- 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.
-
-
-
Machine Learning Models
- 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.
@@ -75,37 +67,14 @@
Community Platform
- 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.
-
- enviPath employs a unique combination of rule-based and machine
- learning approaches to predict biotransformation pathways:
-
-
enviPath is backed by leading research institutions and collaborators:
@@ -128,66 +97,41 @@
/>
-
- 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.
-
-
-
- Since its inception, enviPath has contributed to numerous scientific
- publications and environmental assessments. Our tools are used by:
-
-
- 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.
-
-
-
-
-
Get Involved
-
- Join our community, contribute data, or collaborate on research
- projects.
-
-
-
Visit Community
-
Contact Us
+
+
+
+
Get Involved
+
+ Join our community, contribute data, or collaborate on research
+ projects.
+
+
+
+
+
+
+
Cite Us
+
+ To learn more about the science behind enviPath, please visit
+ our publications page for key publications and how to cite our
+ work.
+
+
-
-
Publications
-
- To learn more about the science behind enviPath, please visit our
- citations page for key
- publications and how to cite our work.
-
-
@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"
+ @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"
+}
+
+
+
+ enviPath – The environmental contaminant biotransformation pathway
+ resource
+
+
+ Authors: Wicker, J., Lorsbach, T., Gütlein, M.,
+ Schmid, E., Latino, D., Kramer, S., Fenner, K.
+ Journal: Nucleic Acids Research, 44(D1),
+ D502-D508
+ Year: 2016
+ DOI:
+ 10.1093/nar/gkv1229
+
+
+
+
Show BibTeX
+
+
@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"
}
@@ -103,57 +148,47 @@ doi = "10.1186/s13321-024-00881-6"
- Predicting Biodegradation Pathways Using a Hybrid Relative
- Reasoning Model
+ A Hybrid Machine Learning and Knowledge Based Approach to Limit
+ Combinatorial Explosion in Biodegradation Prediction
- Authors: Wicker, J., Fenner, K., Ellis, L.,
- Kramer, S.
- Journal: Biotechnology and Bioengineering,
- 110(3), 837-846
- Year: 2013
+ Authors: Wicker, J., Fenner, K., Kramer, S.
+ Book: Computational Sustainability, 75-97
+ Year: 2016
DOI:
10.1002/bit.2474410.1007/978-3-319-31858-5_5
Show BibTeX
-
@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}
+ @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"
}
-
- Machine Learning Models
-
-
-
- enviPath-Transformer (Latest ML Model)
-
-
- If you use the Transformer-based prediction model, please cite:
-
+
+ Predictive modeling of biodegradation pathways using transformer
+ architectures
+
Authors: Brydon, L., Zhang, K., Dobbie, G.,
Taškova, K., and Wicker, J.
@@ -167,31 +202,118 @@ doi = "10.1186/s13321-024-00881-6"
>10.1186/s13321-025-00969-7
+
+
+
Show BibTeX
+
+
@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",
+}
+
+
+
+ Machine Learning Models
+
+
Relative Reasoning Models
+
+ For relative reasoning and machine learning approaches, please cite:
+
-
- For relative reasoning and machine learning approaches:
-
+
+ Predicting biodegradation products and pathways: a hybrid
+ knowledge- and machine learning-based approach
+
- Authors: Fenner, K., Gao, J., Kramer, S., Ellis,
- L., Wackett, L.
- Journal: Environmental Science & Technology,
- 42(15), 5761-5767
+ Authors: Wicker, J., Fenner, K., Ellis, L.,
+ Wackett, L., Kramer, S.
+ Journal: Bioinformatics, 26(6), 814-821
+ Year: 2010
+ DOI:
+ 10.1093/bioinformatics/btq024
+
+
+
+
Show BibTeX
+
+
@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"
+}
+
+
+
+
+
+
+
+
+ Data-driven extraction of relative reasoning rules to limit
+ combinatorial explosion in biodegradation pathway prediction
+
+
+ Authors: Fenner, K., Junfeng, G., Kramer, S.,
+ Ellis, L., Wackett, L.
+ Journal: Bioinformatics, 26(18), 2079-2085
Year: 2008
DOI:
10.1021/es800408g10.1093/bioinformatics/btn378
+
+
+
Show BibTeX
+
+
@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"
+}
+
+
@@ -234,22 +356,13 @@ doi = "10.1186/s13321-024-00881-6"
diff --git a/templates/static/contact.html b/templates/static/contact.html
index cb38034b..ea4f3cd3 100644
--- a/templates/static/contact.html
+++ b/templates/static/contact.html
@@ -79,7 +79,7 @@
Browse our comprehensive documentation and tutorials.
Read DocsenviPath Ltd.
Biodegradation prediction since 2015