forked from enviPath/enviPy
Frontpage update (#179)
This PR introduces an overhaul for the front page and login features while keeping the rest of the application intact. ## Major Changes - TailwindCSS + DaisyUI Integration: Add modern CSS framework for component-based utility styling - Build System: Added pnpm for CSS building; can be extended for updated frontend builds in the future - Navbar + Footer: Redesigned and includable; old version retained for unstyled elements - Optimized Assets: Added minified and CSS-stylable logos ## New Features - Static Pages: Added comprehensive mockups of static pages (legal, privacy policy, terms of use, contact, etc.). **Note:** These have to be fixed before a public release, as their content is largely unreviewed and incorrect. Probably best to do in a separate PR that only contains updates to these. - Discourse API: Implement minimal features based on RestAPI for controllable results. ## Current bugs - [x] The static pages include the default navbar and footer on the login page. This will likely not work, as users need to access it before logging in; no good workaround so far (problem with Django templating system). - [ ] The front page predict link is currently non-functional; the redesigned page is almost ready but better done in a separate PR as it also touches Django code. - [x] Visual bug with the news cards. Still intend to fix for this PR Co-authored-by: Tim Lorsbach <tim@lorsba.ch> Reviewed-on: enviPath/enviPy#179 Reviewed-by: jebus <lorsbach@envipath.com> Co-authored-by: Tobias O <tobias.olenyi@envipath.com> Co-committed-by: Tobias O <tobias.olenyi@envipath.com>
This commit is contained in:
204
templates/static/cite.html
Normal file
204
templates/static/cite.html
Normal file
@ -0,0 +1,204 @@
|
||||
{% extends "framework_modern.html" %}
|
||||
{% load static %}
|
||||
|
||||
{% block main_content %}
|
||||
<div class="max-w-4xl mx-auto px-4 py-8">
|
||||
<!-- Breadcrumbs -->
|
||||
<div class="text-sm breadcrumbs mb-4">
|
||||
<ul>
|
||||
<li><a href="/">Home</a></li>
|
||||
<li>How to Cite enviPath</li>
|
||||
</ul>
|
||||
</div>
|
||||
|
||||
<!-- Main Content -->
|
||||
<div class="bg-base-100 shadow-xl rounded-lg p-8">
|
||||
<h1 class="text-4xl font-bold mb-6">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="alert alert-info mb-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="M13 16h-1v-4h-1m1-4h.01M21 12a9 9 0 11-18 0 9 9 0 0118 0z"></path>
|
||||
</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:
|
||||
</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>
|
||||
</p>
|
||||
<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{Hafner2024,
|
||||
title = "Advancements in biotransformation pathway prediction:
|
||||
enhancements, datasets, and novel functionalities in enviPath",
|
||||
author = "Hafner, Jasmin and Lorsbach, Tim and Schmidt, Sebastian and
|
||||
Brydon, Liam and Dost, Katharina and Zhang, Kunyang and Fenner,
|
||||
Kathrin and Wicker, J{\"o}rg",
|
||||
journal = "J. Cheminform.",
|
||||
publisher = "Springer Science and Business Media LLC",
|
||||
volume = 16,
|
||||
number = 1,
|
||||
pages = "93",
|
||||
month = aug,
|
||||
year = 2024,
|
||||
doi = "10.1186/s13321-024-00881-6"
|
||||
}</code></pre>
|
||||
</div>
|
||||
</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:
|
||||
</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>
|
||||
<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,
|
||||
title={Predicting biodegradation pathways using a hybrid relative reasoning model},
|
||||
author={Wicker, J{\"o}rg and Fenner, Kathrin and Ellis, Lynda and Kramer, Stefan},
|
||||
journal={Biotechnology and Bioengineering},
|
||||
volume={110},
|
||||
number={3},
|
||||
pages={837--846},
|
||||
year={2013},
|
||||
publisher={Wiley Online Library},
|
||||
doi={10.1002/bit.24744}
|
||||
}</code></pre>
|
||||
</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" />
|
||||
</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>
|
||||
</div>
|
||||
{% endblock main_content %}
|
||||
Reference in New Issue
Block a user