forked from enviPath/enviPy
Tobias O
ddf1fd3515
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>
205 lines
10 KiB
HTML
205 lines
10 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">Advancements in biotransformation pathway prediction: enhancements, datasets, and novel functionalities in enviPath</h3>
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<p class="text-sm mb-4">
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<strong>Authors:</strong> Hafner, J., Lorsbach, T., Schmidt, S., 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> <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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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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<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> Brydon, L., Zhang, K., Dobbie, G., 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> <a href="https://doi.org/10.1186/s13321-025-00969-7" target="_blank" class="link link-primary">10.1186/s13321-025-00969-7</a>
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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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