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Sarwar DM, Nickerson DP. CellML Model Discovery with the Physiome Model Repository. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11681-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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2
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Altamirano-Diaz L, Kassay AD, Serajelahi B, McIntyre CW, Filler G, Kharche SR. Arterial Hypertension and Unusual Ascending Aortic Dilatation in a Neonate With Acute Kidney Injury: Mechanistic Computer Modeling. Front Physiol 2019; 10:1391. [PMID: 31780955 PMCID: PMC6856675 DOI: 10.3389/fphys.2019.01391] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 10/25/2019] [Indexed: 01/23/2023] Open
Abstract
Background Neonatal asphyxia caused kidney injury and severe hypertension in a newborn. An unusually dilatated ascending aorta developed. Dialysis and pharmacological treatment led to partial recovery of the ascending aortic diameters. It was hypothesized that the aortic dilatation may be associated with aortic stiffening, peripheral resistance, and cardiovascular changes. Mathematical modeling was used to better understand the potential causes of the hypertension, and to confirm our clinical treatment within the confines of the model's capabilities. Methods The patient's systolic arterial blood pressure showed hypertension. Echocardiographic exams showed ascending aorta dilatation during hypertension, which partially normalized upon antihypertensive treatment. To explore the underlying mechanisms of the aortic dilatation and hypertension, an existing lumped parameter hemodynamics model was deployed. Hypertension was simulated using realistic literature informed parameter values. It was also simulated using large parameter perturbations to demonstrate effects. Simulations were designed to permit examination of causal mechanisms. The hypertension inducing effects of aortic stiffnesses, vascular resistances, and cardiac hypertrophy on blood flow and pressure were simulated. Sensitivity analysis was used to stratify causes. Results In agreement with our clinical diagnosis, the model showed that an increase of aortic stiffness followed by augmentation of peripheral resistance are the prime causes of realistic hypertension. Increased left ventricular elastance may also cause hypertension. Ascending aortic pressure and flow increased in the simultaneous presence of left ventricle hypertrophy and augmented small vessel resistance, which indicate a plausible condition for ascending aorta dilatation. In case of realistic hypertension, sensitivity analysis showed that the treatment of both the large vessel stiffness and small vessel resistance are more important in comparison to cardiac hypertrophy. Conclusion and Discussion Large vessel stiffness was found to be the prime factor in arterial hypertension, which confirmed the clinical treatment. Treatment of cardiac hypertrophy appears to provide significant benefit but may be secondary to treatment of large vessel stiffness. The quantitative grading of pathophysiological mechanisms provided by the modeling may contribute to treatment recommendations. The model was limited due to a lack of data suitable to permit model identification.
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Affiliation(s)
- Luis Altamirano-Diaz
- Department of Paediatrics, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Children's Health Research Institute, London, ON, Canada.,Paediatric Cardiopulmonary Research Laboratory, LHSC, London, ON, Canada
| | | | - Baran Serajelahi
- Department of Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Christopher W McIntyre
- Department of Paediatrics, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Lawson Health Research Institute, London, ON, Canada.,Department of Medical Biophysics, Western University, London, ON, Canada
| | - Guido Filler
- Department of Paediatrics, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Children's Health Research Institute, London, ON, Canada.,Lawson Health Research Institute, London, ON, Canada.,Department of Medical Biophysics, Western University, London, ON, Canada
| | - Sanjay R Kharche
- Lawson Health Research Institute, London, ON, Canada.,Department of Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada.,Department of Medical Biophysics, Western University, London, ON, Canada
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Cowan AE, Mendes P, Blinov ML. ModelBricks-modules for reproducible modeling improving model annotation and provenance. NPJ Syst Biol Appl 2019; 5:37. [PMID: 31602314 PMCID: PMC6783478 DOI: 10.1038/s41540-019-0114-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 08/28/2019] [Indexed: 01/27/2023] Open
Abstract
Most computational models in biology are built and intended for "single-use"; the lack of appropriate annotation creates models where the assumptions are unknown, and model elements are not uniquely identified. Simply recreating a simulation result from a publication can be daunting; expanding models to new and more complex situations is a herculean task. As a result, new models are almost always created anew, repeating literature searches for kinetic parameters, initial conditions and modeling specifics. It is akin to building a brick house starting with a pile of clay. Here we discuss a concept for building annotated, reusable models, by starting with small well-annotated modules we call ModelBricks. Curated ModelBricks, accessible through an open database, could be used to construct new models that will inherit ModelBricks annotations and thus be easier to understand and reuse. Key features of ModelBricks include reliance on a commonly used standard language (SBML), rule-based specification describing species as a collection of uniquely identifiable molecules, association with model specific numerical parameters, and more common annotations. Physical bricks can vary substantively; likewise, to be useful the structure of ModelBricks must be highly flexible-it should encapsulate mechanisms from single reactions to multiple reactions in a complex process. Ultimately, a modeler would be able to construct large models by using multiple ModelBricks, preserving annotations and provenance of model elements, resulting in a highly annotated model. We envision the library of ModelBricks to rapidly grow from community contributions. Persistent citable references will incentivize model creators to contribute new ModelBricks.
