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Schreiber F, Gleeson P, Golebiewski M, Gorochowski TE, Hucka M, Keating SM, König M, Myers CJ, Nickerson DP, Sommer B, Waltemath D. Specifications of standards in systems and synthetic biology: status and developments in 2021. J Integr Bioinform 2021; 18:jib-2021-0026. [PMID: 34674411 PMCID: PMC8573232 DOI: 10.1515/jib-2021-0026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
This special issue of the Journal of Integrative Bioinformatics contains updated specifications of COMBINE standards in systems and synthetic biology. The 2021 special issue presents four updates of standards: Synthetic Biology Open Language Visual Version 2.3, Synthetic Biology Open Language Visual Version 3.0, Simulation Experiment Description Markup Language Level 1 Version 4, and OMEX Metadata specification Version 1.2. This document can also be consulted to identify the latest specifications of all COMBINE standards.
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Affiliation(s)
- Falk Schreiber
- Department of Computer and Information Science, University of Konstanz, Konstanz, Germany
- Faculty of Information Technology, Monash University, Clayton, Australia
| | | | - Martin Golebiewski
- Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | | | | | | | - Matthias König
- Institute for Theoretical Biology, Humboldt-University Berlin, Berlin, Germany
| | - Chris J. Myers
- Department of Electrical, Computer, and Energy Eng., University of Colorado Boulder, Boulder, USA
| | - David P. Nickerson
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
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Brunak S, Bjerre Collin C, Eva Ó Cathaoir K, Golebiewski M, Kirschner M, Kockum I, Moser H, Waltemath D. Towards standardization guidelines for in silico approaches in personalized medicine. J Integr Bioinform 2020; 17:jib-2020-0006. [PMID: 32827396 PMCID: PMC7756614 DOI: 10.1515/jib-2020-0006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/26/2020] [Indexed: 01/11/2023] Open
Abstract
Despite the ever-progressing technological advances in producing data in health and clinical research, the generation of new knowledge for medical benefits through advanced analytics still lags behind its full potential. Reasons for this obstacle are the inherent heterogeneity of data sources and the lack of broadly accepted standards. Further hurdles are associated with legal and ethical issues surrounding the use of personal/patient data across disciplines and borders. Consequently, there is a need for broadly applicable standards compliant with legal and ethical regulations that allow interpretation of heterogeneous health data through in silico methodologies to advance personalized medicine. To tackle these standardization challenges, the Horizon2020 Coordinating and Support Action EU-STANDS4PM initiated an EU-wide mapping process to evaluate strategies for data integration and data-driven in silico modelling approaches to develop standards, recommendations and guidelines for personalized medicine. A first step towards this goal is a broad stakeholder consultation process initiated by an EU-STANDS4PM workshop at the annual COMBINE meeting (COMBINE 2019 workshop report in same issue). This forum analysed the status quo of data and model standards and reflected on possibilities as well as challenges for cross-domain data integration to facilitate in silico modelling approaches for personalized medicine.
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Affiliation(s)
| | | | | | | | - Marc Kirschner
- University of Copenhagen, Copenhagen, Denmark.,Forschungszentrum Jülich GmbH, Project Management Jülich, Jülich, Germany
| | | | - Heike Moser
- German Institute for Standardization, Berlin, Germany
| | - Dagmar Waltemath
- Medical Informatics Laboratory, Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
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Schreiber F, Sommer B, Czauderna T, Golebiewski M, Gorochowski TE, Hucka M, Keating SM, König M, Myers C, Nickerson D, Waltemath D. Specifications of standards in systems and synthetic biology: status and developments in 2020. J Integr Bioinform 2020; 17:jib-2020-0022. [PMID: 32598316 PMCID: PMC7756620 DOI: 10.1515/jib-2020-0022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 04/27/2020] [Indexed: 12/14/2022] Open
Abstract
This special issue of the Journal of Integrative Bioinformatics presents papers related to the 10th COMBINE meeting together with the annual update of COMBINE standards in systems and synthetic biology.
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Affiliation(s)
- Falk Schreiber
- Dept. of Computer and Information Science, University of Konstanz, Konstanz, Germany
- Faculty of Information Technology, Monash University, Melbourne, Australia
| | | | - Tobias Czauderna
- Faculty of Information Technology, Monash University, Melbourne, Australia
| | - Martin Golebiewski
- Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | | | | | | | - Matthias König
- Institute for Theoretical Biology, Humboldt-University Berlin, Berlin, Germany
| | - Chris Myers
- Dept. of Electrical and Computer Engineering, University of Utah, Salt Lake City, USA
| | - David Nickerson
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
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Waltemath D, Golebiewski M, Blinov ML, Gleeson P, Hermjakob H, Hucka M, Inau ET, Keating SM, König M, Krebs O, Malik-Sheriff RS, Nickerson D, Oberortner E, Sauro HM, Schreiber F, Smith L, Stefan MI, Wittig U, Myers CJ. The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). J Integr Bioinform 2020; 17:jib-2020-0005. [PMID: 32598315 PMCID: PMC7756615 DOI: 10.1515/jib-2020-0005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/14/2020] [Indexed: 01/23/2023] Open
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.
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Affiliation(s)
- Dagmar Waltemath
- Medical Informatics, University Medicine Greifswald, Greifswald, Germany
| | - Martin Golebiewski
- Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | | | - Padraig Gleeson
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
| | | | - Michael Hucka
- Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Esther Thea Inau
- Medical Informatics, University Medicine Greifswald, Greifswald, Germany
| | | | - Matthias König
- Institute for Theoretical Biology, Humboldt-University Berlin, Berlin, Germany
| | - Olga Krebs
- Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | | | - David Nickerson
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Ernst Oberortner
- U.S. Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Labs, Berkeley, CA, USA
| | - Herbert M Sauro
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Falk Schreiber
- Department of Computer and Information Science, University ofKonstanz, Germany.,Faculty of IT, Monash University, Melbourne, VIC, Australia
| | - Lucian Smith
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Melanie I Stefan
- Centre for Discovery Brain Sciences, The University of Edinburgh, Edinburgh, UK.,ZJU-UoE Institute, Zhejiang University, Haining, China.,University of Utah, Salt Lake City, UT, USA
| | - Ulrike Wittig
- Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Chris J Myers
- Centre for Discovery Brain Sciences, The University of Edinburgh, Edinburgh, UK
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Hucka M. SBMLPkgSpec: a LaTeX style file for SBML package specification documents. BMC Res Notes 2017; 10:451. [PMID: 28877760 PMCID: PMC5588604 DOI: 10.1186/s13104-017-2788-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/31/2017] [Indexed: 12/04/2022] Open
Abstract
OBJECTIVE The Systems Biology Markup Language (SBML) is a popular open format for storing and exchanging computational models in biology. The definition of SBML is captured in formal specification documents. SBMLPkgSpec is a LaTeX document style intended to fill the need for a standard format for writing such specification documents. RESULTS Specification documents for SBML Level 3 extensions (known as packages in SBML) are made more uniform with the use of a standard template. SBMLPkgSpec is a LaTeX class that provides a document framework for SBML Level 3 package specifications, to simplify the work of document authors while improving the overall quality of the family of SBML specifications.
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Affiliation(s)
- Michael Hucka
- Department of Computing and Mathematical Sciences, California Institute of Technology, 1200 E. California Blvd., Pasadena, California, 91125, USA.
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