forked from enviPath/enviPy
[Refactor] Large scale formatting/linting (#193)
All html files now prettier formatted and fixes for incompatible blocks applied Co-authored-by: Tim Lorsbach <tim@lorsba.ch> Reviewed-on: enviPath/enviPy#193 Co-authored-by: Tobias O <tobias.olenyi@envipath.com> Co-committed-by: Tobias O <tobias.olenyi@envipath.com>
This commit is contained in:
@ -2,56 +2,78 @@
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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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<div class="mx-auto max-w-4xl 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>
|
||||
<li>How to Cite enviPath</li>
|
||||
</ul>
|
||||
<div class="breadcrumbs mb-4 text-sm">
|
||||
<ul>
|
||||
<li><a href="/">Home</a></li>
|
||||
<li>How to Cite enviPath</li>
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||||
</ul>
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||||
</div>
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||||
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||||
<!-- Main Content -->
|
||||
<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>
|
||||
<div class="bg-base-100 rounded-lg p-8 shadow-xl">
|
||||
<h1 class="mb-6 text-4xl font-bold">How to Cite enviPath</h1>
|
||||
|
||||
<div class="prose max-w-none">
|
||||
<p class="text-lg mb-6">
|
||||
If you use enviPath in your research, please cite our work. Citations help us demonstrate the
|
||||
impact of our platform and support continued development and maintenance.
|
||||
</p>
|
||||
<div class="prose max-w-none">
|
||||
<p class="mb-6 text-lg">
|
||||
If you use enviPath in your research, please cite our work. Citations
|
||||
help us demonstrate the impact of our platform and support continued
|
||||
development and maintenance.
|
||||
</p>
|
||||
|
||||
<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>
|
||||
<h3 class="font-bold">Quick Reference</h3>
|
||||
<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 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>
|
||||
<div>
|
||||
<h3 class="font-bold">Quick Reference</h3>
|
||||
<div class="text-sm">
|
||||
The citation depends on which specific tools or models you used.
|
||||
Please cite the relevant publications below.
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<h2 class="text-2xl font-semibold mt-8 mb-4">Main Platform Citation</h2>
|
||||
<p class="mb-4">
|
||||
If you use the enviPath platform in general, please cite:
|
||||
<h2 class="mt-8 mb-4 text-2xl font-semibold">Main Platform Citation</h2>
|
||||
<p class="mb-4">
|
||||
If you use the enviPath platform in general, please cite:
|
||||
</p>
|
||||
|
||||
<div class="card bg-base-200 mb-6">
|
||||
<div class="card-body">
|
||||
<h3 class="mb-2 font-semibold">
|
||||
Advancements in biotransformation pathway prediction:
|
||||
enhancements, datasets, and novel functionalities in enviPath
|
||||
</h3>
|
||||
<p class="mb-4 text-sm">
|
||||
<strong>Authors:</strong> Hafner, J., Lorsbach, T., Schmidt, S.,
|
||||
Brydon, L., Dost, K., Zhang, K., Fenner, K., and Wicker, J.<br />
|
||||
<strong>Journal:</strong> Journal of Cheminformatics, 16(1), 93<br />
|
||||
<strong>Year:</strong> 2024<br />
|
||||
<strong>DOI:</strong>
|
||||
<a
|
||||
href="https://doi.org/10.1186/s13321-024-00881-6"
|
||||
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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>
|
||||
</p>
|
||||
|
||||
<div class="card bg-base-200 mb-6">
|
||||
<div class="card-body">
|
||||
<h3 class="font-semibold mb-2">Advancements in biotransformation pathway prediction: enhancements, datasets, and novel functionalities in enviPath</h3>
|
||||
<p class="text-sm mb-4">
|
||||
<strong>Authors:</strong> Hafner, J., Lorsbach, T., Schmidt, S., Brydon, L., Dost, K., Zhang, K., Fenner, K., and Wicker, J.<br>
|
||||
<strong>Journal:</strong> Journal of Cheminformatics, 16(1), 93<br>
|
||||
<strong>Year:</strong> 2024<br>
|
||||
<strong>DOI:</strong> <a href="https://doi.org/10.1186/s13321-024-00881-6" target="_blank" class="link link-primary">10.1186/s13321-024-00881-6</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{Hafner2024,
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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>
|
||||
<div class="collapse-content">
|
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<pre class="overflow-x-auto text-xs"><code>@ARTICLE{Hafner2024,
