Static pages update (#299)

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>
This commit is contained in:
2026-01-19 23:37:08 +13:00
committed by jebus
parent 5f5ae76182
commit 2a2fe4f147
5 changed files with 235 additions and 169 deletions

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@ -17,10 +17,7 @@
{% endif %}
<nav>
<h6 class="footer-title">Company</h6>
<a class="link link-hover" href="/about">About us</a>
<a class="link link-hover" href="/contact">Contact us</a>
<a class="link link-hover" href="/careers">Careers</a>
<a class="link link-hover" href="/legal">Legal</a>
<a class="link link-hover" href="/about" target="_blank">About us</a>
</nav>
<nav>
<h6 class="footer-title">Legal</h6>

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@ -287,7 +287,7 @@
</p>
<div class="float-right flex flex-row gap-4">
<a href="/about" class="btn btn-ghost-neutral">Read More</a>
<a href="/about" class="btn btn-neutral">Publications</a>
<a href="/cite" class="btn btn-neutral">Publications</a>
</div>
</div>
</div>

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@ -33,23 +33,15 @@
biodegradation pathways.
</p>
<h2 class="mt-8 mb-4 text-2xl font-semibold">Our Mission</h2>
<p class="mb-4">
Our mission is to advance environmental science through innovative
computational tools that predict and analyze the biotransformation of
chemical compounds. We strive to provide researchers, regulators, and
industry professionals with accurate, accessible tools for
understanding environmental fate and behavior.
</p>
<h2 class="mt-8 mb-4 text-2xl font-semibold">What We Offer</h2>
<h2 class="mt-8 mb-4 text-2xl font-semibold">Services</h2>
<div class="mb-6 grid gap-6 md:grid-cols-2">
<div class="card bg-base-200 shadow-md">
<div class="card-body">
<h3 class="card-title text-primary">Pathway Database</h3>
<p>
Access experimentally observed biotransformation pathways and
reactions from curated scientific literature.
reactions from curated scientific literature and assessment
reports.
</p>
</div>
</div>
@ -57,8 +49,8 @@
<div class="card-body">
<h3 class="card-title text-primary">Prediction System</h3>
<p>
Use our relative reasoning models to predict likely
biotransformation pathways and products for new compounds.
Use our models to predict likely biotransformation pathways and
products for new compounds.
</p>
</div>
</div>
@ -66,8 +58,8 @@
<div class="card-body">
<h3 class="card-title text-primary">Machine Learning Models</h3>
<p>
Leverage advanced ML algorithms trained on extensive
biodegradation data for accurate predictions.
Leverage advanced Machine Learning algorithms trained on
extensive biodegradation data for accurate predictions.
</p>
</div>
</div>
@ -75,37 +67,14 @@
<div class="card-body">
<h3 class="card-title text-primary">Community Platform</h3>
<p>
Join our active community of researchers to share knowledge,
discuss findings, and collaborate.
Join our active community of researchers to access
documentation, get help, share knowledge, discuss findings, and
collaborate.
</p>
</div>
</div>
</div>
<h2 class="mt-8 mb-4 text-2xl font-semibold">Our Technology</h2>
<p class="mb-4">
enviPath employs a unique combination of rule-based and machine
learning approaches to predict biotransformation pathways:
</p>
<ul class="mb-4 list-inside list-disc space-y-2">
<li>
<strong>Relative Reasoning:</strong> Uses structural similarity to
known biotransformations
</li>
<li>
<strong>Rule-Based Systems:</strong> Applies expert-curated
transformation rules
</li>
<li>
<strong>Machine Learning:</strong> Leverages neural networks for
pattern recognition
</li>
<li>
<strong>Hybrid Models:</strong> Combines multiple approaches for
optimal accuracy
</li>
</ul>
<h2 class="mt-8 mb-4 text-2xl font-semibold">Our Partners</h2>
<p class="mb-4">
enviPath is backed by leading research institutions and collaborators:
@ -128,66 +97,41 @@
/>
</div>
<h2 class="mt-8 mb-4 text-2xl font-semibold">Our Team</h2>
<p class="mb-4">
enviPath is developed and maintained by a dedicated team of
computational chemists, environmental scientists, and software
engineers. Our interdisciplinary approach ensures that the platform
meets the needs of the scientific community while remaining accessible
and user-friendly.
