-text sidebar-link">
 <span class="menu-text">Datasets</span></a>
          <a class="sidebar-item-toggle text-start collapsed" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-6" aria-expanded="false" aria-label="Toggle section">
            <i class="bi bi-chevron-right ms-2"></i>
          </a> 
      </div>
      <ul id="quarto-sidebar-section-6" class="collapse list-unstyled sidebar-section depth1 ">  
          <li class="sidebar-item sidebar-item-section">
      <div class="sidebar-item-container"> 
            <a class="sidebar-item-text sidebar-link text-start collapsed" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="false">
 <span class="menu-text">Ion mobility</span></a>
          <a class="sidebar-item-toggle text-start collapsed" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-7" aria-expanded="false" aria-label="Toggle section">
            <i class="bi bi-chevron-right ms-2"></i>
          </a> 
      </div>
      <ul id="quarto-sidebar-section-7" class="collapse list-unstyled sidebar-section depth2 ">  
          <li class="sidebar-item">
  <div class="sidebar-item-container"> 
  <a href="./datasets/ionmobility/Meier_TIMS.html" class="sidebar-item-text sidebar-link">
 <span class="menu-text">Meier et al.&nbsp;TIMS</span></a>
  </div>
</li>
          <li class="sidebar-item">
  <div class="sidebar-item-container"> 
  <a href="./datasets/ionmobility/VanPuyvelde_TWIMS.html" class="sidebar-item-text sidebar-link">
 <span class="menu-text">Van Puyvelde et al.&nbsp;TWIMS</span></a>
  </div>
</li>
      </ul>
  </li>
          <li class="sidebar-item sidebar-item-section">
      <div class="sidebar-item-container"> 
            <a class="sidebar-item-text sidebar-link text-start collapsed" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="false">
 <span class="menu-text">Fragmentation</span></a>
          <a class="sidebar-item-toggle text-start collapsed" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-8" aria-expanded="false" aria-label="Toggle section">
            <i class="bi bi-chevron-right ms-2"></i>
          </a> 
      </div>
      <ul id="quarto-sidebar-section-8" class="collapse list-unstyled sidebar-section depth2 ">  
          <li class="sidebar-item">
  <div class="sidebar-item-container"> 
  <a href="./datasets/fragmentation/nist.html" class="sidebar-item-text sidebar-link">
 <span class="menu-text">NIST Peptide libraries</span></a>
  </div>
</li>
          <li class="sidebar-item">
  <div class="sidebar-item-container"> 
  <a href="./datasets/fragmentation/ProteomeTools_FI.html" class="sidebar-item-text sidebar-link">
 <span class="menu-text">ProteomeTools</span></a>
  </div>
</li>
      </ul>
  </li>
          <li class="sidebar-item sidebar-item-section">
      <div class="sidebar-item-container"> 
            <a class="sidebar-item-text sidebar-link text-start collapsed" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-9" aria-expanded="false">
 <span class="menu-text">Detectability</span></a>
          <a class="sidebar-item-toggle text-start collapsed" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-9" aria-expanded="false" aria-label="Toggle section">
            <i class="bi bi-chevron-right ms-2"></i>
          </a> 
      </div>
      <ul id="quarto-sidebar-section-9" class="collapse list-unstyled sidebar-section depth2 ">  
          <li class="sidebar-item">
  <div class="sidebar-item-container"> 
  <a href="./datasets/detectability/ArabidopsisLightDarkProteome.html" class="sidebar-item-text sidebar-link">
 <span class="menu-text">Arabidopsis PeptideAtlas Light and Dark Proteome</span></a>
  </div>
</li>
      </ul>
  </li>
          <li class="sidebar-item sidebar-item-section">
      <div class="sidebar-item-container"> 
            <a class="sidebar-item-text sidebar-link text-start collapsed" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-10" aria-expanded="false">
 <span class="menu-text">Retention time</span></a>
          <a class="sidebar-item-toggle text-start collapsed" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar-section-10" aria-expanded="false" aria-label="Toggle section">
            <i class="bi bi-chevron-right ms-2"></i>
          </a> 
      </div>
      <ul id="quarto-sidebar-section-10" class="collapse list-unstyled sidebar-section depth2 ">  
          <li class="sidebar-item">
  <div class="sidebar-item-container"> 
  <a href="./datasets/retentiontime/DLOmix_RT.html" class="sidebar-item-text sidebar-link">
 <span class="menu-text">DLOmix</span></a>
  </div>
</li>
          <li class="sidebar-item">
  <div class="sidebar-item-container"> 
  <a href="./datasets/retentiontime/ProteomeTools_RT.html" class="sidebar-item-text sidebar-link">
 <span class="menu-text">ProteomeTools</span></a>
  </div>
</li>