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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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@ -66,32 +88,45 @@ 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>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<h2 class="text-2xl font-semibold mt-8 mb-4">Pathway Prediction System</h2>
|
||||
<p class="mb-4">
|
||||
If you use the pathway prediction functionality, please also cite:
|
||||
<h2 class="mt-8 mb-4 text-2xl font-semibold">
|
||||
Pathway Prediction System
|
||||
</h2>
|
||||
<p class="mb-4">
|
||||
If you use the pathway prediction functionality, please also cite:
|
||||
</p>
|
||||
|
||||
<div class="card bg-base-200 mb-6">
|
||||
<div class="card-body">
|
||||
<h3 class="mb-2 font-semibold">
|
||||
Predicting Biodegradation Pathways Using a Hybrid Relative
|
||||
Reasoning Model
|
||||
</h3>
|
||||
<p class="mb-4 text-sm">
|
||||
<strong>Authors:</strong> Wicker, J., Fenner, K., Ellis, L.,
|
||||
Kramer, S.<br />
|
||||
<strong>Journal:</strong> Biotechnology and Bioengineering,
|
||||
110(3), 837-846<br />
|
||||
<strong>Year:</strong> 2013<br />
|
||||
<strong>DOI:</strong>
|
||||
<a
|
||||
href="https://doi.org/10.1002/bit.24744"
|
||||
target="_blank"
|
||||
class="link link-primary"
|
||||
>10.1002/bit.24744</a
|
||||
>
|
||||
</p>
|
||||
|
||||
<div class="card bg-base-200 mb-6">
|
||||
<div class="card-body">
|
||||
<h3 class="font-semibold mb-2">Predicting Biodegradation Pathways Using a Hybrid Relative Reasoning Model</h3>
|
||||
<p class="text-sm mb-4">
|
||||
<strong>Authors:</strong> Wicker, J., Fenner, K., Ellis, L., Kramer, S.<br>
|
||||
<strong>Journal:</strong> Biotechnology and Bioengineering, 110(3), 837-846<br>
|
||||
<strong>Year:</strong> 2013<br>
|
||||
<strong>DOI:</strong> <a href="https://doi.org/10.1002/bit.24744" target="_blank" class="link link-primary">10.1002/bit.24744</a>
|
||||
</p>
|
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<div class="collapse collapse-arrow bg-base-300">
|
||||
<input type="checkbox" />
|
||||
<div class="collapse-title font-medium text-sm">
|
||||
Show BibTeX
|
||||
</div>
|
||||
<div class="collapse-content">
|
||||
<pre class="text-xs overflow-x-auto"><code>@article{wicker2013predicting,
|
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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">
|
||||
<pre
|
||||
class="overflow-x-auto text-xs"
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><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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@ -102,103 +137,161 @@ doi = "10.1186/s13321-024-00881-6"
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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>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<h2 class="text-2xl font-semibold mt-8 mb-4">Machine Learning Models</h2>
|
||||
|
||||
<h3 class="text-xl font-semibold mt-6 mb-3">enviPath-Transformer (Latest ML Model)</h3>
|
||||
<div class="card bg-base-200 mb-6">
|
||||
<div class="card-body">
|
||||
<p class="text-sm mb-2">
|
||||
If you use the Transformer-based prediction model, please cite:
|
||||
</p>
|
||||
<p class="text-sm mb-4">
|
||||
<strong>Authors:</strong> Brydon, L., Zhang, K., Dobbie, G., Taškova, K., and Wicker, J.<br>
|
||||
<strong>Journal:</strong> Journal of Cheminformatics, 17(1), 21<br>
|
||||
<strong>Year:</strong> 2025<br>
|
||||
<strong>DOI:</strong> <a href="https://doi.org/10.1186/s13321-025-00969-7" target="_blank" class="link link-primary">10.1186/s13321-025-00969-7</a>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<h3 class="text-xl font-semibold mt-6 mb-3">Relative Reasoning Models</h3>
|
||||
<div class="card bg-base-200 mb-6">
|
||||
<div class="card-body">
|
||||
<p class="text-sm mb-2">
|
||||
For relative reasoning and machine learning approaches:
|
||||
</p>
|
||||
<p class="text-sm mb-4">
|
||||
<strong>Authors:</strong> Fenner, K., Gao, J., Kramer, S., Ellis, L., Wackett, L.<br>
|
||||
<strong>Journal:</strong> Environmental Science & Technology, 42(15), 5761-5767<br>
|
||||
<strong>Year:</strong> 2008<br>
|
||||
<strong>DOI:</strong> <a href="https://doi.org/10.1021/es800408g" target="_blank" class="link link-primary">10.1021/es800408g</a>
|
||||
</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<h2 class="text-2xl font-semibold mt-8 mb-4">Package-Specific Citations</h2>
|
||||
<p class="mb-4">
|
||||
If you use data from a specific package within enviPath, please also acknowledge the package creators
|
||||
and cite any relevant publications associated with that package. Package-specific citation information
|
||||
is available on each package's detail page.
