forked from enviPath/enviPy
Liam Brydon
2a2fe4f147
I have updated the static pages following @wicker comments on #275 Co-authored-by: Tobias O <tobias.olenyi@envipath.com> Reviewed-on: enviPath/enviPy#299 Co-authored-by: Liam Brydon <lbry121@aucklanduni.ac.nz> Co-committed-by: Liam Brydon <lbry121@aucklanduni.ac.nz>
411 lines
15 KiB
HTML
411 lines
15 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="mx-auto max-w-4xl px-4 py-8">
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<!-- Breadcrumbs -->
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<div class="breadcrumbs mb-4 text-sm">
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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 rounded-lg p-8 shadow-xl">
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<h1 class="mb-6 text-4xl font-bold">How to Cite enviPath</h1>
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<div class="prose max-w-none">
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<p class="mb-6 text-lg">
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If you use enviPath in your research, please cite our work. Citations
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help us demonstrate the impact of our platform and support continued
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development and maintenance.
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</p>
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<div class="alert alert-info mb-8">
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<svg
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xmlns="http://www.w3.org/2000/svg"
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fill="none"
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viewBox="0 0 24 24"
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class="h-6 w-6 shrink-0 stroke-current"
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>
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<path
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stroke-linecap="round"
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stroke-linejoin="round"
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stroke-width="2"
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d="M13 16h-1v-4h-1m1-4h.01M21 12a9 9 0 11-18 0 9 9 0 0118 0z"
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></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">
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The citation depends on which specific tools or models you used.
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Please cite the relevant publications below.
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</div>
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</div>
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</div>
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<h2 class="mt-8 mb-4 text-2xl font-semibold">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="mb-2 font-semibold">
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Advancements in biotransformation pathway prediction:
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enhancements, datasets, and novel functionalities in enviPath
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</h3>
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<p class="mb-4 text-sm">
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<strong>Authors:</strong> Hafner, J., Lorsbach, T., Schmidt, S.,
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Brydon, L., Dost, K., Zhang, K., Fenner, K., and Wicker, J.<br />
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<strong>Journal:</strong> Journal of Cheminformatics, 16(1), 93<br />
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<strong>Year:</strong> 2024<br />
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<strong>DOI:</strong>
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<a
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href="https://doi.org/10.1186/s13321-024-00881-6"
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target="_blank"
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class="link link-primary"
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>10.1186/s13321-024-00881-6</a
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>
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</p>
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<div class="collapse-arrow bg-base-300 collapse">
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<input type="checkbox" />
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<div class="collapse-title text-sm font-medium">Show BibTeX</div>
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<div class="collapse-content">
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<pre
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class="overflow-x-auto text-xs"
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><code>@ARTICLE{Hafner2024enviPath,
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title = "Advancements in biotransformation pathway prediction:
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enhancements, datasets, and novel functionalities in enviPath",
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author = "Hafner, Jasmin and Lorsbach, Tim and Schmidt, Sebastian and
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Brydon, Liam and Dost, Katharina and Zhang, Kunyang and Fenner,
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Kathrin and Wicker, J{\"o}rg",
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journal = "J. Cheminform.",
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publisher = "Springer Science and Business Media LLC",
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volume = 16,
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number = 1,
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pages = "93",
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month = aug,
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year = 2024,
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doi = "10.1186/s13321-024-00881-6"
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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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<div class="card bg-base-200 mb-6">
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<div class="card-body">
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<h3 class="mb-2 font-semibold">
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enviPath – The environmental contaminant biotransformation pathway
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resource
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</h3>
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<p class="mb-4 text-sm">
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<strong>Authors:</strong> Wicker, J., Lorsbach, T., Gütlein, M.,
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Schmid, E., Latino, D., Kramer, S., Fenner, K.<br />
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<strong>Journal:</strong> Nucleic Acids Research, 44(D1),
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D502-D508<br />
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<strong>Year:</strong> 2016<br />
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<strong>DOI:</strong>
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<a
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href="https://doi.org/10.1093/nar/gkv1229"
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target="_blank"
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class="link link-primary"
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>10.1093/nar/gkv1229</a
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>
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</p>
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<div class="collapse-arrow bg-base-300 collapse">
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<input type="checkbox" />
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<div class="collapse-title text-sm font-medium">Show BibTeX</div>
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<div class="collapse-content">
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<pre
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class="overflow-x-auto text-xs"
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><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 Gütlein, Martin and Schmid,
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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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month = jan,
