forked from enviPath/enviPy
204 lines
9.9 KiB
HTML
204 lines
9.9 KiB
HTML
{% extends "framework_modern.html" %}
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{% load static %}
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{% block main_content %}
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<div class="max-w-4xl mx-auto px-4 py-8">
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<!-- Breadcrumbs -->
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<div class="text-sm breadcrumbs mb-4">
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<ul>
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<li><a href="/">Home</a></li>
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<li>How to Cite enviPath</li>
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</ul>
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</div>
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<!-- Main Content -->
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<div class="bg-base-100 shadow-xl rounded-lg p-8">
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<h1 class="text-4xl font-bold mb-6">How to Cite enviPath</h1>
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<div class="prose max-w-none">
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<p class="text-lg mb-6">
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If you use enviPath in your research, please cite our work. Citations help us demonstrate the
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impact of our platform and support continued development and maintenance.
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</p>
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<div class="alert alert-info mb-8">
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<svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" class="stroke-current shrink-0 w-6 h-6">
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<path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M13 16h-1v-4h-1m1-4h.01M21 12a9 9 0 11-18 0 9 9 0 0118 0z"></path>
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</svg>
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<div>
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<h3 class="font-bold">Quick Reference</h3>
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<div class="text-sm">The citation depends on which specific tools or models you used. Please cite the relevant publications below.</div>
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</div>
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</div>
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<h2 class="text-2xl font-semibold mt-8 mb-4">Main Platform Citation</h2>
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<p class="mb-4">
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If you use the enviPath platform in general, please cite:
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</p>
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<div class="card bg-base-200 mb-6">
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<div class="card-body">
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<h3 class="font-semibold mb-2">enviPath - The Environmental Contaminant Biotransformation Pathway Resource</h3>
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<p class="text-sm mb-4">
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<strong>Authors:</strong> Wicker, J., Lorsbach, T., Gütlein, M., Schmid, E., Latino, D.,
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Kramer, S., Fenner, K.<br>
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<strong>Journal:</strong> Nucleic Acids Research, 44(D1), D502-D508<br>
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<strong>Year:</strong> 2016<br>
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<strong>DOI:</strong> <a href="https://doi.org/10.1093/nar/gkv1229" target="_blank" class="link link-primary">10.1093/nar/gkv1229</a>
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</p>
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<div class="collapse collapse-arrow bg-base-300">
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<input type="checkbox" />
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<div class="collapse-title font-medium text-sm">
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Show BibTeX
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</div>
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<div class="collapse-content">
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<pre class="text-xs overflow-x-auto"><code>@article{wicker2016envipath,
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title={enviPath--the environmental contaminant biotransformation pathway resource},
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author={Wicker, J{\"o}rg and Lorsbach, Tim and G{\"u}tlein, Martin and Schmid, Emanuel and Latino, Diogo and Kramer, Stefan and Fenner, Kathrin},
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journal={Nucleic Acids Research},
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volume={44},
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number={D1},
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pages={D502--D508},
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year={2016},
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publisher={Oxford University Press},
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doi={10.1093/nar/gkv1229}
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}</code></pre>
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</div>
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</div>
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</div>
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</div>
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<h2 class="text-2xl font-semibold mt-8 mb-4">Pathway Prediction System</h2>
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<p class="mb-4">
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If you use the pathway prediction functionality, please also cite:
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</p>
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<div class="card bg-base-200 mb-6">
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<div class="card-body">
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<h3 class="font-semibold mb-2">Predicting Biodegradation Pathways Using a Hybrid Relative Reasoning Model</h3>
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<p class="text-sm mb-4">
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<strong>Authors:</strong> Wicker, J., Fenner, K., Ellis, L., Kramer, S.<br>
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<strong>Journal:</strong> Biotechnology and Bioengineering, 110(3), 837-846<br>
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<strong>Year:</strong> 2013<br>
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<strong>DOI:</strong> <a href="https://doi.org/10.1002/bit.24744" target="_blank" class="link link-primary">10.1002/bit.24744</a>
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</p>
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<div class="collapse collapse-arrow bg-base-300">
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<input type="checkbox" />
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<div class="collapse-title font-medium text-sm">
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Show BibTeX
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</div>
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<div class="collapse-content">
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<pre class="text-xs overflow-x-auto"><code>@article{wicker2013predicting,
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title={Predicting biodegradation pathways using a hybrid relative reasoning model},
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author={Wicker, J{\"o}rg and Fenner, Kathrin and Ellis, Lynda and Kramer, Stefan},
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journal={Biotechnology and Bioengineering},
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volume={110},
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number={3},
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pages={837--846},
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year={2013},
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publisher={Wiley Online Library},
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doi={10.1002/bit.24744}
