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Static pages update (#299)

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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:
Liam Brydon
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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{% endif %} {% endif %}
<nav> <nav>
<h6 class="footer-title">Company</h6> <h6 class="footer-title">Company</h6>
<a class="link link-hover" href="/about">About us</a> <a class="link link-hover" href="/about" target="_blank">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>
</nav> </nav>
<nav> <nav>
<h6 class="footer-title">Legal</h6> <h6 class="footer-title">Legal</h6>

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@ -287,7 +287,7 @@
</p> </p>
<div class="float-right flex flex-row gap-4"> <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-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> </div>
</div> </div>

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

241
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@ -73,20 +73,65 @@
<input type="checkbox" /> <input type="checkbox" />
<div class="collapse-title text-sm font-medium">Show BibTeX</div> <div class="collapse-title text-sm font-medium">Show BibTeX</div>
<div class="collapse-content"> <div class="collapse-content">
<pre class="overflow-x-auto text-xs"><code>@ARTICLE{Hafner2024, <pre
title = "Advancements in biotransformation pathway prediction: class="overflow-x-auto text-xs"
enhancements, datasets, and novel functionalities in enviPath", ><code>@ARTICLE{Hafner2024enviPath,
author = "Hafner, Jasmin and Lorsbach, Tim and Schmidt, Sebastian and title = "Advancements in biotransformation pathway prediction:
Brydon, Liam and Dost, Katharina and Zhang, Kunyang and Fenner, enhancements, datasets, and novel functionalities in enviPath",
Kathrin and Wicker, J{\"o}rg", author = "Hafner, Jasmin and Lorsbach, Tim and Schmidt, Sebastian and
journal = "J. Cheminform.", Brydon, Liam and Dost, Katharina and Zhang, Kunyang and Fenner,
publisher = "Springer Science and Business Media LLC", Kathrin and Wicker, J{\"o}rg",
volume = 16, journal = "J. Cheminform.",
number = 1, publisher = "Springer Science and Business Media LLC",
pages = "93", volume = 16,
month = aug, number = 1,
year = 2024, pages = "93",
doi = "10.1186/s13321-024-00881-6" 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> }</code></pre>
</div> </div>
</div> </div>
@ -103,57 +148,47 @@ doi = "10.1186/s13321-024-00881-6"
<div class="card bg-base-200 mb-6"> <div class="card bg-base-200 mb-6">
<div class="card-body"> <div class="card-body">
<h3 class="mb-2 font-semibold"> <h3 class="mb-2 font-semibold">
Predicting Biodegradation Pathways Using a Hybrid Relative A Hybrid Machine Learning and Knowledge Based Approach to Limit
Reasoning Model Combinatorial Explosion in Biodegradation Prediction
</h3> </h3>
<p class="mb-4 text-sm"> <p class="mb-4 text-sm">
<strong>Authors:</strong> Wicker, J., Fenner, K., Ellis, L., <strong>Authors:</strong> Wicker, J., Fenner, K., Kramer, S.<br />
Kramer, S.<br /> <strong>Book:</strong> Computational Sustainability, 75-97<br />
<strong>Journal:</strong> Biotechnology and Bioengineering, <strong>Year:</strong> 2016<br />
110(3), 837-846<br />
<strong>Year:</strong> 2013<br />
<strong>DOI:</strong> <strong>DOI:</strong>
<a <a
href="https://doi.org/10.1002/bit.24744" href="https://doi.org/10.1007/978-3-319-31858-5_5"
target="_blank" target="_blank"
class="link link-primary" class="link link-primary"
>10.1002/bit.24744</a >10.1007/978-3-319-31858-5_5</a
> >
</p> </p>
<div class="collapse-arrow bg-base-300 collapse"> <div class="collapse-arrow bg-base-300 collapse">
<input type="checkbox" /> <input type="checkbox" />
<div class="collapse-title text-sm font-medium">Show BibTeX</div> <div class="collapse-title text-sm font-medium">Show BibTeX</div>
