COMBINE (Computational Modeling in Biology Network)

This is the exchange platform of the COMBINE network.

COMBINE is an initiative to coordinate the development of various community standards and formats for computational models: BioPax, CellML, NeuroML, Synthetic Biology Open Language (SBOL), Systems Biology Graphical Notation (SBGN), Systems Biology Markup Language (SBML), Simulation Experiment Description Markup Language (SED-ML).

Web page: http://co.mbine.org

Funding details:
No funding details specified

Related items

Frank Bergmann

Projects: de.NBI-SysBio, EnzymeML, COMBINE Multicellular Modelling, Standardization of enzyme-catalyzed reaction measurement, Standardization of enzyme-catalyzed reaction modelling

Institutions: University of Heidelberg

https://orcid.org/0000-0001-5553-4702
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
Chris Evelo

Projects: HUMET Startup, COMBINE Multicellular Modelling, COVID-19 Disease Map

Institutions: University Maastricht

https://orcid.org/0000-0002-5301-3142
Juliano Ferrari Gianlupi

Projects: COMBINE Multicellular Modelling

Institutions: Indiana University Bloomington

Samuel Friedman

Projects: COMBINE Multicellular Modelling

Institutions: Indiana University Bloomington

https://orcid.org/0000-0001-8003-6860
Padraig Gleeson

Projects: COMBINE Multicellular Modelling

Institutions: University College London (UCL)

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

Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)

https://orcid.org/0000-0002-8683-7084
Randy Heiland

Projects: COMBINE Multicellular Modelling

Institutions: Indiana University Bloomington

https://orcid.org/0000-0002-7440-2905
Henning Hermjakob project_administrator

Projects: COVID-19 Disease Map, ModeleXchange initiative

Institutions: The European Bioinformatics Institute < EMBL-EBI

Xiaoming Hu admin

Projects: FAIRDOM, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", COVID-19 Disease Map, COVID-19 related studies and tools in Germany, nfdi4health - German National Research Data Infrastructure for Personal Health Data, LiSyM Core Infrastructure and Management (LiSyM-PD), ModeleXchange initiative

Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)

Tim Johann

Projects: COMBINE Multicellular Modelling

Institutions: Leibniz-Institut für Arbeitsforschung (IfADo)

https://orcid.org/0000-0001-5792-1562
Jonathan Karr

Projects: MycoSynVac - Engineering Mycoplasma pneumoniae as a broad-spectrum animal vaccine, COVID-19 Disease Map, ModeleXchange initiative

Institutions: ICAHN Icahn School of Medicine at Mount Sinai

Jochen Kursawe

Projects: COMBINE Multicellular Modelling

Institutions: University of St Andrews

Matthias König project_administratorasset_housekeeperasset_gatekeeper

Projects: Kinetics on the move - Workshop 2016, Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), FAIRDOM user meeting, COMBINE Multicellular Modelling, FAIRDOM & LiSyM & de.NBI Data Structuring Training

Institutions: Charité University Medicine Berlin, Humboldt-Universität zu Berlin, Humboldt University Berlin

https://orcid.org/0000-0003-1725-179X
James Alastair McLaughlin

Projects: COMBINE Multicellular Modelling

Institutions: University of Newcastle-upon-Tyne

https://orcid.org/0000-0002-8361-2795
Wolfgang Müller project_administratorasset_housekeeperasset_gatekeeperprogramme_administrator

Projects: SysMO DB, FAIRDOM, ICYSB 2015 - International Practical Course in Systems Biology, de.NBI-SysBio, Regeneration and Repair in Acute-on-Chronic Liver Failure (LiSyM-ACLF - Pillar III), Early Metabolic Injury (LiSyM-EMI - Pillar I), Chronic Liver Disease Progression (LiSyM-DP - Pillar II), LiSyM Core Infrastructure and Management (LiSyM-PD), Liver Function Diagnostics (LiSyM-LiFuDi - Pillar IV), Molecular Steatosis - Imaging & Modeling (LiSyM-MSIM), Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), Model Guided Pharmacotherapy In Chronic Liver Disease (LiSyM-MGP), The Hedgehog Signalling Pathway (LiSyM-JGMMS), Kinetics on the move - Workshop 2016, Example use cases, SBEpo - Systems Biology of Erythropoietin, FAIRDOM & LiSyM & de.NBI Data Structuring Training, MESI-STRAT, INCOME, EnzymeML, PoLiMeR - Polymers in the Liver: Metabolism and Regulation, MS_DILI, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", COMBINE Multicellular Modelling, COVID-19 Disease Map, COVID-19 related studies and tools in Germany, nfdi4health - German National Research Data Infrastructure for Personal Health Data, NMTrypI - New Medicines for Trypanosomatidic Infections, ModeleXchange initiative, SNAPPER: Synergistic Neurotoxicology APP for Environmental Regulation