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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="mt-8 mb-4 text-2xl font-semibold">
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Pathway Prediction System
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</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="mb-2 font-semibold">
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A Hybrid Machine Learning and Knowledge Based Approach to Limit
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Combinatorial Explosion in Biodegradation Prediction
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</h3>
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<p class="mb-4 text-sm">
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<strong>Authors:</strong> Wicker, J., Fenner, K., Kramer, S.<br />
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<strong>Book:</strong> Computational Sustainability, 75-97<br />
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<strong>Year:</strong> 2016<br />
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<strong>DOI:</strong>
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<a
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href="https://doi.org/10.1007/978-3-319-31858-5_5"
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target="_blank"
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class="link link-primary"
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>10.1007/978-3-319-31858-5_5</a
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>
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</p>
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<div class="collapse-arrow bg-base-300 collapse">
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<input type="checkbox" />
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<div class="collapse-title text-sm font-medium">Show BibTeX</div>
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<div class="collapse-content">
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<pre class="overflow-x-auto text-xs"><code>@INBOOK{Wicker2016ML,
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title="A Hybrid Machine Learning and Knowledge Based Approach to
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Limit Combinatorial Explosion in Biodegradation Prediction",
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author="Wicker, J{\"o}rg and Fenner, Kathrin and Kramer, Stefan",
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editor="L{\"a}ssig, J{\"o}rg and Kersting, Kristian and Morik, Katharina",
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bookTitle="Computational Sustainability",
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year=2016,
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publisher="Springer International Publishing",
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pages="75--97",
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doi="10.1007/978-3-319-31858-5_5"
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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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<div class="card bg-base-200 mb-6">
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<div class="card-body">
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<h3 class="mb-2 font-semibold">
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Predictive modeling of biodegradation pathways using transformer
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architectures
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</h3>
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<p class="mb-4 text-sm">
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<strong>Authors:</strong> Brydon, L., Zhang, K., Dobbie, G.,
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Taškova, K., and Wicker, J.<br />
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<strong>Journal:</strong> Journal of Cheminformatics, 17(1), 21<br />
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<strong>Year:</strong> 2025<br />
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<strong>DOI:</strong>
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<a
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href="https://doi.org/10.1186/s13321-025-00969-7"
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target="_blank"
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class="link link-primary"
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>10.1186/s13321-025-00969-7</a
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>
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</p>
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<div class="collapse-arrow bg-base-300 collapse">
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<input type="checkbox" />
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<div class="collapse-title text-sm font-medium">Show BibTeX</div>
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<div class="collapse-content">
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<pre
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class="overflow-x-auto text-xs"
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><code>@article{Brydon2025Transformer,
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title = "Predictive modeling of biodegradation pathways using transformer architectures",
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author = "Brydon, Liam and Zhang, Kunyang and Dobbie, Gillian and
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Ta\v{s}kova, Katerina and Wicker, J{\"o}rg Simon",
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journal = "Journal of Cheminformatics",
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volume = 17,
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number = 1,
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pages = "1--16",
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year = 2025,
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month = feb,
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doi = "10.1186/s13321-025-00969-7",
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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="mt-8 mb-4 text-2xl font-semibold">
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Machine Learning Models
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</h2>
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<h3 class="mt-6 mb-3 text-xl font-semibold">
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Relative Reasoning Models
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</h3>
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<p class="mb-4">
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For relative reasoning and machine learning approaches, 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="mb-2 font-semibold">
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Predicting biodegradation products and pathways: a hybrid
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knowledge- and machine learning-based approach
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</h3>
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<p class="mb-4 text-sm">
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<strong>Authors:</strong> Wicker, J., Fenner, K., Ellis, L.,
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Wackett, L., Kramer, S.<br />
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<strong>Journal:</strong> Bioinformatics, 26(6), 814-821<br />
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<strong>Year:</strong> 2010<br />
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<strong>DOI:</strong>
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<a
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href="https://doi.org/10.1093/bioinformatics/btq024"
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target="_blank"
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class="link link-primary"
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>10.1093/bioinformatics/btq024</a
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>
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</p>
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<div class="collapse-arrow bg-base-300 collapse">
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<input type="checkbox" />
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<div class="collapse-title text-sm font-medium">Show BibTeX</div>
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<div class="collapse-content">
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<pre class="overflow-x-auto text-xs"><code>@ARTICLE{Wicker2010,
