2 Search Results for "Ebbels, Timothy"

Document
DOI: 10.4230/DagRep.14.4.124
Computational Metabolomics: Towards Molecules, Models, and their Meaning (Dagstuhl Seminar 24181)

Authors: Timothy M. D. Ebbels, Soha Hassoun, Ewy A. Mathé, Justin J. J. van der Hooft, and Haley Chatelaine

Published in: Dagstuhl Reports, Volume 14, Issue 4 (2024)

Abstract
Dagstuhl Seminar "Computational Metabolomics: Towards Molecules, Models, and their Meaning," (24181) is the fifth edition of the Computational Metabolomics seminars. Experts in fields ranging from cheminformatics, computer science, bioinformatics, analytical chemistry, and epidemiology attended to address the current state and future directions of this multi-disciplinary field. Specific topics of discussion were decided by participants but largely revolved around the seminar’s titular themes of molecules (i.e., utilizing and annotating individual metabolites for use in models), models (i.e., generating systems from which to derive meaning), and meaning (i.e., deriving actionable insights to further understanding of biological systems). New to this seminar, topics of education and training, as well as the use of large language models to enhance access to resources, were also discussed. Participants identified community needs for a balance of standardization and flexibility in realms of repository-scale data deposition and analysis, spectral library generation, automation best practices, and biological pathway interpretation. Participants also identified a number of action items toward these ends, fostering international collaborations among them. For example, one topic evolved around creating a benchmarking dataset for structure annotation based on MS/MS spectral data. Discussions represented balanced perspectives, thanks to varied session facilitators and active participation of all members. The report contained herein reflects highlights of each session, including informal evening sessions and ideas for future directions.
Cite as

Timothy M. D. Ebbels, Soha Hassoun, Ewy A. Mathé, Justin J. J. van der Hooft, and Haley Chatelaine. Computational Metabolomics: Towards Molecules, Models, and their Meaning (Dagstuhl Seminar 24181). In Dagstuhl Reports, Volume 14, Issue 4, pp. 124-141, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@Article{ebbels_et_al:DagRep.14.4.124,
  author =	{Ebbels, Timothy M. D. and Hassoun, Soha and Math\'{e}, Ewy A. and van der Hooft, Justin J. J. and Chatelaine, Haley},
  title =	{{Computational Metabolomics: Towards Molecules, Models, and their Meaning (Dagstuhl Seminar 24181)}},
  pages =	{124--141},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2024},
  volume =	{14},
  number =	{4},
  editor =	{Ebbels, Timothy M. D. and Hassoun, Soha and Math\'{e}, Ewy A. and van der Hooft, Justin J. J. and Chatelaine, Haley},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagRep.14.4.124},
  URN =		{urn:nbn:de:0030-drops-213492},
  doi =		{10.4230/DagRep.14.4.124},
  annote =	{Keywords: bioinformatics, cheminformatics, data integration, machine learning, mass spectrometry, metabolite identification, metabolomics, pathway analysis, repository-scale analysis, training and education}
}
Document
DOI: 10.4230/DagRep.12.5.1
Computational Metabolomics: From Spectra to Knowledge (Dagstuhl Seminar 22181)

Authors: Corey Broeckling, Timothy Ebbels, Ewy Mathé, Nicola Zamboni, and Cecilia Wieder

Published in: Dagstuhl Reports, Volume 12, Issue 5 (2022)

Abstract
The fourth edition of the Computational Metabolomics seminars, Dagstuhl Seminar 22181, brought together a wide range of computational and experimental experts to share state-of-the art methodologies and push our collective understanding of how to interpret and maximise insight of metabolomic data. With increasing amounts of metabolomic data being generated, including large-scale epidemiological studies, and increasing sensitivity of instrumentation, development of sophisticated and robust computational solutions is required. Further, community agreement on which data standards should be used and which data sets are most apt for benchmarking computational tools is needed in the field. Building upon the previous successful formats of previous seminars (17491, 15492, and 20051) on this topic, attendees gathered each morning to collectively agree on the number of sessions and topics to discuss. A summary of the daily sessions were shared amongst all participants after dinner during each day’s final formal session. Further, informal evening sessions were spontaneously created to further dive into specific topics. As with past seminars, this format was very well received and enabled all participants to weigh in. Of particular note, this seminar was delayed and travel was complicated due to the pandemic. Despite these setbacks, this seminar brought together a balanced number of previous and new, seasoned and early career participants. All participants were active in these discussions, and a true sense of renewed energy ensued from the seminar. This report provides highlights of formal and informal evening sessions, including future anticipated research directions rooted from this seminar. Possible future workshops, such as a next phase of this Computational Metabolomics Dagstuhl seminar in late 2023 or 2024 were also discussed and will be applied for.
Cite as

Corey Broeckling, Timothy Ebbels, Ewy Mathé, Nicola Zamboni, and Cecilia Wieder. Computational Metabolomics: From Spectra to Knowledge (Dagstuhl Seminar 22181). In Dagstuhl Reports, Volume 12, Issue 5, pp. 1-16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@Article{broeckling_et_al:DagRep.12.5.1,
  author =	{Broeckling, Corey and Ebbels, Timothy and Math\'{e}, Ewy and Zamboni, Nicola and Wieder, Cecilia},
  title =	{{Computational Metabolomics: From Spectra to Knowledge (Dagstuhl Seminar 22181)}},
  pages =	{1--16},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2022},
  volume =	{12},
  number =	{5},
  editor =	{Broeckling, Corey and Ebbels, Timothy and Math\'{e}, Ewy and Zamboni, Nicola and Wieder, Cecilia},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagRep.12.5.1},
  URN =		{urn:nbn:de:0030-drops-174410},
  doi =		{10.4230/DagRep.12.5.1},
  annote =	{Keywords: bioinformatics, cheminformatics, computational mass spectrometry, metabolite identification, computational metabolomics, machine learning, data integration, pathway analysis}
}
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