Institutions: Heidelberg Institute for Theoretical Studies (HITS gGmbH)

https://orcid.org/0000-0002-4980-3512
David Nickerson

Projects: COMBINE Multicellular Modelling, COVID-19 Disease Map, ModeleXchange initiative

Institutions: Auckland Bioengineering Institute

https://orcid.org/0000-0003-4667-9779
Marco Nobile

Projects: COMBINE Multicellular Modelling

Institutions: Bioinformatics MIlan Bicocca (BIMIB) - Università degli Studi di Milano Bicocca

https://orcid.org/0000-0002-7692-7203
Jürgen Pahle

Projects: COMBINE Multicellular Modelling

Institutions: University of Heidelberg

https://orcid.org/0000-0002-7637-7547
Rahuman Sheriff

Projects: ModeleXchange initiative

Institutions: The European Bioinformatics Institute < EMBL-EBI

https://orcid.org/0000-0003-0705-9809
ModeleXchange initiative
No description specified

Programme: COMBINE (Computational Modeling in Biology Network)

Public web page: Not specified

COMBINE Multicellular Modelling
No description specified

Programme: COMBINE (Computational Modeling in Biology Network)

Public web page: https://multicellml.org/

Auckland Bioengineering Institute

Country:  New Zealand

City: Auckland

Web page: http://www.abi.auckland.ac.nz/

Bioinformatics MIlan Bicocca (BIMIB) - Università degli Studi di Milano Bicocca

Country:  Italy

City: Milano

Web page: http://bimib.disco.unimib.it/

Heidelberg Institute for Theoretical Studies (HITS gGmbH)

Country:  Germany

City: Heidelberg

Web page: http://www.h-its.org/

Humboldt-Universität zu Berlin

Country:  Germany

City: Berlin

Web page: http://www.hu-berlin.de/

ICAHN Icahn School of Medicine at Mount Sinai

Country:  United States

City: New York

Web page: http://icahn.mssm.edu/

Indiana University Bloomington

Country:  United States

City: Bloomington

Web page: https://www.indiana.edu

Leibniz-Institut für Arbeitsforschung (IfADo)

Country:  Germany

City: 44139 Dortmund

Web page: http://www.ifado.de/

Norwegian University of Science and Technology

Country:  Norway

City: Trondheim

Web page: http://www.ntnu.edu/

Stellenbosch University

Country:  South Africa

City: Not specified

Web page: Not specified

Technische Universität Dresden

Country:  Germany

City: Dresden

Web page: http://tu-dresden.de/en

The European Bioinformatics Institute < EMBL-EBI

Country:  United Kingdom

City: Hinxton, Cambridgeshire

Web page: Not specified

University College London (UCL)

Country:  United Kingdom

City: London

Web page: https://www.ucl.ac.uk

University Maastricht

Country:  Netherlands

City: Maastricht

Web page: Not specified

University of Heidelberg

Country:  Germany

City: Heidelberg

Web page: http://www.uni-heidelberg.de/index_e.html

University of Newcastle-upon-Tyne

Country:  United Kingdom

City: Not specified

Web page: Not specified

University of Rostock

Country:  Germany

City: Rostock

Web page: http://www.uni-rostock.de

University of St Andrews

Country:  United Kingdom

City: St Andrews

Web page: https://www.st-andrews.ac.uk

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Abstract booklet of the Multicellular Mini-Symposium at ECMTB 2014 in Gothenburgh
COMBINE Multicellular Modelling

This mini-symposium, colocated at the ECMTB in Gothenburg, presents the state-of-the-art in computational methods for multicellular systems biology. It brings together developers and users of this software to identify common approaches and future challenges concerning multiscale integration, model specification, model exchange, scalability, workflow management as well as compliance to standards and guidelines. The session thus aims to provide an overview of the available modeling and simulation ...

