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>

templates/components/footer.html

@@ -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="/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>
       <h6 class="footer-title">Legal</h6>

templates/index/index.html

@@ -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>

templates/static/about_us.html

@@ -33,23 +33,15 @@
           biodegradation pathways.
         </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="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
+                Use our models to predict likely biotransformation pathways and
-                biotransformation pathways and products for new compounds.
+                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
+                Leverage advanced Machine Learning algorithms trained on
-                biodegradation data for accurate predictions.
+                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,
+                Join our active community of researchers to access
-                discuss findings, and collaborate.
+                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:
@@ -128,41 +97,7 @@
           />
         </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">
-          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>
@@ -181,13 +116,22 @@
               </div>
             </div>
           </div>
-
+          <div class="card bg-primary text-primary-content mt-8">
-        <h2 class="mt-8 mb-4 text-2xl font-semibold">Publications</h2>
+            <div class="card-body">
-        <p class="mb-4">
+              <h3 class="card-title">Cite Us</h3>
-          To learn more about the science behind enviPath, please visit our
+              <p>
-          <a href="/cite" class="link link-primary">citations page</a> for key
+                To learn more about the science behind enviPath, please visit
-          publications and how to cite our work.
+                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>
       </div>
     </div>
   </div>

templates/static/cite.html

@@ -73,7 +73,9 @@
               <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,
+                <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
@@ -93,6 +95,49 @@ doi       = "10.1186/s13321-024-00881-6"
           </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>
+          </div>
+        </div>
+
         <h2 class="mt-8 mb-4 text-2xl font-semibold">
           Pathway Prediction System
         </h2>
@@ -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
+              A Hybrid Machine Learning and Knowledge Based Approach to Limit
-              Reasoning Model
+              Combinatorial Explosion in Biodegradation Prediction
             </h3>
             <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>
               <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
+                <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>
               </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">
+            <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">
               <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">
+            <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">
-              <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>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">

templates/static/contact.html

@@ -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