          <li class="sidebar-item">
  <div class="sidebar-item-container"> 
  <a href="./datasets/retentiontime/PXD028248_RT.html" class="sidebar-item-text sidebar-link">
 <span class="menu-text">PXD028248</span></a>
  </div>
</li>
      </ul>
  </li>
      </ul>
  </li>
        <li class="sidebar-item">
  <div class="sidebar-item-container"> 
  <a href="./contributing.html" class="sidebar-item-text sidebar-link">
 <span class="menu-text">Contributing</span></a>
  </div>
</li>
        <li class="sidebar-item">
  <div class="sidebar-item-container"> 
  <a href="./code-of-conduct.html" class="sidebar-item-text sidebar-link active">
 <span class="menu-text">Code of Conduct</span></a>
  </div>
</li>
    </ul>
    </div>
</nav>
<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
<!-- margin-sidebar -->
    <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
        <nav id="TOC" role="doc-toc" class="toc-active">
    <h2 id="toc-title">On this page</h2>
   
  <ul>
  <li><a href="#contributor-covenant-code-of-conduct" id="toc-contributor-covenant-code-of-conduct" class="nav-link active" data-scroll-target="#contributor-covenant-code-of-conduct">Contributor Covenant Code of Conduct</a>
  <ul>
  <li><a href="#our-pledge" id="toc-our-pledge" class="nav-link" data-scroll-target="#our-pledge">Our Pledge</a></li>
  <li><a href="#our-standards" id="toc-our-standards" class="nav-link" data-scroll-target="#our-standards">Our Standards</a></li>
  <li><a href="#enforcement-responsibilities" id="toc-enforcement-responsibilities" class="nav-link" data-scroll-target="#enforcement-responsibilities">Enforcement Responsibilities</a></li>
  <li><a href="#scope" id="toc-scope" class="nav-link" data-scroll-target="#scope">Scope</a></li>
  <li><a href="#enforcement" id="toc-enforcement" class="nav-link" data-scroll-target="#enforcement">Enforcement</a></li>
  <li><a href="#enforcement-guidelines" id="toc-enforcement-guidelines" class="nav-link" data-scroll-target="#enforcement-guidelines">Enforcement Guidelines</a>
  <ul class="collapse">
  <li><a href="#correction" id="toc-correction" class="nav-link" data-scroll-target="#correction">1. Correction</a></li>
  <li><a href="#warning" id="toc-warning" class="nav-link" data-scroll-target="#warning">2. Warning</a></li>
  <li><a href="#temporary-ban" id="toc-temporary-ban" class="nav-link" data-scroll-target="#temporary-ban">3. Temporary Ban</a></li>
  <li><a href="#permanent-ban" id="toc-permanent-ban" class="nav-link" data-scroll-target="#permanent-ban">4. Permanent Ban</a></li>
  </ul></li>
  <li><a href="#attribution" id="toc-attribution" class="nav-link" data-scroll-target="#attribution">Attribution</a></li>
  </ul></li>
  </ul>
<div class="toc-actions"><div><i class="bi bi-github"></i></div><div class="action-links"><p><a href="https://github.com/ProteomicsML/ProteomicsML/blob/main/CODE_OF_CONDUCT.md" class="toc-action">View source</a></p><p><a href="https://github.com/ProteomicsML/ProteomicsML/edit/main/CODE_OF_CONDUCT.md" class="toc-action">Edit this page</a></p></div></div></nav>
    </div>
<!-- main -->
<main class="content" id="quarto-document-content">


<section id="contributor-covenant-code-of-conduct" class="level1">
<h1>Contributor Covenant Code of Conduct</h1>
<section id="our-pledge" class="level2">
<h2 class="anchored" data-anchor-id="our-pledge">Our Pledge</h2>
<p>We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, religion, or sexual identity and orientation.</p>
<p>We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community.</p>
</section>
<section id="our-standards" class="level2">
<h2 class="anchored" data-anchor-id="our-standards">Our Standards</h2>
<p>Examples of behavior that contributes to a positive environment for our community include:</p>
<ul>
<li>Demonstrating empathy and kindness toward other people</li>
<li>Being respectful of differing opinions, viewpoints, and experiences</li>
<li>Giving and gracefully accepting constructive feedback</li>
<li>Accepting responsibility and apologizing to those affected by our mistakes, and learning from the experience</li>
<li>Focusing on what is best not just for us as individuals, but for the overall community</li>
</ul>
<p>Examples of unacceptable behavior include:</p>
<ul>
<li>The use of sexualized language or imagery, and sexual attention or advances of any kind</li>
<li>Trolling, insulting or derogatory comments, and personal or political attacks</li>
<li>Public or private harassment</li>
<li>Publishing others’ private information, such as a physical or email address, without their explicit permission</li>
<li>Other conduct which could reasonably be considered inappropriate in a professional setting</li>
</ul>
</section>
<section id="enforcement-responsibilities" class="level2">