</p>
<h2 class="mt-8 mb-4 text-2xl font-semibold">Research Impact</h2>
<p class="mb-4">
Since its inception, enviPath has contributed to numerous scientific
publications and environmental assessments. Our tools are used by:
</p>
<ul class="mb-4 list-inside list-disc space-y-2">
<li>
Academic researchers in environmental chemistry and toxicology
</li>
<li>Regulatory agencies for chemical risk assessment</li>
<li>
Chemical manufacturers for product development and safety evaluation
</li>
<li>Environmental consultants for contamination studies</li>
</ul>
<h2 class="mt-8 mb-4 text-2xl font-semibold">
Open Science Commitment
</h2>
<p class="mb-4">
We are committed to open science principles. enviPath provides free
access to our database and prediction tools for academic research. We
actively contribute to the scientific community through publications,
open-source software, and collaboration.
</p>
<div class="card bg-primary text-primary-content mt-8">
<div class="card-body">
<h3 class="card-title">Get Involved</h3>
<p>
Join our community, contribute data, or collaborate on research
projects.
</p>
<div class="card-actions mt-4 justify-end">
<a
href="https://community.envipath.org/"
target="_blank"
class="btn btn-secondary"
>Visit Community</a
>
<a href="/contact" class="btn btn-ghost">Contact Us</a>
<div class="mb-6 grid gap-6 md:grid-cols-2">
<div class="card bg-primary text-primary-content mt-8">
<div class="card-body">
<h3 class="card-title">Get Involved</h3>
<p>
Join our community, contribute data, or collaborate on research
projects.
</p>
<div class="card-actions mt-4 justify-end">
<a
href="https://community.envipath.org/"
target="_blank"
class="btn btn-secondary"
>Visit Community</a
>
<a href="/contact" class="btn btn-ghost">Contact Us</a>
</div>
</div>
</div>
<div class="card bg-primary text-primary-content mt-8">
<div class="card-body">
<h3 class="card-title">Cite Us</h3>
<p>
To learn more about the science behind enviPath, please visit
our publications page for key publications and how to cite our
work.
</p>
<div class="card-actions mt-4 justify-end">
<a href="/cite" target="_blank" class="btn btn-secondary"
>Publications</a
>
</div>
</div>
</div>
</div>
<h2 class="mt-8 mb-4 text-2xl font-semibold">Publications</h2>
<p class="mb-4">
To learn more about the science behind enviPath, please visit our
<a href="/cite" class="link link-primary">citations page</a> for key
publications and how to cite our work.