<div class="collapse-content"> <div class="collapse-content">
<pre <pre class="overflow-x-auto text-xs"><code>@INBOOK{Wicker2016ML,
class="overflow-x-auto text-xs" title="A Hybrid Machine Learning and Knowledge Based Approach to
><code>@article{wicker2013predicting, Limit Combinatorial Explosion in Biodegradation Prediction",
title={Predicting biodegradation pathways using a hybrid relative reasoning model}, author="Wicker, J{\"o}rg and Fenner, Kathrin and Kramer, Stefan",
author={Wicker, J{\"o}rg and Fenner, Kathrin and Ellis, Lynda and Kramer, Stefan}, editor="L{\"a}ssig, J{\"o}rg and Kersting, Kristian and Morik, Katharina",
journal={Biotechnology and Bioengineering}, bookTitle="Computational Sustainability",
volume={110}, year=2016,
number={3}, publisher="Springer International Publishing",
pages={837--846}, pages="75--97",
year={2013}, doi="10.1007/978-3-319-31858-5_5"
publisher={Wiley Online Library},
doi={10.1002/bit.24744}
}</code></pre> }</code></pre>
</div> </div>
</div> </div>
</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 bg-base-200 mb-6">
<div class="card-body"> <div class="card-body">
<p class="mb-2 text-sm"> <h3 class="mb-2 font-semibold">
If you use the Transformer-based prediction model, please cite: Predictive modeling of biodegradation pathways using transformer
</p> architectures
</h3>
<p class="mb-4 text-sm"> <p class="mb-4 text-sm">
<strong>Authors:</strong> Brydon, L., Zhang, K., Dobbie, G., <strong>Authors:</strong> Brydon, L., Zhang, K., Dobbie, G.,
Taškova, K., and Wicker, J.<br /> Taškova, K., and Wicker, J.<br />
@ -167,31 +202,118 @@ doi = "10.1186/s13321-024-00881-6"
>10.1186/s13321-025-00969-7</a >10.1186/s13321-025-00969-7</a
> >
</p> </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>
</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"> <h3 class="mt-6 mb-3 text-xl font-semibold">
Relative Reasoning Models Relative Reasoning Models
</h3> </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 bg-base-200 mb-6">
<div class="card-body"> <div class="card-body">
<p class="mb-2 text-sm"> <h3 class="mb-2 font-semibold">
For relative reasoning and machine learning approaches: Predicting biodegradation products and pathways: a hybrid
</p> knowledge- and machine learning-based approach
</h3>
<p class="mb-4 text-sm"> <p class="mb-4 text-sm">
<strong>Authors:</strong> Fenner, K., Gao, J., Kramer, S., Ellis, <strong>Authors:</strong> Wicker, J., Fenner, K., Ellis, L.,
L., Wackett, L.<br /> Wackett, L., Kramer, S.<br />
<strong>Journal:</strong> Environmental Science & Technology, <strong>Journal:</strong> Bioinformatics, 26(6), 814-821<br />
42(15), 5761-5767<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>Year:</strong> 2008<br />
<strong>DOI:</strong> <strong>DOI:</strong>
<a <a
href="https://doi.org/10.1021/es800408g" href="https://doi.org/10.1093/bioinformatics/btn378"
target="_blank" target="_blank"
class="link link-primary" class="link link-primary"
>10.1021/es800408g</a >10.1093/bioinformatics/btn378</a
> >
</p> </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>
</div> </div>
@ -234,22 +356,13 @@ doi = "10.1186/s13321-024-00881-6"
<ul class="mb-6 list-inside list-disc space-y-2"> <ul class="mb-6 list-inside list-disc space-y-2">
<li> <li>
<a <a
href="https://community.envipath.org/" href="https://community.envipath.org/t/envipath-publications/"
target="_blank" target="_blank"
class="link link-primary" class="link link-primary"
> >
enviPath Community - Publications Section enviPath Community - Publications Section
</a> </a>
</li> </li>
<li>
<a
href="https://wiki.envipath.org/"
target="_blank"
class="link link-primary"
>
enviPath Documentation - References
</a>
</li>
</ul> </ul>
<div class="alert alert-success mt-8"> <div class="alert alert-success mt-8">

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