<h2 class="anchored" data-anchor-id="enforcement-responsibilities">Enforcement Responsibilities</h2>
<p>Community leaders are responsible for clarifying and enforcing our standards of acceptable behavior and will take appropriate and fair corrective action in response to any behavior that they deem inappropriate, threatening, offensive, or harmful.</p>
<p>Community leaders have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, and will communicate reasons for moderation decisions when appropriate.</p>
</section>
<section id="scope" class="level2">
<h2 class="anchored" data-anchor-id="scope">Scope</h2>
<p>This Code of Conduct applies within all community spaces, and also applies when an individual is officially representing the community in public spaces. Examples of representing our community include using an official e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event.</p>
</section>
<section id="enforcement" class="level2">
<h2 class="anchored" data-anchor-id="enforcement">Enforcement</h2>
<p>Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to the community leaders responsible for enforcement at <a href="mailto:eric.deutsch@isbscience.org">eric.deutsch@isbscience.org</a>. All complaints will be reviewed and investigated promptly and fairly.</p>
<p>All community leaders are obligated to respect the privacy and security of the reporter of any incident.</p>
</section>
<section id="enforcement-guidelines" class="level2">
<h2 class="anchored" data-anchor-id="enforcement-guidelines">Enforcement Guidelines</h2>
<p>Community leaders will follow these Community Impact Guidelines in determining the consequences for any action they deem in violation of this Code of Conduct:</p>
<section id="correction" class="level3">
<h3 class="anchored" data-anchor-id="correction">1. Correction</h3>
<p><strong>Community Impact</strong>: Use of inappropriate language or other behavior deemed unprofessional or unwelcome in the community.</p>
<p><strong>Consequence</strong>: A private, written warning from community leaders, providing clarity around the nature of the violation and an explanation of why the behavior was inappropriate. A public apology may be requested.</p>
</section>
<section id="warning" class="level3">
<h3 class="anchored" data-anchor-id="warning">2. Warning</h3>
<p><strong>Community Impact</strong>: A violation through a single incident or series of actions.</p>
<p><strong>Consequence</strong>: A warning with consequences for continued behavior. No interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, for a specified period of time. This includes avoiding interactions in community spaces as well as external channels like social media. Violating these terms may lead to a temporary or permanent ban.</p>
</section>
<section id="temporary-ban" class="level3">
<h3 class="anchored" data-anchor-id="temporary-ban">3. Temporary Ban</h3>
<p><strong>Community Impact</strong>: A serious violation of community standards, including sustained inappropriate behavior.</p>
<p><strong>Consequence</strong>: A temporary ban from any sort of interaction or public communication with the community for a specified period of time. No public or private interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, is allowed during this period. Violating these terms may lead to a permanent ban.</p>
</section>
<section id="permanent-ban" class="level3">
<h3 class="anchored" data-anchor-id="permanent-ban">4. Permanent Ban</h3>
<p><strong>Community Impact</strong>: Demonstrating a pattern of violation of community standards, including sustained inappropriate behavior, harassment of an individual, or aggression toward or disparagement of classes of individuals.</p>
<p><strong>Consequence</strong>: A permanent ban from any sort of public interaction within the community.</p>
</section>
</section>
<section id="attribution" class="level2">
<h2 class="anchored" data-anchor-id="attribution">Attribution</h2>
<p>This Code of Conduct is adapted from the <a href="https://www.contributor-covenant.org">Contributor Covenant</a>, version 2.0, available at <a href="https://www.contributor-covenant.org/version/2/0/code_of_conduct.html">https://www.contributor-covenant.org/version/2/0/code_of_conduct.html</a>.</p>
<p>Community Impact Guidelines were inspired by <a href="https://github.com/mozilla/diversity">Mozilla’s code of conduct enforcement ladder</a>.</p>
<p>For answers to common questions about this code of conduct, see the FAQ at <a href="https://www.contributor-covenant.org/faq">https://www.contributor-covenant.org/faq</a>. Translations are available at <a href="https://www.contributor-covenant.org/translations">https://www.contributor-covenant.org/translations</a>.</p>


</section>
</section>

</main> <!-- /main -->
<script id="quarto-html-after-body" type="application/javascript">
