forked from enviPath/enviPy
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:
@ -17,10 +17,7 @@
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{% endif %}
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<nav>
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||||
<h6 class="footer-title">Company</h6>
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||||
<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>
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||||
<a class="link link-hover" href="/legal">Legal</a>
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||||
<a class="link link-hover" href="/about" target="_blank">About us</a>
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||||
</nav>
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||||
<nav>
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||||
<h6 class="footer-title">Legal</h6>
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||||
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||||
@ -287,7 +287,7 @@
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</p>
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||||
<div class="float-right flex flex-row gap-4">
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||||
<a href="/about" class="btn btn-ghost-neutral">Read More</a>
|
||||
<a href="/about" class="btn btn-neutral">Publications</a>
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||||
<a href="/cite" class="btn btn-neutral">Publications</a>
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</div>
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||||
</div>
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</div>
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@ -33,23 +33,15 @@
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biodegradation pathways.
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</p>
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<h2 class="mt-8 mb-4 text-2xl font-semibold">Our Mission</h2>
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||||
<p class="mb-4">
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||||
Our mission is to advance environmental science through innovative
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computational tools that predict and analyze the biotransformation of
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chemical compounds. We strive to provide researchers, regulators, and
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industry professionals with accurate, accessible tools for
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understanding environmental fate and behavior.
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||||
</p>
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||||
|
||||
<h2 class="mt-8 mb-4 text-2xl font-semibold">What We Offer</h2>
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||||
<h2 class="mt-8 mb-4 text-2xl font-semibold">Services</h2>
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<div class="mb-6 grid gap-6 md:grid-cols-2">
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<div class="card bg-base-200 shadow-md">
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<div class="card-body">
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<h3 class="card-title text-primary">Pathway Database</h3>
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<p>
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Access experimentally observed biotransformation pathways and
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reactions from curated scientific literature.
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reactions from curated scientific literature and assessment
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reports.
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</p>
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</div>
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</div>
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@ -57,8 +49,8 @@
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<div class="card-body">
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<h3 class="card-title text-primary">Prediction System</h3>
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<p>
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Use our relative reasoning models to predict likely
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biotransformation pathways and products for new compounds.
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Use our models to predict likely biotransformation pathways and
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products for new compounds.
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</p>
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</div>
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</div>
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@ -66,8 +58,8 @@
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<div class="card-body">
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<h3 class="card-title text-primary">Machine Learning Models</h3>
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<p>
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Leverage advanced ML algorithms trained on extensive
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biodegradation data for accurate predictions.
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Leverage advanced Machine Learning algorithms trained on
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extensive biodegradation data for accurate predictions.
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</p>
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</div>
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</div>
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@ -75,37 +67,14 @@
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<div class="card-body">
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<h3 class="card-title text-primary">Community Platform</h3>
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<p>
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Join our active community of researchers to share knowledge,
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discuss findings, and collaborate.
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Join our active community of researchers to access
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documentation, get help, share knowledge, discuss findings, and
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collaborate.
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</p>
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</div>
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</div>
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</div>
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<h2 class="mt-8 mb-4 text-2xl font-semibold">Our Technology</h2>
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<p class="mb-4">
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enviPath employs a unique combination of rule-based and machine
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learning approaches to predict biotransformation pathways:
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</p>
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<ul class="mb-4 list-inside list-disc space-y-2">
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<li>
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<strong>Relative Reasoning:</strong> Uses structural similarity to
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known biotransformations
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</li>
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<li>
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<strong>Rule-Based Systems:</strong> Applies expert-curated
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transformation rules
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</li>
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<li>
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<strong>Machine Learning:</strong> Leverages neural networks for
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pattern recognition
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</li>
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<li>
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<strong>Hybrid Models:</strong> Combines multiple approaches for
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optimal accuracy
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</li>
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</ul>
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<h2 class="mt-8 mb-4 text-2xl font-semibold">Our Partners</h2>
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<p class="mb-4">
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enviPath is backed by leading research institutions and collaborators:
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@ -128,66 +97,41 @@
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/>
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</div>
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<h2 class="mt-8 mb-4 text-2xl font-semibold">Our Team</h2>
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||||
<p class="mb-4">
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||||
enviPath is developed and maintained by a dedicated team of
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||||
computational chemists, environmental scientists, and software
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||||
engineers. Our interdisciplinary approach ensures that the platform
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||||
meets the needs of the scientific community while remaining accessible
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||||
and user-friendly.
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||||
</p>
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||||
<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
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||||
publications and environmental assessments. Our tools are used by:
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||||
</p>
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||||
<ul class="mb-4 list-inside list-disc space-y-2">
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<li>
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||||
Academic researchers in environmental chemistry and toxicology
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||||
</li>
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||||
<li>Regulatory agencies for chemical risk assessment</li>
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||||
<li>
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||||
Chemical manufacturers for product development and safety evaluation
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||||
</li>
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||||
<li>Environmental consultants for contamination studies</li>
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||||
</ul>
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||||
|
||||
<h2 class="mt-8 mb-4 text-2xl font-semibold">
|
||||
Open Science Commitment
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||||
</h2>
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||||
<p class="mb-4">
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||||
We are committed to open science principles. enviPath provides free
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||||
access to our database and prediction tools for academic research. We
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||||
actively contribute to the scientific community through publications,
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open-source software, and collaboration.
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||||
</p>
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||||
|
||||
<div class="card bg-primary text-primary-content mt-8">
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||||
<div class="card-body">
|
||||
<h3 class="card-title">Get Involved</h3>
|
||||
<p>
|
||||
Join our community, contribute data, or collaborate on research
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||||
projects.
|
||||
</p>
|
||||
<div class="card-actions mt-4 justify-end">
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||||
<a
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||||
href="https://community.envipath.org/"
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||||
target="_blank"
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||||
class="btn btn-secondary"
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||||
>Visit Community</a
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||||
>
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||||
<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"
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||||
class="btn btn-secondary"
|
||||
>Visit Community</a
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||||
>
|
||||
<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.
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||||
</p>
|
||||
<div class="card-actions mt-4 justify-end">
|
||||
<a href="/cite" target="_blank" class="btn btn-secondary"
|
||||
>Publications</a
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||||
>
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||||
</div>
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||||
</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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||||
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||||
@ -73,20 +73,65 @@
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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">
|
||||
<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",
|
||||
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,
|
||||
doi = "10.1186/s13321-024-00881-6"
|
||||
<pre
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||||
class="overflow-x-auto text-xs"
|
||||
><code>@ARTICLE{Hafner2024enviPath,
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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,
|
||||
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>
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||||
</div>
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||||
</div>
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||||
</div>
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||||
</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
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||||
resource
|
||||
</h3>
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||||
<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
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||||
class="overflow-x-auto text-xs"
|
||||
><code>@ARTICLE{Wicker2016enviPath,
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||||
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">
|
||||
|
||||
@ -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
|
||||
|
||||
Reference in New Issue
Block a user