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title = "Predicting biodegradation products and pathways:
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a hybrid knowledge- and machine learning-based approach",
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author = "Wicker, J{\"o}rg and Fenner, Kathrin and Ellis, Lynda and Wackett, Larry and Kramer, Stefan",
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journal = "Bioinformatics",
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volume = 26,
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number = 6,
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pages = "814-821",
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year = 2010,
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month = jan,
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doi = "10.1093/bioinformatics/btq024"
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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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<div class="card bg-base-200 mb-6">
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<div class="card-body">
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<h3 class="mb-2 font-semibold">
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Data-driven extraction of relative reasoning rules to limit
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combinatorial explosion in biodegradation pathway prediction
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</h3>
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<p class="mb-4 text-sm">
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<strong>Authors:</strong> Fenner, K., Junfeng, G., Kramer, S.,
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Ellis, L., Wackett, L.<br />
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<strong>Journal:</strong> Bioinformatics, 26(18), 2079-2085<br />
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<strong>Year:</strong> 2008<br />
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<strong>DOI:</strong>
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<a
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href="https://doi.org/10.1093/bioinformatics/btn378"
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target="_blank"
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class="link link-primary"
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>10.1093/bioinformatics/btn378</a
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>
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</p>
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<div class="collapse-arrow bg-base-300 collapse">
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<input type="checkbox" />
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<div class="collapse-title text-sm font-medium">Show BibTeX</div>
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<div class="collapse-content">
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<pre
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class="overflow-x-auto text-xs"
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><code>@ARTICLE{Fenner2008Reason,
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title = "Data-driven extraction of relative reasoning rules to
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limit combinatorial explosion in biodegradation pathway prediction",
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author = "Fenner, Kathrin and Gao, Junfeng and Kramer, Stefan and Ellis, Lynda and Wackett, Larry",
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journal = "Bioinformatics",
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volume = 24,
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number = 18,
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pages = "2079-2085",
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year = 2008,
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month = 07,
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doi = "10.1093/bioinformatics/btn378"
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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="mt-8 mb-4 text-2xl font-semibold">
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Package-Specific Citations
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</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
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acknowledge the package creators and cite any relevant publications
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associated with that package. Package-specific citation information is
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available on each package's detail page.
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</p>
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<h2 class="mt-8 mb-4 text-2xl font-semibold">
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Example Acknowledgment Text
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</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="text-sm italic">
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"Biotransformation pathway predictions were performed using
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enviPath (<a
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href="https://envipath.org"
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target="_blank"
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class="link link-primary"
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>https://envipath.org</a
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>), a database and prediction system for microbial
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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="mt-8 mb-4 text-2xl font-semibold">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="mb-6 list-inside list-disc space-y-2">
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<li>
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<a
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href="https://community.envipath.org/t/envipath-publications/"
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target="_blank"
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class="link link-primary"
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>
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enviPath Community - Publications Section
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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
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xmlns="http://www.w3.org/2000/svg"
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fill="none"
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viewBox="0 0 24 24"
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class="h-6 w-6 shrink-0 stroke-current"
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>
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<path
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stroke-linecap="round"
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stroke-linejoin="round"
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stroke-width="2"
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d="M9 12l2 2 4-4m6 2a9 9 0 11-18 0 9 9 0 0118 0z"
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/>
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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
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impact of our work and enable us to continue providing this
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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="mt-8 mb-4 text-2xl font-semibold">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
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||
citations, please
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<a href="/contact" class="link link-primary">contact us</a> or ask on
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our
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<a
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||
href="https://community.envipath.org/"
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target="_blank"
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class="link link-primary"
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>community forums</a
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>.
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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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