|
||||
</p>
|
||||
|
||||
<h2 class="text-2xl font-semibold mt-8 mb-4">Example Acknowledgment Text</h2>
|
||||
<p class="mb-4">
|
||||
You may use the following text in your acknowledgments section:
|
||||
</p>
|
||||
|
||||
<div class="card bg-base-200 mb-6">
|
||||
<div class="card-body">
|
||||
<p class="italic text-sm">
|
||||
"Biotransformation pathway predictions were performed using enviPath
|
||||
(<a href="https://envipath.org" target="_blank" class="link link-primary">https://envipath.org</a>),
|
||||
a database and prediction system for microbial biotransformation of organic environmental contaminants."
|
||||
</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<h2 class="text-2xl font-semibold mt-8 mb-4">Additional Resources</h2>
|
||||
<p class="mb-4">
|
||||
For a complete list of publications related to enviPath, please visit:
|
||||
</p>
|
||||
<ul class="list-disc list-inside mb-6 space-y-2">
|
||||
<li>
|
||||
<a href="https://community.envipath.org/" target="_blank" class="link link-primary">
|
||||
enviPath Community - Publications Section
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="https://wiki.envipath.org/" target="_blank" class="link link-primary">
|
||||
enviPath Documentation - References
|
||||
</a>
|
||||
</li>
|
||||
</ul>
|
||||
|
||||
<div class="alert alert-success mt-8">
|
||||
<svg xmlns="http://www.w3.org/2000/svg" fill="none" viewBox="0 0 24 24" class="stroke-current shrink-0 w-6 h-6">
|
||||
<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>
|
||||
<div>
|
||||
<h3 class="font-bold">Thank You!</h3>
|
||||
<div class="text-sm">
|
||||
Thank you for citing enviPath. Your citations help demonstrate the impact of our work and
|
||||
enable us to continue providing this resource to the scientific community.
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div class="divider my-8"></div>
|
||||
|
||||
<h2 class="text-2xl font-semibold mt-8 mb-4">Questions?</h2>
|
||||
<p class="mb-4">
|
||||
If you're unsure which papers to cite or have questions about citations, please
|
||||
<a href="/contact" class="link link-primary">contact us</a> or ask on our
|
||||
<a href="https://community.envipath.org/" target="_blank" class="link link-primary">community forums</a>.