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Affiliation(s)
- Ann E. Cowan
- Center for Cell Analysis and Modeling, UConn Health, Farmington, CT USA
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT USA
| | - Pedro Mendes
- Center for Cell Analysis and Modeling, UConn Health, Farmington, CT USA
- Center for Quantitative Medicine, UConn Health, Farmington, CT USA
- Department of Cell Biology, UConn Health, Farmington, CT USA
| | - Michael L. Blinov
- Center for Cell Analysis and Modeling, UConn Health, Farmington, CT USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT USA
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4
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Neal ML, König M, Nickerson D, Mısırlı G, Kalbasi R, Dräger A, Atalag K, Chelliah V, Cooling MT, Cook DL, Crook S, de Alba M, Friedman SH, Garny A, Gennari JH, Gleeson P, Golebiewski M, Hucka M, Juty N, Myers C, Olivier BG, Sauro HM, Scharm M, Snoep JL, Touré V, Wipat A, Wolkenhauer O, Waltemath D. Harmonizing semantic annotations for computational models in biology. Brief Bioinform 2019; 20:540-550. [PMID: 30462164 PMCID: PMC6433895 DOI: 10.1093/bib/bby087] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/08/2018] [Accepted: 08/17/2018] [Indexed: 02/06/2023] Open
Abstract
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.
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Affiliation(s)
- Maxwell Lewis Neal
- Seattle Children’s Research Institute, Center for Global Infectious Disease Research, Seattle, USA
| | - Matthias König
- Department of Biology, Humboldt-University Berlin, Institute for Theoretical Biology, Berlin, Germany
| | - David Nickerson
- Auckland Bioengineering Institute, University of Auckland, Auckland, NZ
| | - Göksel Mısırlı
- School of Computing and Mathematics, Keele University, Keele, UK
| | - Reza Kalbasi
- Auckland Bioengineering Institute, University of Auckland, Auckland, NZ
| | - Andreas Dräger
- Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens, Center for Bioinformatics Tübingen (ZBIT), University of Tübingen, Tübingen, Germany
- Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Koray Atalag
- Auckland Bioengineering Institute, University of Auckland, Auckland, NZ
| | - Vijayalakshmi Chelliah
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Michael T Cooling
- Auckland Bioengineering Institute, University of Auckland, Auckland, NZ
| | - Daniel L Cook
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA
| | - Sharon Crook
- School of Mathematical and Statistical Sciences, Arizona State University, Tempe, USA
| | - Miguel de Alba
- German Federal Institute for Risk Assessment, Berlin, Germany
| | | | - Alan Garny
- Auckland Bioengineering Institute, University of Auckland, Auckland, NZ
| | - John H Gennari
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA, USA
| | - Padraig Gleeson
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
| | - Martin Golebiewski
- Heidelberg Institute for Theoretical Studies (HITS gGmbH), Heidelberg, Germany
| | - Michael Hucka
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA
| | - Nick Juty
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Chris Myers
- Department of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT, USA
| | - Brett G Olivier
- Systems Bioinformatics, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Modelling of Biological Processes, BioQUANT/COS, Heidelberg University, Germany
| | - Herbert M Sauro
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Martin Scharm
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
| | - Jacky L Snoep
- Department of Biochemistry, Stellenbosch University, Matieland, South Africa
- Department of Molecular Cell Physiology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Manchester Institute for Biotechnology, University of Manchester, Manchester, UK
| | - Vasundra Touré
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Anil Wipat
- School of Computing Science, Newcastle University, Newcastle upon Tyne, UK
| | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
- Stellenbosch Institute for Advanced Study (STIAS), Stellenbosch, South Africa
| | - Dagmar Waltemath
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
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Stanford NJ, Scharm M, Dobson PD, Golebiewski M, Hucka M, Kothamachu VB, Nickerson D, Owen S, Pahle J, Wittig U, Waltemath D, Goble C, Mendes P, Snoep J. Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. Methods Mol Biol 2019; 2049:285-314. [PMID: 31602618 DOI: 10.1007/978-1-4939-9736-7_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
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.