Creator: Walter de Back, TU Dresden

Submitter: Lutz Brusch

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Morpheus model of spatio-temporal YAP/Hippo pathway activation during liver regeneration
Early Metabolic Injury (LiSyM-EMI - Pillar I), COMBINE Multicellular Modelling

For the spatio-temporal dynamics of bile transport, bile canalicular dilation, mechanical stimulation and transduction of YAP signaling during liver regeneration see the open access publication and its appendix: Meyer et al. (2020) Bile canaliculi remodeling activates YAP via the actin cytoskeleton during liver regeneration. Molecular Systems Biology 16:e8985. https://doi.org/10.15252/msb.20198985

The model format is MorpheusML that can readily be loaded and run in the free and open source software ...

Creator: Lutz Brusch

Submitter: Lutz Brusch

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Morpheus model of spatio-temporal liver zonation from Wnt-Hh crosstalk
Early Metabolic Injury (LiSyM-EMI - Pillar I), COMBINE Multicellular Modelling

Spatio-temporal liver zonation in mouse and human with Wnt-Hh crosstalk and transport are modeled using coupled partial differential equations. The model file is in MorpheusML format and can be opened in the free, open-source multicellular modeling software Morpheus (https://morpheus.gitlab.io). In Morpheus, the model will simulate the time course (movie) of dynamic liver zonation for a 2D cross-section of several liver lobules, showing the patterns of Wnt ligands, intracellular Wnt signaling, ...

Creators: Lutz Brusch, Jörn Starruß, Michael Kücken

Submitter: Lutz Brusch

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The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE)
FAIRDOM, LiSyM Core Infrastructure and Management (LiSyM-PD), COMBINE Multicellular Modelling, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", COVID-19 Disease Map

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

Specifications of standards in systems and synthetic biology: status and developments in 2020
FAIRDOM, LiSyM Core Infrastructure and Management (LiSyM-PD), COMBINE Multicellular Modelling, COVID-19 Disease Map

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

Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices.
FAIRDOM, LiSyM Core Infrastructure and Management (LiSyM-PD), COMBINE Multicellular Modelling, COVID-19 Disease Map

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 2019
FAIRDOM, LiSyM Core Infrastructure and Management (LiSyM-PD), COMBINE Multicellular Modelling, COVID-19 Disease Map

Abstract (Expand)

This special issue of the Journal of Integrative Bioinformatics presents an overview of COMBINE standards and their latest specifications. The standards cover representation formats for computational … modeling in synthetic and systems biology and include BioPAX, CellML, NeuroML, SBML, SBGN, SBOL and SED-ML. The articles in this issue contain updated specifications of SBGN Process Description Level 1 Version 2, SBML Level 3 Core Version 2 Release 2, SBOL Version 2.3.0, and SBOL Visual Version 2.1.

Authors: Falk Schreiber, Björn Sommer, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Sarah M. Keating, Matthias König, Chris Myers, David Nickerson, Dagmar Waltemath

Date Published: 13th Jul 2019

Publication Type: Journal

Harmonizing semantic annotations for computational models in biology
FAIRDOM, LiSyM Core Infrastructure and Management (LiSyM-PD), COMBINE Multicellular Modelling, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", COVID-19 Disease Map

Abstract (Expand)

Life science researchers use computational models to articulate and test hypotheses about the behavior of biological systems. Semantic annotation is a critical component for enhancing the interoperability … and reusability of such models as well as for the integration of the data needed for model parameterization and validation. Encoded as machine-readable links to knowledge resource terms, semantic annotations describe the computational or biological meaning of what models and data represent. These annotations help researchers find and repurpose models, accelerate model composition and enable knowledge integration across model repositories and experimental data stores. However, realizing the potential benefits of semantic annotation requires the development of model annotation standards that adhere to a community-based annotation protocol. Without such standards, tool developers must account for a variety of annotation formats and approaches, a situation that can become prohibitively cumbersome and which can defeat the purpose of linking model elements to controlled knowledge resource terms. Currently, no consensus protocol for semantic annotation exists among the larger biological modeling community. Here, we report on the landscape of current annotation practices among the COmputational Modeling in BIology NEtwork community and provide a set of recommendations for building a consensus approach to semantic annotation.

