James Glazier

Projects: COMBINE Multicellular Modelling

Institutions: Indiana University Bloomington

https://orcid.org/0000-0003-3634-190X
Rahuman Sheriff

Projects: ModeleXchange initiative, COMBINE Multicellular Modelling

Institutions: The European Bioinformatics Institute < EMBL-EBI, European Bioinformatics Institute

https://orcid.org/0000-0003-0705-9809
Sebastian Höpfl project_administrator

Projects: Working Group Nicole Radde, SteaPKMod

Institutions: University of Stuttgart

https://orcid.org/0000-0002-5300-0915
Lukrécia Mertová project_administrator

Projects: FAIRDOM, BioCreative VII, The BeeProject, SDBV/HITS, Semantic Table Interpretation in Chemistry

Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)

https://orcid.org/0000-0002-7585-4479
Hans V. Westerhoff project_administratorasset_housekeeperasset_gatekeeperprogramme_administrator

Projects: SysMO-LAB, MOSES, PSYSMO, SulfoSys, SulfoSys - Biotec, EraCoBiotech 2 nd call proposal preparation, Make Me My Model, Mechanism based modeling viral disease ( COVID-19 ) dynamics in human population, Modelling COVID-19 epidemics, SNAPPER: Synergistic Neurotoxicology APP for Environmental Regulation, Xenophiles Systems Biology, Thermodynamics, Non equilibrium thermodynamics, Book on Thermodynamics, and kinetics, Teaching Alien Biology, Outdated material, Fusion-fission-mitophagy, Stochastics and bursting

Institutions: Manchester Centre for Integrative Systems Biology, University of Manchester, VU University Amsterdam, University of Amsterdam, Systems Biology Amsterdam

https://orcid.org/0000-0002-0443-6114
Tobias Czauderna

Projects: COVID-19 Disease Map

Institutions: University of Applied Sciences Mittweida

https://orcid.org/0000-0002-1788-9593
Carsten Kettner project_administrator

Projects: EnzymeML, Standardization of enzyme-catalyzed reaction measurement, Standardization of enzyme-catalyzed reaction modelling

Institutions: Beilstein Institut

https://orcid.org/0000-0002-8697-6842
Cornelius Erbelding project_administratorasset_housekeeperasset_gatekeeperprogramme_administrator

Projects: WG Infrastructure for Translational Research, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", Translational Bioinformatics, Medical Biometry, Epidemiology, Medical Informatics

Institutions: University Medical Center Göttingen, University of Tübingen, University of Saarland

https://orcid.org/0000-0002-1505-594X
Lutz Brusch project_administrator

Projects: COMBINE Multicellular Modelling, Early Metabolic Injury (LiSyM-EMI - Pillar I)

Institutions: Technische Universität Dresden

https://orcid.org/0000-0003-0137-5106
Randy Heiland

Projects: COMBINE Multicellular Modelling

Institutions: Indiana University Bloomington

https://orcid.org/0000-0002-7440-2905
James Sluka

Projects: COMBINE Multicellular Modelling

Institutions: Indiana University Bloomington

https://orcid.org/0000-0002-5901-1404
Padraig Gleeson

Projects: COMBINE Multicellular Modelling

Institutions: University College London (UCL)

https://orcid.org/0000-0001-5963-8576
Brett Olivier

Projects: Not specified

Institutions: Not specified

https://orcid.org/0000-0002-5293-5321
Martin Golebiewski project_administratorasset_housekeeperasset_gatekeeperprogramme_administrator

Projects: FAIRDOM, Early Metabolic Injury (LiSyM-EMI - Pillar I), Chronic Liver Disease Progression (LiSyM-DP - Pillar II), Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF - Pillar III), LiSyM Core Infrastructure and Management (LiSyM-PD), Liver Function Diagnostics (LiSyM-LiFuDi - Pillar IV), Model Guided Pharmacotherapy In Chronic Liver Disease (LiSyM-MGP), Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), The Hedgehog Signalling Pathway (LiSyM-JGMMS), Molecular Steatosis - Imaging & Modeling (LiSyM-MSIM), Kinetics on the move - Workshop 2016, Example use cases, FAIRDOM user meeting, MS_DILI, COMBINE Multicellular Modelling, FAIRDOM & LiSyM & de.NBI Data Structuring Training, EnzymeML, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", FAIRDOM Community Workers, COVID-19 Disease Map, COVID-19 related studies and tools in Germany, nfdi4health - German National Research Data Infrastructure for Personal Health Data, ModeleXchange initiative, SDBV/HITS, EDITH (Ecosystem Digital Twins in Health) test project

Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)

https://orcid.org/0000-0002-8683-7084
Dagmar Waltemath

Projects: de.NBI-SysBio, GenoSysFat, Kinetics on the move - Workshop 2016, Example use cases, COMBINE Multicellular Modelling, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", COVID-19 related studies and tools in Germany, nfdi4health - German National Research Data Infrastructure for Personal Health Data