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Affiliation(s)
| | - Martin Scharm
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
| | - Paul D Dobson
- School of Computer Science, University of Manchester, Manchester, UK
| | - Martin Golebiewski
- Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Michael Hucka
- Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA, USA
| | | | - David Nickerson
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Stuart Owen
- School of Computer Science, University of Manchester, Manchester, UK
| | - Jürgen Pahle
- BIOMS/BioQuant, Heidelberg University, Heidelberg, Germany.
| | - Ulrike Wittig
- Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Dagmar Waltemath
- Medical Informatics, University Medicine Greifswald, Greifswald, Germany
| | - Carole Goble
- School of Computer Science, University of Manchester, Manchester, UK
| | - Pedro Mendes
- Centre for Quantitative Medicine, University of Connecticut, Farmington, CT, USA
| | - Jacky Snoep
- School of Computer Science, University of Manchester, Manchester, UK.,Biochemistry, Stellenbosch University, Stellenbosch, South Africa
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6
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Viswan NA, HarshaRani GV, Stefan MI, Bhalla US. FindSim: A Framework for Integrating Neuronal Data and Signaling Models. Front Neuroinform 2018; 12:38. [PMID: 29997492 PMCID: PMC6028806 DOI: 10.3389/fninf.2018.00038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 06/05/2018] [Indexed: 12/30/2022] Open
Abstract
Current experiments touch only small but overlapping parts of very complex subcellular signaling networks in neurons. Even with modern optical reporters and pharmacological manipulations, a given experiment can only monitor and control a very small subset of the diverse, multiscale processes of neuronal signaling. We have developed FindSim (Framework for Integrating Neuronal Data and SIgnaling Models) to anchor models to structured experimental datasets. FindSim is a framework for integrating many individual electrophysiological and biochemical experiments with large, multiscale models so as to systematically refine and validate the model. We use a structured format for encoding the conditions of many standard physiological and pharmacological experiments, specifying which parts of the model are involved, and comparing experiment outcomes with model output. A database of such experiments is run against successive generations of composite cellular models to iteratively improve the model against each experiment, while retaining global model validity. We suggest that this toolchain provides a principled and scalable way to tackle model complexity and diversity of data sources.