window.document.addEventListener("DOMContentLoaded", function (event) {
  const toggleBodyColorMode = (bsSheetEl) => {
    const mode = bsSheetEl.getAttribute("data-mode");
    const bodyEl = window.document.querySelector("body");
    if (mode === "dark") {
      bodyEl.classList.add("quarto-dark");
      bodyEl.classList.remove("quarto-light");
    } else {
      bodyEl.classList.add("quarto-light");
      bodyEl.classList.remove("quarto-dark");
    }
  }
  const toggleBodyColorPrimary = () => {
    const bsSheetEl = window.document.querySelector("link#quarto-bootstrap");
    if (bsSheetEl) {
      toggleBodyColorMode(bsSheetEl);
    }
  }
  toggleBodyColorPrimary();  
  const icon = "";
  const anchorJS = new window.AnchorJS();
  anchorJS.options = {
    placement: 'right',
    icon: icon
  };
  anchorJS.add('.anchored');
  const isCodeAnnotation = (el) => {
    for (const clz of el.classList) {
      if (clz.startsWith('code-annotation-')) {                     
        return true;
      }
    }
    return false;
  }
  const clipboard = new window.ClipboardJS('.code-copy-button', {
    text: function(trigger) {
      const codeEl = trigger.previousElementSibling.cloneNode(true);
      for (const childEl of codeEl.children) {
        if (isCodeAnnotation(childEl)) {
          childEl.remove();
        }
      }
      return codeEl.innerText;
    }
  });
  clipboard.on('success', function(e) {
    // button target
    const button = e.trigger;
    // don't keep focus
    button.blur();
    // flash "checked"
    button.classList.add('code-copy-button-checked');
    var currentTitle = button.getAttribute("title");
    button.setAttribute("title", "Copied!");
    let tooltip;
    if (window.bootstrap) {
      button.setAttribute("data-bs-toggle", "tooltip");
      button.setAttribute("data-bs-placement", "left");
      button.setAttribute("data-bs-title", "Copied!");
      tooltip = new bootstrap.Tooltip(button, 
        { trigger: "manual", 
          customClass: "code-copy-button-tooltip",
          offset: [0, -8]});
      tooltip.show();    
    }
    setTimeout(function() {
      if (tooltip) {
        tooltip.hide();
        button.removeAttribute("data-bs-title");
        button.removeAttribute("data-bs-toggle");
        button.removeAttribute("data-bs-placement");
      }
      button.setAttribute("title", currentTitle);
      button.classList.remove('code-copy-button-checked');
    }, 1000);
    // clear code selection
    e.clearSelection();
  });
  function tippyHover(el, contentFn) {
    const config = {
      allowHTML: true,
      content: contentFn,
      maxWidth: 500,
      delay: 100,
      arrow: false,
      appendTo: function(el) {
          return el.parentElement;
      },
      interactive: true,
      interactiveBorder: 10,
      theme: 'quarto',
      placement: 'bottom-start'
    };
    window.tippy(el, config); 
  }
  const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]');
  for (var i=0; i<noterefs.length; i++) {
    const ref = noterefs[i];
    tippyHover(ref, function() {
      // use id or data attribute instead here
      let href = ref.getAttribute('data-footnote-href') || ref.getAttribute('href');
      try { href = new URL(href).hash; } catch {}
      const id = href.replace(/^#\/?/, "");
      const note = window.document.getElementById(id);
      return note.innerHTML;
    });
  }
      let selectedAnnoteEl;
      const selectorForAnnotation = ( cell, annotation) => {
        let cellAttr = 'data-code-cell="' + cell + '"';
        let lineAttr = 'data-code-annotation="' +  annotation + '"';
        const selector = 'span[' + cellAttr + '][' + lineAttr + ']';
        return selector;
      }
      const selectCodeLines = (annoteEl) => {
        const doc = window.document;
        const targetCell = annoteEl.getAttribute("data-target-cell");
        const targetAnnotation = annoteEl.getAttribute("data-target-annotation");
        const annoteSpan = window.document.querySelector(selectorForAnnotation(targetCell, targetAnnotation));
        const lines = annoteSpan.getAttribute("data-code-lines").split(",");
        const lineIds = lines.map((line) => {
          return targetCell + "-" + line;
        })
        let top = null;
        let height = null;
        let parent = null;
        if (lineIds.length > 0) {
            //compute the position of the single el (top and bottom and make a div)
            const el = window.document.getElementById(lineIds[0]);
            top = el.offsetTop;
            height = el.offsetHeight;
            parent = el.parentElement.parentElement;
          if (lineIds.length > 1) {
            const lastEl = window.document.getElementById(lineIds[lineIds.length - 1]);
            const bottom = lastEl.offsetTop + lastEl.offsetHeight;