Authors: Maxwell Lewis Neal, Matthias König, David Nickerson, Göksel Mısırlı, Reza Kalbasi, Andreas Dräger, Koray Atalag, Vijayalakshmi Chelliah, Michael T Cooling, Daniel L Cook, Sharon Crook, Miguel de Alba, Samuel H Friedman, Alan Garny, John H Gennari, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nick Juty, Chris Myers, Brett G Olivier, Herbert M Sauro, Martin Scharm, Jacky L Snoep, Vasundra Touré, Anil Wipat, Olaf Wolkenhauer, Dagmar Waltemath

Date Published: 1st Mar 2019

Publication Type: Journal

Data Formats for Systems Biology and Quantitative Modeling
FAIRDOM, LiSyM Core Infrastructure and Management (LiSyM-PD), COMBINE Multicellular Modelling, COVID-19 Disease Map

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

A brief history of COMBINE
FAIRDOM, LiSyM Core Infrastructure and Management (LiSyM-PD), COMBINE Multicellular Modelling, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik"

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

FAIRDOMHub: a repository and collaboration environment for sharing systems biology research.
LiSyM Core Infrastructure and Management (LiSyM-PD), COMBINE Multicellular Modelling, TRALAMINOL, GMDS Project Group "FAIRe Dateninfrastrukturen für die Biomedizinische Informatik", COVID-19 Disease Map

Abstract (Expand)

The FAIRDOMHub is a repository for publishing FAIR (Findable, Accessible, Interoperable and Reusable) Data, Operating procedures and Models (https://fairdomhub.org/) for the Systems Biology community. … It is a web-accessible repository for storing and sharing systems biology research assets. It enables researchers to organize, share and publish data, models and protocols, interlink them in the context of the systems biology investigations that produced them, and to interrogate them via API interfaces. By using the FAIRDOMHub, researchers can achieve more effective exchange with geographically distributed collaborators during projects, ensure results are sustained and preserved and generate reproducible publications that adhere to the FAIR guiding principles of data stewardship.

Authors: K. Wolstencroft, O. Krebs, J. L. Snoep, N. J. Stanford, F. Bacall, M. Golebiewski, R. Kuzyakiv, Q. Nguyen, S. Owen, S. Soiland-Reyes, J. Straszewski, D. D. van Niekerk, A. R. Williams, L. Malmstrom, B. Rinn, W. Muller, C. Goble

Date Published: 4th Jan 2017

Publication Type: Journal

Lessons from SBML Level 3 extensions
Multi-Scale Models for Personalized Liver Function Tests (LiSyM-MM-PLF), COMBINE Multicellular Modelling

An overview over important lessons from the experience with SBML Level 3 extension for the MultiCellML language.

Creator: Matthias König

Submitter: Matthias König

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

Creator: Lutz Brusch

Submitter: Lutz Brusch

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Workshop and Hackathon "Multicellular model description and cross-simulator exchange"

Aim Multicellular spatial models have become an essential tool in quantitative biology and multiple model formalisms and simulation frameworks coexist. Progress towards software interoperability and reproducibility requires a novel model description language and conversion library, complementing SBML. Building on the community‘s practical experiences with multiple formalisms and simulators, we aim at (1) defining the concept for a multicellular language while simultaneously (2) exploring automated ...

Start Date: 1st Sep 2019

End Date: 4th Sep 2019

Event Website: https://multicellml.org/wiki/doku.php?id=hackathon

Country:  Germany

City: Dresden

Multi-scale modeling platforms in multicellular systems biology

This mini-symposium, colocated at the ECMTB in Gothenburg, presents the state-of-the-art in computational methods for multicellular systems biology. It brings together developers and users of this software to identify common approaches and future challenges concerning multiscale integration, model specification, model exchange, scalability, workflow management as well as compliance to standards and guidelines. The session thus aims to provide an overview of the available modeling and simulation ...

Start Date: 19th Jun 2014

End Date: 19th Jun 2014

Event Website: https://imc.zih.tu-dresden.de/wiki/multisysbio2014/

Country:  Sweden

City: Gothenburg

Morpheus Simulator Overview
COMBINE Multicellular Modelling
No description specified

Creators: Lutz Brusch, Jörn Starruß

Submitter: Lutz Brusch

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Chaste Simulator Overview
COMBINE Multicellular Modelling
No description specified

Creators: Lutz Brusch, Jochen Kursawe, Jörn Starruß

Submitter: Lutz Brusch

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CompuCell3D Simulator Overview
COMBINE Multicellular Modelling
No description specified

Creators: Juliano Ferrari Gianlupi, Lutz Brusch, Jörn Starruß

Submitter: Juliano Ferrari Gianlupi

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