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Affiliation(s)
- Nisha A Viswan
- National Centre for Biological Sciences, Bangalore, India.,Tata Institute of Fundamental Research, The University of Trans-Disciplinary Health Sciences and Technology, Bangalore, India
| | | | - Melanie I Stefan
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom.,ZJU-UoE Institute, Zhejiang University, Hangzhou, China
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7
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de Boer TP, van der Werf S, Hennekam B, Nickerson DP, Garny A, Gerbrands M, Bouwmeester RAM, Rozendal AP, Torfs E, van Rijen HVM. eSolv, a CellML-based simulation front-end for online teaching. ADVANCES IN PHYSIOLOGY EDUCATION 2017; 41:425-427. [PMID: 28679581 DOI: 10.1152/advan.00127.2016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 04/04/2017] [Accepted: 04/04/2017] [Indexed: 06/07/2023]
Affiliation(s)
- Teun P de Boer
- Department of Medical Physiology, Division Heart and Lungs, University Medical Center, Utrecht, The Netherlands;
| | - Sape van der Werf
- Center for Research and Development of Education, Education Center, University Medical Center, Utrecht, The Netherlands
| | - Bas Hennekam
- Center for Research and Development of Education, Education Center, University Medical Center, Utrecht, The Netherlands
| | | | - Alan Garny
- The University of Auckland, Auckland, New Zealand; and
| | - Michèle Gerbrands
- Center for Research and Development of Education, Education Center, University Medical Center, Utrecht, The Netherlands
- Biomedical Sciences, Education Center, University Medical Center, Utrecht, The Netherlands
| | - Rianne A M Bouwmeester
- Department of Medical Physiology, Division Heart and Lungs, University Medical Center, Utrecht, The Netherlands
- Biomedical Sciences, Education Center, University Medical Center, Utrecht, The Netherlands
| | - Anne-Petra Rozendal
- Center for Research and Development of Education, Education Center, University Medical Center, Utrecht, The Netherlands
| | - Ellen Torfs
- Center for Research and Development of Education, Education Center, University Medical Center, Utrecht, The Netherlands
| | - Harold V M van Rijen
- Department of Medical Physiology, Division Heart and Lungs, University Medical Center, Utrecht, The Netherlands
- Biomedical Sciences, Education Center, University Medical Center, Utrecht, The Netherlands
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8
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Hoekstra AG, Alowayyed S, Lorenz E, Melnikova N, Mountrakis L, van Rooij B, Svitenkov A, Závodszky G, Zun P. Towards the virtual artery: a multiscale model for vascular physiology at the physics-chemistry-biology interface. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2016.0146. [PMID: 27698036 PMCID: PMC5052730 DOI: 10.1098/rsta.2016.0146] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/14/2016] [Indexed: 05/27/2023]
Abstract
This discussion paper introduces the concept of the Virtual Artery as a multiscale model for arterial physiology and pathologies at the physics-chemistry-biology (PCB) interface. The cellular level is identified as the mesoscopic level, and we argue that by coupling cell-based models with other relevant models on the macro- and microscale, a versatile model of arterial health and disease can be composed. We review the necessary ingredients, both models of arteries at many different scales, as well as generic methods to compose multiscale models. Next, we discuss how this can be combined into the virtual artery. Finally, we argue that the concept of models at the PCB interface could or perhaps should become a powerful paradigm, not only as in our case for studying physiology, but also for many other systems that have such PCB interfaces.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.
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Affiliation(s)
- Alfons G Hoekstra
- Computational Science Laboratory, Institute for Informatics, Faculty of Science, University of Amsterdam, Sciencepark 904, 1098 XH Amsterdam, The Netherlands High Performance Computing Department, ITMO University, Saint Petersburg, Russia
| | - Saad Alowayyed
- Computational Science Laboratory, Institute for Informatics, Faculty of Science, University of Amsterdam, Sciencepark 904, 1098 XH Amsterdam, The Netherlands King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Eric Lorenz
- Computational Science Laboratory, Institute for Informatics, Faculty of Science, University of Amsterdam, Sciencepark 904, 1098 XH Amsterdam, The Netherlands Electric Ant Lab BV, Panamalaan 4 K, 1019AZ Amsterdam, The Netherlands
| | - Natalia Melnikova
- High Performance Computing Department, ITMO University, Saint Petersburg, Russia
| | - Lampros Mountrakis
- Computational Science Laboratory, Institute for Informatics, Faculty of Science, University of Amsterdam, Sciencepark 904, 1098 XH Amsterdam, The Netherlands
| | - Britt van Rooij
- Computational Science Laboratory, Institute for Informatics, Faculty of Science, University of Amsterdam, Sciencepark 904, 1098 XH Amsterdam, The Netherlands
| | - Andrew Svitenkov
- High Performance Computing Department, ITMO University, Saint Petersburg, Russia