            height = bottom - top;
          }
          if (top !== null && height !== null && parent !== null) {
            // cook up a div (if necessary) and position it 
            let div = window.document.getElementById("code-annotation-line-highlight");
            if (div === null) {
              div = window.document.createElement("div");
              div.setAttribute("id", "code-annotation-line-highlight");
              div.style.position = 'absolute';
              parent.appendChild(div);
            }
            div.style.top = top - 2 + "px";
            div.style.height = height + 4 + "px";
            let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter");
            if (gutterDiv === null) {
              gutterDiv = window.document.createElement("div");
              gutterDiv.setAttribute("id", "code-annotation-line-highlight-gutter");
              gutterDiv.style.position = 'absolute';
              const codeCell = window.document.getElementById(targetCell);
              const gutter = codeCell.querySelector('.code-annotation-gutter');
              gutter.appendChild(gutterDiv);
            }
            gutterDiv.style.top = top - 2 + "px";
            gutterDiv.style.height = height + 4 + "px";
          }
          selectedAnnoteEl = annoteEl;
        }
      };
      const unselectCodeLines = () => {
        const elementsIds = ["code-annotation-line-highlight", "code-annotation-line-highlight-gutter"];
        elementsIds.forEach((elId) => {
          const div = window.document.getElementById(elId);
          if (div) {
            div.remove();
          }
        });
        selectedAnnoteEl = undefined;
      };
      // Attach click handler to the DT
      const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
      for (const annoteDlNode of annoteDls) {
        annoteDlNode.addEventListener('click', (event) => {
          const clickedEl = event.target;
          if (clickedEl !== selectedAnnoteEl) {
            unselectCodeLines();
            const activeEl = window.document.querySelector('dt[data-target-cell].code-annotation-active');
            if (activeEl) {
              activeEl.classList.remove('code-annotation-active');
            }
            selectCodeLines(clickedEl);
            clickedEl.classList.add('code-annotation-active');
          } else {
            // Unselect the line
            unselectCodeLines();
            clickedEl.classList.remove('code-annotation-active');
          }
        });
      }
  const findCites = (el) => {
    const parentEl = el.parentElement;
    if (parentEl) {
      const cites = parentEl.dataset.cites;
      if (cites) {
        return {
          el,
          cites: cites.split(' ')
        };
      } else {
        return findCites(el.parentElement)
      }
    } else {
      return undefined;
    }
  };
  var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]');
  for (var i=0; i<bibliorefs.length; i++) {
    const ref = bibliorefs[i];
    const citeInfo = findCites(ref);
    if (citeInfo) {
      tippyHover(citeInfo.el, function() {
        var popup = window.document.createElement('div');
        citeInfo.cites.forEach(function(cite) {
          var citeDiv = window.document.createElement('div');
          citeDiv.classList.add('hanging-indent');
          citeDiv.classList.add('csl-entry');
          var biblioDiv = window.document.getElementById('ref-' + cite);
          if (biblioDiv) {
            citeDiv.innerHTML = biblioDiv.innerHTML;
          }
          popup.appendChild(citeDiv);
        });
        return popup.innerHTML;
      });
    }
  }
    var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
      var filterRegex = new RegExp("https:\/\/www\.proteomicsml\.org");
    var isInternal = (href) => {
        return filterRegex.test(href) || localhostRegex.test(href);
    }
    // Inspect non-navigation links and adorn them if external
 	var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item)');
    for (var i=0; i<links.length; i++) {
      const link = links[i];
      if (!isInternal(link.href)) {
          // target, if specified
          link.setAttribute("target", "_blank");
      }
    }
});
</script>
</div> <!-- /content -->
<footer class="footer">
  <div class="nav-footer">
    <div class="nav-footer-left">
      &nbsp;
    </div>   
    <div class="nav-footer-center"><small>This work is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons CC BY 4.0</a> license.</small><div class="cookie-consent-footer"><a href="#" id="open_preferences_center">Cookie Preferences</a></div></div>
    <div class="nav-footer-right">
      &nbsp;
    </div>
  </div>
</footer>


<script src="site_libs/quarto-html/zenscroll-min.js"></script>
</body></html>