Institutions: University of Rostock, University of Greifswald, University Medicine of Greifswald

https://orcid.org/0000-0002-5886-5563
Carole Goble

Projects: SysMO DB, FAIRDOM, FAIRDOM user meeting, COVID-19 Disease Map

Institutions: University of Manchester - Department of Computer Science, Manchester Centre for Integrative Systems Biology, University of Manchester

https://orcid.org/0000-0003-1219-2137
Norman Morrison

Projects: FAIRDOM

Institutions: University of Manchester - Department of Computer Science

https://orcid.org/0000-0003-1604-1512
A brief history of COMBINE

Abstract (Expand)

Standards for data exchange are critical to the development of any field. They enable researchers and practitioners to transport information reliably, to apply a variety of tools to their problems, and … to reproduce scientific results. Over the past two decades, a range of standards have been developed to facilitate the exchange and reuse of information in the domain of representation and modeling of biological systems. These standards are complementary, so the interactions between their developers increased over time. By the end of the last decade, the community of researchers decided that more interoperability is required between the standards, and that common development is needed to make better use of effort, time, and money devoted to this activity. The COmputational MOdeling in Biology NEtwork (COMBINE) was created to enable the sharing of resources, tools, and other infrastructure. This paper provides a brief history of this endeavor and the challenges that remain.

Authors: Chris J. Myers, Gary Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nicolas Le Novere, David P. Nickerson, Falk Schreiber, Dagmar Waltemath

Date Published: 1st Dec 2017

Publication Type: InProceedings

Data Formats for Systems Biology and Quantitative Modeling

Abstract (Expand)

Data standards support the reliable exchange of information, the interoperability of tools, and the reproducibility of scientific results. In systems biology standards are agreed ways of structuring, … describing, and associating models and data, as well as their respective parts, graphical visualization, and information about applied experimental or computational methods. Such standards also assist with describing how constituent parts interact together, or are linked, and how they are embedded in their environmental and experimental context. Here the focus will be on standards for formatting models and their content, and on metadata checklists and ontologies that support modeling.

Author: Martin Golebiewski

Date Published: 2019

Publication Type: InBook

Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices.

Abstract (Expand)

Computational systems biology involves integrating heterogeneous datasets in order to generate models. These models can assist with understanding and prediction of biological phenomena. Generating … datasets and integrating them into models involves a wide range of scientific expertise. As a result these datasets are often collected by one set of researchers, and exchanged with others researchers for constructing the models. For this process to run smoothly the data and models must be FAIR-findable, accessible, interoperable, and reusable. In order for data and models to be FAIR they must be structured in consistent and predictable ways, and described sufficiently for other researchers to understand them. Furthermore, these data and models must be shared with other researchers, with appropriately controlled sharing permissions, before and after publication. In this chapter we explore the different data and model standards that assist with structuring, describing, and sharing. We also highlight the popular standards and sharing databases within computational systems biology.

Authors: N. J. Stanford, M. Scharm, P. D. Dobson, M. Golebiewski, M. Hucka, V. B. Kothamachu, D. Nickerson, S. Owen, J. Pahle, U. Wittig, D. Waltemath, C. Goble, P. Mendes, J. Snoep

Date Published: 12th Oct 2019

Publication Type: Journal

Specifications of standards in systems and synthetic biology: status and developments in 2020

Abstract (Expand)

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. …Not specified

Authors: Falk Schreiber, Björn Sommer, Tobias Czauderna, Martin Golebiewski, Thomas E. Gorochowski, Michael Hucka, Sarah M. Keating, Matthias König, Chris Myers, David Nickerson, Dagmar Waltemath

Date Published: 29th Jun 2020

Publication Type: Journal

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

Abstract (Expand)

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.

Authors: Dagmar Waltemath, Martin Golebiewski, Michael L Blinov, Padraig Gleeson, Henning Hermjakob, Michael Hucka, Esther Thea Inau, Sarah M Keating, Matthias König, Olga Krebs, Rahuman S Malik-Sheriff, David Nickerson, Ernst Oberortner, Herbert M Sauro, Falk Schreiber, Lucian Smith, Melanie I Stefan, Ulrike Wittig, Chris J Myers

Date Published: 29th Jun 2020

Publication Type: Journal

The German Corona Consensus Dataset (GECCO): A standardized dataset for COVID-19 research

Abstract (Expand)

Background: The current COVID-19 pandemic has led to a surge of research activity. While this research provides important insights, the multitude of studies results in an increasing segmentation of … information. To ensure comparability across projects and institutions, standard datasets are needed. Here, we introduce the "German Corona Consensus Dataset" (GECCO), a uniform dataset that uses international terminologies and health IT standards to improve interoperability of COVID-19 data. Methods: Based on previous work (e.g., the ISARIC-WHO COVID-19 case report form) and in coordination with experts from university hospitals, professional associations and research initiatives, data elements relevant for COVID-19 research were collected, prioritized and consolidated into a compact core dataset. The dataset was mapped to international terminologies, and the Fast Healthcare Interoperability Resources (FHIR) standard was used to define interoperable, machine-readable data formats. Results: A core dataset consisting of 81 data elements with 281 response options was defined, including information about, for example, demography, anamnesis, symptoms, therapy, medications or laboratory values of COVID-19 patients. Data elements and response options were mapped to SNOMED CT, LOINC, UCUM, ICD-10-GM and ATC, and FHIR profiles for interoperable data exchange were defined. Conclusion: GECCO provides a compact, interoperable dataset that can help to make COVID-19 research data more comparable across studies and institutions. The dataset will be further refined in the future by adding domain-specific extension modules for more specialized use cases.