</p>
</div>
</div>
</div>

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@ -73,20 +73,65 @@
<input type="checkbox" />
<div class="collapse-title text-sm font-medium">Show BibTeX</div>
<div class="collapse-content">
<pre class="overflow-x-auto text-xs"><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"
<pre
class="overflow-x-auto text-xs"
><code>@ARTICLE{Hafner2024enviPath,
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>
<div class="card bg-base-200 mb-6">
<div class="card-body">
<h3 class="mb-2 font-semibold">
enviPath The environmental contaminant biotransformation pathway
resource
</h3>
<p class="mb-4 text-sm">
<strong>Authors:</strong> Wicker, J., Lorsbach, T., Gütlein, M.,
Schmid, E., Latino, D., Kramer, S., Fenner, K.<br />
<strong>Journal:</strong> Nucleic Acids Research, 44(D1),
D502-D508<br />
<strong>Year:</strong> 2016<br />
<strong>DOI:</strong>
<a
href="https://doi.org/10.1093/nar/gkv1229"
target="_blank"
class="link link-primary"
>10.1093/nar/gkv1229</a
>
</p>
<div class="collapse-arrow bg-base-300 collapse">
<input type="checkbox" />
<div class="collapse-title text-sm font-medium">Show BibTeX</div>
<div class="collapse-content">
<pre
class="overflow-x-auto text-xs"
><code>@ARTICLE{Wicker2016enviPath,
title = "enviPath The environmental contaminant biotransformation pathway resource",
author = "Wicker, J{\"o}rg and Lorsbach, Tim and Gütlein, Martin and Schmid,
Emanuel and Latino, Diogo and Kramer, Stefan and Fenner, Kathrin",
journal = "Nucleic Acids Research",
volume = 44,
number = "D1",
pages = "D502-D508",
year = 2016,
month = jan,
doi = "10.1093/nar/gkv1229"
}</code></pre>
</div>
</div>
@ -103,57 +148,47 @@ doi = "10.1186/s13321-024-00881-6"
<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
A Hybrid Machine Learning and Knowledge Based Approach to Limit
Combinatorial Explosion in Biodegradation Prediction
</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>Authors:</strong> Wicker, J., Fenner, K., Kramer, S.<br />
<strong>Book:</strong> Computational Sustainability, 75-97<br />
<strong>Year:</strong> 2016<br />
<strong>DOI:</strong>
<a
href="https://doi.org/10.1002/bit.24744"
href="https://doi.org/10.1007/978-3-319-31858-5_5"
target="_blank"
class="link link-primary"
>10.1002/bit.24744</a
>10.1007/978-3-319-31858-5_5</a
>
</p>
<div class="collapse-arrow bg-base-300 collapse">
<input type="checkbox" />
<div class="collapse-title text-sm font-medium">Show BibTeX</div>
<div class="collapse-content">
<pre
class="overflow-x-auto text-xs"
><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}
<pre class="overflow-x-auto text-xs"><code>@INBOOK{Wicker2016ML,
title="A Hybrid Machine Learning and Knowledge Based Approach to
Limit Combinatorial Explosion in Biodegradation Prediction",
author="Wicker, J{\"o}rg and Fenner, Kathrin and Kramer, Stefan",
editor="L{\"a}ssig, J{\"o}rg and Kersting, Kristian and Morik, Katharina",
bookTitle="Computational Sustainability",
year=2016,
publisher="Springer International Publishing",
pages="75--97",
doi="10.1007/978-3-319-31858-5_5"
}</code></pre>
</div>
</div>
</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>
<h3 class="mb-2 font-semibold">
Predictive modeling of biodegradation pathways using transformer
architectures
</h3>
<p class="mb-4 text-sm">
<strong>Authors:</strong> Brydon, L., Zhang, K., Dobbie, G.,
Taškova, K., and Wicker, J.<br />
@ -167,31 +202,118 @@ doi = "10.1186/s13321-024-00881-6"
>10.1186/s13321-025-00969-7</a
>
</p>
<div class="collapse-arrow bg-base-300 collapse">
<input type="checkbox" />
<div class="collapse-title text-sm font-medium">Show BibTeX</div>
<div class="collapse-content">
<pre
class="overflow-x-auto text-xs"
><code>@article{Brydon2025Transformer,
title = "Predictive modeling of biodegradation pathways using transformer architectures",
author = "Brydon, Liam and Zhang, Kunyang and Dobbie, Gillian and
Ta\v{s}kova, Katerina and Wicker, J{\"o}rg Simon",
journal = "Journal of Cheminformatics",
volume = 17,
number = 1,
pages = "1--16",
year = 2025,
month = feb,