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}</code></pre>
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</div>
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</div>
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</div>
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</div>
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<h2 class="text-2xl font-semibold mt-8 mb-4">Machine Learning Models</h2>
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<h3 class="text-xl font-semibold mt-6 mb-3">enviPath-Transformer (Latest ML Model)</h3>
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<div class="card bg-base-200 mb-6">
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<div class="card-body">
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<p class="text-sm mb-2">
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If you use the Transformer-based prediction model, please cite:
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</p>
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<p class="text-sm mb-4">
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<strong>Authors:</strong> Probst, D., Manica, M., Nana Teukam, Y.G., Castrogiovanni, A.,
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Paratore, F., Laino, T.<br>
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<strong>Journal:</strong> [Journal information]<br>
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<strong>Year:</strong> 2022<br>
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<strong>Note:</strong> Please check the latest publication details
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</p>
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</div>
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</div>
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<h3 class="text-xl font-semibold mt-6 mb-3">Relative Reasoning Models</h3>
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<div class="card bg-base-200 mb-6">
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<div class="card-body">
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<p class="text-sm mb-2">
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For relative reasoning and machine learning approaches:
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</p>
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<p class="text-sm mb-4">
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<strong>Authors:</strong> Fenner, K., Gao, J., Kramer, S., Ellis, L., Wackett, L.<br>
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<strong>Journal:</strong> Environmental Science & Technology, 42(15), 5761-5767<br>
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<strong>Year:</strong> 2008<br>
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<strong>DOI:</strong> <a href="https://doi.org/10.1021/es800408g" target="_blank" class="link link-primary">10.1021/es800408g</a>
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</p>
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</div>
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</div>
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<h2 class="text-2xl font-semibold mt-8 mb-4">Package-Specific Citations</h2>
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<p class="mb-4">
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If you use data from a specific package within enviPath, please also acknowledge the package creators
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and cite any relevant publications associated with that package. Package-specific citation information
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is available on each package's detail page.
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</p>
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<h2 class="text-2xl font-semibold mt-8 mb-4">Example Acknowledgment Text</h2>
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<p class="mb-4">
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You may use the following text in your acknowledgments section:
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</p>
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<div class="card bg-base-200 mb-6">
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<div class="card-body">
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<p class="italic text-sm">
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"Biotransformation pathway predictions were performed using enviPath
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(<a href="https://envipath.org" target="_blank" class="link link-primary">https://envipath.org</a>),
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a database and prediction system for microbial biotransformation of organic environmental contaminants."
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</p>
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</div>
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</div>
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<h2 class="text-2xl font-semibold mt-8 mb-4">Additional Resources</h2>
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<p class="mb-4">
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For a complete list of publications related to enviPath, please visit:
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</p>
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<ul class="list-disc list-inside mb-6 space-y-2">
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<li>
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<a href="https://community.envipath.org/" target="_blank" class="link link-primary">
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enviPath Community - Publications Section
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</a>
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</li>
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<li>
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<a href="https://wiki.envipath.org/" target="_blank" class="link link-primary">
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enviPath Documentation - References
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</a>
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</li>
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</ul>
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<div class="alert alert-success mt-8">
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<svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" class="stroke-current shrink-0 w-6 h-6">
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<path stroke-linecap="round" stroke-linejoin="round" stroke-width="2" d="M9 12l2 2 4-4m6 2a9 9 0 11-18 0 9 9 0 0118 0z" />
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</svg>
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<div>
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<h3 class="font-bold">Thank You!</h3>
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<div class="text-sm">
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Thank you for citing enviPath. Your citations help demonstrate the impact of our work and
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enable us to continue providing this resource to the scientific community.
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</div>
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</div>
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</div>
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<div class="divider my-8"></div>
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<h2 class="text-2xl font-semibold mt-8 mb-4">Questions?</h2>
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<p class="mb-4">
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If you're unsure which papers to cite or have questions about citations, please
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<a href="/contact" class="link link-primary">contact us</a> or ask on our
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<a href="https://community.envipath.org/" target="_blank" class="link link-primary">community forums</a>.
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</p>
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</div>
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</div>
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</div>
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{% endblock main_content %}
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