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The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE)

Waltemath, Dagmar and Golebiewski, Martin and Blinov, Michael L. and Gleeson, Padraig and Hermjakob, Henning and Hucka, Michael and Inau, Esther Thea and Keating, Sarah M. and König, Matthias and Krebs, Olga and Malik-Sheriff, Rahuman S. and Nickerson, David and Oberortner, Ernst and Sauro, Herbert M. and Schreiber, Falk and Smith, Lucian and Stefan, Melanie I. and Wittig, Ulrike and Myers, Chris J. (2020) The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). Journal of Integrative Bioinformatics, 17 (2-3). Art. No. 20200005. ISSN 1613-4516. https://resolver.caltech.edu/CaltechAUTHORS:20200708-073700691

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Abstract

This paper presents a report on outcomes of the 10th Computational Modeling in Biology Network (COMBINE) meeting that was held in Heidelberg, Germany, in July of 2019. The annual event brings together researchers, biocurators and software engineers to present recent results and discuss future work in the area of standards for systems and synthetic biology. The COMBINE initiative coordinates the development of various community standards and formats for computational models in the life sciences. Over the past 10 years, COMBINE has brought together standard communities that have further developed and harmonized their standards for better interoperability of models and data. COMBINE 2019 was co-located with a stakeholder workshop of the European EU-STANDS4PM initiative that aims at harmonized data and model standardization for in silico models in the field of personalized medicine, as well as with the FAIRDOM PALs meeting to discuss findable, accessible, interoperable and reusable (FAIR) data sharing. This report briefly describes the work discussed in invited and contributed talks as well as during breakout sessions. It also highlights recent advancements in data, model, and annotation standardization efforts. Finally, this report concludes with some challenges and opportunities that this community will face during the next 10 years.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1515/jib-2020-0005DOIArticle
ORCID:
AuthorORCID
Waltemath, Dagmar0000-0002-5886-5563
Hucka, Michael0000-0001-9105-5960
Keating, Sarah M.0000-0002-3356-3542
König, Matthias0000-0003-1725-179X
Nickerson, David0000-0003-4667-9779
Smith, Lucian0000-0001-7002-6386
Myers, Chris J.0000-0002-8762-8444
Additional Information:© 2020 Dagmar Waltemath et al., published by De Gruyter, Berlin/Boston. This work is licensed under the Creative Commons Attribution 4.0 Public License. BY 4.0 Received: 2020-02-18; Accepted: 2020-05-14; Published Online: 2020-06-29. The 2019 COMBINE meeting was supported by the German Research Foundation DFG (grant #MU 3099/4-1), by the Heidelberg Institute for Theoretical Studies (HITS), by the European coordination action EU-STANDS4PM (grant #825843 in the EU H2020 programme under the Health research collaborative programme), the German Federal Ministry of Education and Research (BMBF) through the German Network for Bioinformatics Infrastructure (de.NBI) and the German research network Systems Medicine of the Liver (LiSyM), as well as from the Klaus Tschira Foundation (KTS) and the University Medicine Greifswald. Travel grants for US-based students were provided by the NSF (grant #1928838). Author contribution: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission. Research funding: This research was funded by the was supported by the German Research Foundation DFG (grant #MU 3099/4-1), by the Heidelberg Institute for Theoretical Studies (HITS), by the European coordination action EU-STANDS4PM (grant #825843 in the EU H2020 programme under the Health research collaborative programme), the German Federal Ministry of Education and Research (BMBF) through the German Network for Bioinformatics Infrastructure (de.NBI) and the German research network Systems Medicine of the Liver (LiSyM), as well as from the Klaus Tschira Foundation (KTS) and the University Medicine Greifswald. Travel grants for US-based students were provided by the NSF (grant #1928838). Employment or leadership: None declared. Honorarium: None declared. The authors declare no conflicts of interest regarding this article.
Funders:
Funding AgencyGrant Number
Deutsche Forschungsgemeinschaft (DFG)MU 3099/4-1
Heidelberg Institute for Theoretical Studies (HITS)UNSPECIFIED
European Research Council (ERC)825843
Bundesministerium für Bildung und Forschung (BMBF)UNSPECIFIED
German Network for Bioinformatics InfrastructureUNSPECIFIED
German Research Network Systems Medicine of the LiverUNSPECIFIED
Klaus Tschira Foundation (KTS)UNSPECIFIED
University Medicine GreifswaldUNSPECIFIED
NSFCCF-1928838
Subject Keywords:COMBINE; community building; meeting report; standardization
Issue or Number:2-3
Record Number:CaltechAUTHORS:20200708-073700691
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20200708-073700691
Official Citation:Waltemath, D., Golebiewski, M., Blinov, M., Gleeson, P., Hermjakob, H., Hucka, M., Inau, E., Keating, S., König, M., Krebs, O., Malik-Sheriff, R., Nickerson, D., Oberortner, E., Sauro, H., Schreiber, F., Smith, L., Stefan, M., Wittig, U., & Myers, C. (2020). The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE), Journal of Integrative Bioinformatics, 17(2-3), 20200005. doi: https://doi.org/10.1515/jib-2020-0005
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:104268
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:08 Jul 2020 15:40
Last Modified:21 Sep 2020 20:25

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