@enviPath

Mastodon: https://xitter.cf/t.co/EQ8izRQ4Jh / @envipath@mstdn.science

 Mainz, Germany
envipath.com
Joined August 2015
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enviPath was first published in 2016. Since then, we have introduced substantial functionality enhancements and updates.We’ve summarized these advancements in our latest update paper. Check it out here: ncbi.nlm.nih.gov/pmc/article…
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New publication alert! 'Making waves: Enhancing pollutant biodegradation via rational engineering of microbial consortia' sciencedirect.com/science/ar…
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New publication alert! 'Systematic Handling of Environmental Fate Data for Model Development─Illustrated for the Case of Biodegradation Half-Life Data' pubs.acs.org/doi/10.1021/acs…
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New data package: EAWAG-SLUDGE ! EAWAG-SLUDGE contains biotransformation data from activated sludge experiments extracted from 27 scientific articles, including our own paper by Trostel et al. (2023) envipath.org/package/7932e57…
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New publication alert! “enviRule: an end-to-end system for automatic extraction of reaction patterns from environmental contaminant biotransformation pathways” academic.oup.com/bioinformat…
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New publication alert! ‘Combining predictive and analytical methods to elucidate pharmaceutical biotransformation in activated sludge’ pubs.rsc.org/en/content/arti…
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Replying to @enviPath
It was great to be there (so many familiar faces) - here's the link to our slides with @pubchem & @lcs doi.org/10.5281/zenodo.81438…
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Throwback Tuesday! The whole enviPath team was present at the International Conference on Chemistry and the Environment 2023 in Venice. We organized a workshop around the enviPath platform, featuring talks regarding databases, predictive models, and applications of enviPath.
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Throwback Tuesday! As part of the enviPath+ project, we aim to bring the enviPath platform to a new level. We held a scoping workshop in July to understand how to best meet the needs of our users and collaborators. We thank the participants for their valuable inputs!
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Just presented this overview at the @enviPath workshop on behalf of Tiejun, @EvanBolton and @pubchem and LCSB-ECI teams. #OpenScience #cheminformatics @lcsb_uni_lu @FnrLux @ZeroPM_H2020 Reaction Data in @pubchem Slides: zenodo.org/record/8143832 Sneak peek (lots of hyperlinks):
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Our new automatic rule extraction tool enviRule - extract transformation rules directly from your data set. Soon available in enviPath: doi.org/10.1093/bioinformati…

enviRule: an end-to-end system for automatic extraction of reaction patterns from environmental...

AbstractMotivation. Transformation products (TPs) of man-made chemicals, formed through microbially mediated transformation in the environment, can have se

academic.oup.com
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new: "Combatting over-specialization bias in growing chemical databases" jcheminf.biomedcentral.com/a…
Fig. 2: Comparison of the Gaussians fitted to a biased dataset.

ALT Fig. 2: Comparison of the Gaussians fitted to a biased dataset.

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Application deadline approaching for two positions to further develop @enviPath, our internationally unique online resource on contaminant biotransformation. Assistant in chemical data science: tinyurl.com/mbbuaxn7 Postdoc in Computational Metabolomics: tinyurl.com/5h8k9w5c
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Join us at ICCE 2023 in Venice! We are planning a satellite event at ICCE 2023 - we will introduce enviPath, with theory sessions and hands-on exercises. We will also have an exciting list of speakers! Register now - more updates soon! icce2023.com/satellite-event…
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Announcing two positions to make @enviPath THE ORD resource on contaminant biotransformation, to be filled ASAP, at @UZH & @EawagResearch. Research assistant in chemical data science: tinyurl.com/mbbuaxn7 Postdoc in Computational Metabolomics: tinyurl.com/5h8k9w5c
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EAWAG-SLUDGE, our latest addition to the enviPath database, is now available at envipath.org/package/4a3cd0f…. It features biodegradation pathways and kinetic information for 91 micropollutants commonly detected in wastewater treatment plants.
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Our paper on the holistic evaluation of predicted biodegradation/metabolism pathways with our partners @enviPath @MLAucklandUni appeared in @jcheminf. Dealing with problems like transient intermediates that are missing in the experimental reference data, or multi-step reactions.
Journal of Cheminformatics@jcheminf4 Sep 2021
new: "Holistic evaluation of biodegradation pathway prediction: assessing multi-step reactions and intermediate products" jcheminf.biomedcentral.com/a…
Figure 1: The pathway Benzyl Sulfide from the EAWAG-BBD package.

ALT Figure 1: The pathway Benzyl Sulfide from the EAWAG-BBD package.

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new: "Holistic evaluation of biodegradation pathway prediction: assessing multi-step reactions and intermediate products" jcheminf.biomedcentral.com/a…
Figure 1: The pathway Benzyl Sulfide from the EAWAG-BBD package.

ALT Figure 1: The pathway Benzyl Sulfide from the EAWAG-BBD package.

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We will add a new evaluation feature to enviPath shortly - Multi-Generation Evaluation. Our preprint is available @ChemRxiv: doi.org/10.26434/chemrxiv.14…
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Great new paper written in collaboration by our partners @MLAucklandUni and @KnowledgeTechn2 . "A comprehensive comparison of molecular feature representations for use in predictive modeling". doi.org/10.1016/j.compbiomed… #MachineLearning #AI
Machine Learning UoA@MLAucklandUni14 Jan 2021
Tomaž Stepišnik, PhD student @KnowledgeTechn2, visited us a while back and started working on his paper "A comprehensive comparison of molecular feature representations for use in predictive modeling", he later finished it back in Ljubljana. It is now published at CBM!
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