doi = "10.1186/s13321-025-00969-7",
}</code></pre>
</div>
</div>
</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">
Relative Reasoning Models
</h3>
<p class="mb-4">
For relative reasoning and machine learning approaches, please cite:
</p>
<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>
<h3 class="mb-2 font-semibold">
Predicting biodegradation products and pathways: a hybrid
knowledge- and machine learning-based approach
</h3>
<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>Authors:</strong> Wicker, J., Fenner, K., Ellis, L.,
Wackett, L., Kramer, S.<br />
<strong>Journal:</strong> Bioinformatics, 26(6), 814-821<br />
<strong>Year:</strong> 2010<br />
<strong>DOI:</strong>
<a
href="https://doi.org/10.1093/bioinformatics/btq024"
target="_blank"
class="link link-primary"
>10.1093/bioinformatics/btq024</a
>
</p>
<div class="collapse-arrow bg-base-300 collapse">
<input type="checkbox" />
<div class="collapse-title text-sm font-medium">Show BibTeX</div>
<div class="collapse-content">
<pre class="overflow-x-auto text-xs"><code>@ARTICLE{Wicker2010,
title = "Predicting biodegradation products and pathways:
a hybrid knowledge- and machine learning-based approach",
author = "Wicker, J{\"o}rg and Fenner, Kathrin and Ellis, Lynda and Wackett, Larry and Kramer, Stefan",
journal = "Bioinformatics",
volume = 26,
number = 6,
pages = "814-821",
year = 2010,
month = jan,
doi = "10.1093/bioinformatics/btq024"
}</code></pre>
</div>
</div>
</div>
</div>
<div class="card bg-base-200 mb-6">
<div class="card-body">
<h3 class="mb-2 font-semibold">
Data-driven extraction of relative reasoning rules to limit
combinatorial explosion in biodegradation pathway prediction
</h3>
<p class="mb-4 text-sm">
<strong>Authors:</strong> Fenner, K., Junfeng, G., Kramer, S.,
Ellis, L., Wackett, L.<br />
<strong>Journal:</strong> Bioinformatics, 26(18), 2079-2085<br />
<strong>Year:</strong> 2008<br />
<strong>DOI:</strong>
<a
href="https://doi.org/10.1021/es800408g"
href="https://doi.org/10.1093/bioinformatics/btn378"
target="_blank"
class="link link-primary"
>10.1021/es800408g</a
>10.1093/bioinformatics/btn378</a
>
</p>
<div class="collapse-arrow bg-base-300 collapse">
<input type="checkbox" />
<div class="collapse-title text-sm font-medium">Show BibTeX</div>
<div class="collapse-content">
<pre
class="overflow-x-auto text-xs"
><code>@ARTICLE{Fenner2008Reason,
title = "Data-driven extraction of relative reasoning rules to
limit combinatorial explosion in biodegradation pathway prediction",
author = "Fenner, Kathrin and Gao, Junfeng and Kramer, Stefan and Ellis, Lynda and Wackett, Larry",
journal = "Bioinformatics",
volume = 24,
number = 18,
pages = "2079-2085",
year = 2008,
month = 07,
doi = "10.1093/bioinformatics/btn378"
}</code></pre>
</div>
</div>
</div>
</div>
@ -234,22 +356,13 @@ doi = "10.1186/s13321-024-00881-6"
<ul class="mb-6 list-inside list-disc space-y-2">
<li>
<a
href="https://community.envipath.org/"
href="https://community.envipath.org/t/envipath-publications/"
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">

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@ -79,7 +79,7 @@
<p>Browse our comprehensive documentation and tutorials.</p>
<div class="card-actions justify-end">
<a
href="https://wiki.envipath.org/"
href="https://community.envipath.org/c/documentation"
target="_blank"
class="btn btn-neutral"
>Read Docs</a
@ -139,6 +139,18 @@
<h3 class="card-title">enviPath Ltd.</h3>
<p>Biodegradation prediction since 2015</p>
<div class="mt-4 flex gap-4">
<a
href="https://envipath.com/"
target="_blank"
class="btn btn-outline btn-sm"
>
<img
src="{% static '/images/logo-square.svg' %}"
width="24"
height="24"
/>
enviPath.com
</a>
<a
href="https://www.linkedin.com/company/envipath/"
target="_blank"
@ -208,7 +220,7 @@
Simply visit our homepage and try the prediction tool! For full
access to all features, create a free account. Check out our
<a
href="https://wiki.envipath.org/"
href="https://community.envipath.org/c/documentation"
target="_blank"
class="link link-primary"
>documentation</a