Authors: Julian Sass, Alexander Bartschke, Moritz Lehne, Andrea Essenwanger, Eugenia Rinaldi, Stefanie Rudolph, Kai Uwe Heitmann, Joerg Janne Vehreschild, Christof von Kalle, Sylvia Thun

Date Published: 29th Jul 2020

Publication Type: Journal

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016.

Abstract (Expand)

Standards are essential to the advancement of science and technology. In systems and synthetic biology, numerous standards and associated tools have been developed over the last 16 years. This special … issue of the Journal of Integrative Bioinformatics aims to support the exchange, distribution and archiving of these standards, as well as to provide centralised and easily citable access to them.

Authors: F. Schreiber, G. D. Bader, P. Gleeson, M. Golebiewski, M. Hucka, N. Le Novere, C. Myers, D. Nickerson, B. Sommer, D. Walthemath

Date Published: 12th Feb 2017

Publication Type: Not specified

The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable

Abstract (Expand)

Reconstructing and understanding the Human Physiome virtually is a complex mathematical problem, and a highly demanding computational challenge. Mathematical models spanning from the molecular level … through to whole populations of individuals must be integrated, then personalized. This requires interoperability with multiple disparate and geographically separated data sources, and myriad computational software tools. Extracting and producing knowledge from such sources, even when the databases and software are readily available, is a challenging task. Despite the difficulties, researchers must frequently perform these tasks so that available knowledge can be continually integrated into the common framework required to realize the Human Physiome. Software and infrastructures that support the communities that generate these, together with their underlying standards to format, describe and interlink the corresponding data and computer models, are pivotal to the Human Physiome being realized. They provide the foundations for integrating, exchanging and re-using data and models efficiently, and correctly, while also supporting the dissemination of growing knowledge in these forms. In this paper, we explore the standards, software tooling, repositories and infrastructures that support this work, and detail what makes them vital to realizing the Human Physiome.

Authors: D. Nickerson, K. Atalag, B. de Bono, J. Geiger, C. Goble, S. Hollmann, J. Lonien, W. Muller, B. Regierer, N. J. Stanford, M. Golebiewski, P. Hunter

Date Published: 7th Apr 2016

Publication Type: Not specified

Workshop and Hackathon poster "Multicellular model description and cross-simulator exchange"
No description specified

Creator: Lutz Brusch

Submitter: Lutz Brusch

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Introduction to FAIRDOMHub

Talk given by Olga Krebs at EmPowerPutida project meeting in Bruxeles 23rd November 2016

Creators: Olga Krebs, Carole Goble, Rostyslav Kuzyakiv, Wolfgang Müller, Quyen Nguyen, Stuart Owen, Bernd Rinn, Jacky Snoep, Natalie Stanford

Submitter: Olga Krebs

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Improving the management of computational models.

Written by Martin Scharm (University of Rostock), Ron Henkel (University of Rostock), Dagmar Waltemath (University of Rostock), Olaf Wolkenhauer (University of Rostock, Stellenbosch University), and presented by Martin Scharm (University of Rostock) as part of the Reproducible and Citable Data and Models Workshop in Warnemünde, Germany. September 14th - 16th 2015.

Creators: Natalie Stanford, Dagmar Waltemath, Olaf Wolkenhauer, Ron Henkel, Martin Scharm (University of Rostock)

Submitter: Natalie Stanford

External Link
JERM templates: overview & recent development.

Talk given by Olga Krebs at SysMO PALs meeting on 18 - 20 September 2013 in Paris

Creator: Olga Krebs

Submitter: Olga Krebs

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RDA response to the global COVID 19 pandemic (press release)

The Research Data Alliance (RDA) is a volunteer community of over 10,500 professionals from 145 countries across the globe. In less than two months, the community responded to an urgent call for action and defined much needed, comprehensive recommendations and guidelines for data sharing under the present COVID-19 circumstances.

Creators: Martin Golebiewski, see full list of members of the RDA COVID-19 working group: https://www.rd-alliance.org/node/68704/members

Submitter: Martin Golebiewski

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RDA COVID-19 Recommendations and Guidelines - 5th Release

This is the fifth and final draft of the Recommendations and Guidelines from the RDA COVID-19 working group, and is open for public comment until 8th of June 2020. Following the open period, feedback will be considered and then the WG will seek endorsement of the document from the RDA governance bodies prior to final publication.

Creators: Martin Golebiewski, see full list of members of the RDA COVID-19 working group: https://www.rd-alliance.org/node/68704/members

Submitter: Martin Golebiewski

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RDA COVID-19 Recommendations and Guidelines - 4th Release

Draft guidelines and recommendations; fourth release, 15 May 2020, version for public review

Creator: see full list of members of the RDA COVID-19 working group: https://www.rd-alliance.org/node/68704/members

Submitter: Martin Golebiewski

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