|
||||
</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<h2 class="mt-8 mb-4 text-2xl font-semibold">
|
||||
Machine Learning Models
|
||||
</h2>
|
||||
|
||||
<h3 class="mt-6 mb-3 text-xl font-semibold">
|
||||
enviPath-Transformer (Latest ML Model)
|
||||
</h3>
|
||||
<div class="card bg-base-200 mb-6">
|
||||
<div class="card-body">
|
||||
<p class="mb-2 text-sm">
|
||||
If you use the Transformer-based prediction model, please cite:
|
||||
</p>
|
||||
<p class="mb-4 text-sm">
|
||||
<strong>Authors:</strong> Brydon, L., Zhang, K., Dobbie, G.,
|
||||
Taškova, K., and Wicker, J.<br />
|
||||
<strong>Journal:</strong> Journal of Cheminformatics, 17(1), 21<br />
|
||||
<strong>Year:</strong> 2025<br />
|
||||
<strong>DOI:</strong>
|
||||
<a
|
||||
href="https://doi.org/10.1186/s13321-025-00969-7"
|
||||
target="_blank"
|
||||
class="link link-primary"
|
||||
>10.1186/s13321-025-00969-7</a
|
||||
>
|
||||
</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<h3 class="mt-6 mb-3 text-xl font-semibold">
|
||||
Relative Reasoning Models
|
||||
</h3>
|
||||
<div class="card bg-base-200 mb-6">
|
||||
<div class="card-body">
|
||||
<p class="mb-2 text-sm">
|
||||
For relative reasoning and machine learning approaches:
|
||||
</p>
|
||||
<p class="mb-4 text-sm">
|
||||
<strong>Authors:</strong> Fenner, K., Gao, J., Kramer, S., Ellis,
|
||||
L., Wackett, L.<br />
|
||||
<strong>Journal:</strong> Environmental Science & Technology,
|
||||
42(15), 5761-5767<br />
|
||||
<strong>Year:</strong> 2008<br />
|
||||
<strong>DOI:</strong>
|
||||
<a
|
||||
href="https://doi.org/10.1021/es800408g"
|
||||
target="_blank"
|
||||
class="link link-primary"
|
||||
>10.1021/es800408g</a
|
||||
>
|
||||
</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<h2 class="mt-8 mb-4 text-2xl font-semibold">
|
||||
Package-Specific Citations
|
||||
</h2>
|
||||
<p class="mb-4">
|
||||
If you use data from a specific package within enviPath, please also
|
||||
acknowledge the package creators and cite any relevant publications
|
||||
associated with that package. Package-specific citation information is
|
||||
available on each package's detail page.
|
||||
</p>
|
||||
|
||||
<h2 class="mt-8 mb-4 text-2xl font-semibold">
|
||||
Example Acknowledgment Text
|
||||
</h2>
|
||||
<p class="mb-4">
|
||||
You may use the following text in your acknowledgments section:
|
||||
</p>
|
||||
|
||||
<div class="card bg-base-200 mb-6">
|
||||
<div class="card-body">
|
||||
<p class="text-sm italic">
|
||||
"Biotransformation pathway predictions were performed using
|
||||
enviPath (<a
|
||||
href="https://envipath.org"
|
||||
target="_blank"
|
||||
class="link link-primary"
|
||||
>https://envipath.org</a
|
||||
>), a database and prediction system for microbial
|
||||
biotransformation of organic environmental contaminants."
|
||||
</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<h2 class="mt-8 mb-4 text-2xl font-semibold">Additional Resources</h2>
|
||||
<p class="mb-4">
|
||||
For a complete list of publications related to enviPath, please visit:
|
||||
</p>
|
||||
<ul class="mb-6 list-inside list-disc space-y-2">
|
||||
<li>
|
||||
<a
|
||||
href="https://community.envipath.org/"
|
||||
target="_blank"
|
||||
class="link link-primary"
|
||||
>
|
||||
enviPath Community - Publications Section
|
||||
</a>
|
||||
</li>
|
||||
<li>
|
||||
<a
|
||||
href="https://wiki.envipath.org/"
|
||||
target="_blank"
|
||||
class="link link-primary"
|
||||
>
|
||||
enviPath Documentation - References
|
||||
</a>
|
||||
</li>
|
||||
</ul>
|
||||
|
||||
<div class="alert alert-success mt-8">
|
||||
<svg
|
||||
xmlns="http://www.w3.org/2000/svg"
|
||||
fill="none"
|
||||
viewBox="0 0 24 24"
|
||||
class="h-6 w-6 shrink-0 stroke-current"
|
||||
>
|
||||
<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"
|
||||
/>
|
||||
</svg>
|
||||
<div>
|
||||
<h3 class="font-bold">Thank You!</h3>
|
||||
<div class="text-sm">
|
||||
Thank you for citing enviPath. Your citations help demonstrate the
|
||||
impact of our work and enable us to continue providing this
|
||||
resource to the scientific community.
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div class="divider my-8"></div>
|
||||
|
||||
<h2 class="mt-8 mb-4 text-2xl font-semibold">Questions?</h2>
|
||||
<p class="mb-4">
|
||||
If you're unsure which papers to cite or have questions about
|
||||
citations, please
|
||||
<a href="/contact" class="link link-primary">contact us</a> or ask on
|
||||
our
|
||||
<a
|
||||
href="https://community.envipath.org/"
|
||||
target="_blank"
|
||||
class="link link-primary"
|
||||
>community forums</a
|
||||
>.
|
||||
</p>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
{% endblock main_content %}
|
||||
|
||||
Reference in New Issue
Block a user