| | - Gábor Závodszky
- Computational Science Laboratory, Institute for Informatics, Faculty of Science, University of Amsterdam, Sciencepark 904, 1098 XH Amsterdam, The Netherlands
| | - Pavel Zun
- High Performance Computing Department, ITMO University, Saint Petersburg, Russia
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9
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Fernandez J, Zhang J, Heidlauf T, Sartori M, Besier T, Röhrle O, Lloyd D. Multiscale musculoskeletal modelling, data-model fusion and electromyography-informed modelling. Interface Focus 2016; 6:20150084. [PMID: 27051510 DOI: 10.1098/rsfs.2015.0084] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
This paper proposes methods and technologies that advance the state of the art for modelling the musculoskeletal system across the spatial and temporal scales; and storing these using efficient ontologies and tools. We present population-based modelling as an efficient method to rapidly generate individual morphology from only a few measurements and to learn from the ever-increasing supply of imaging data available. We present multiscale methods for continuum muscle and bone models; and efficient mechanostatistical methods, both continuum and particle-based, to bridge the scales. Finally, we examine both the importance that muscles play in bone remodelling stimuli and the latest muscle force prediction methods that use electromyography-assisted modelling techniques to compute musculoskeletal forces that best reflect the underlying neuromuscular activity. Our proposal is that, in order to have a clinically relevant virtual physiological human, (i) bone and muscle mechanics must be considered together; (ii) models should be trained on population data to permit rapid generation and use underlying principal modes that describe both muscle patterns and morphology; and (iii) these tools need to be available in an open-source repository so that the scientific community may use, personalize and contribute to the database of models.
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Affiliation(s)
- J Fernandez
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand; Department of Engineering Science, University of Auckland, Auckland, New Zealand
| | - J Zhang
- Auckland Bioengineering Institute , University of Auckland , Auckland , New Zealand
| | - T Heidlauf
- Institut für Mechanik (Bau) , University of Stuttgart , Stuttgart , Germany
| | - M Sartori
- Department of Neurorehabilitation Engineering , University Medical Center Göttingen , Göttingen , Germany
| | - T Besier
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand; Department of Engineering Science, University of Auckland, Auckland, New Zealand
| | - O Röhrle
- Institut für Mechanik (Bau) , University of Stuttgart , Stuttgart , Germany
| | - D Lloyd
- Centre for Musculoskeletal Research, Menzies Health Institute Queensland, Griffith University, Queensland, Australia; School of Rehabilitation Sciences, Griffith University, Queensland, Australia
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Shalbaf F, Du P, Lovell NH, Dokos S, Vaghefi E. A 3D-continuum bidomain model of retinal electrical stimulation using an anatomically detailed mesh. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2016; 2015:2291-4. [PMID: 26736750 DOI: 10.1109/embc.2015.7318850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A continuum bidomain model of sub-retinal electrical stimulation on an anatomically detailed mesh of retina is presented. The underlying geometry is made up of 256 B-scans of optical coherence tomography (OCT) images of a healthy human retina, covering approximately 6×2 mm(2) centered on the macula. The OCT images are initially segmented and digitized into five major retinal layers comprising passive and active retinal cell types. This computational mesh is then used to model a subretinal hexapolar biphasic electrical stimulation. Our results indicate that the ultra-structure of the retina results in an asymmetric spatial extracellular potential distribution, leading to an irregular pattern of retinal ganglion cell activation. This finding is in contrast to focal circular activation previously reported in retinal electrical stimulation modeling with a uniform mesh.
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11
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E-Cyanobacterium.org: A Web-Based Platform for Systems Biology of Cyanobacteria. COMPUTATIONAL METHODS IN SYSTEMS BIOLOGY 2016. [DOI: 10.1007/978-3-319-45177-0_20] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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12
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Cooper J, Spiteri RJ, Mirams GR. Cellular cardiac electrophysiology modeling with Chaste and CellML. Front Physiol 2015; 5:511. [PMID: 25610400 PMCID: PMC4285015 DOI: 10.3389/fphys.2014.00511] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 12/09/2014] [Indexed: 11/18/2022] Open
Abstract
Chaste is an open-source C++ library for computational biology that has well-developed cardiac electrophysiology tissue simulation support. In this paper, we introduce the features available for performing cardiac electrophysiology action potential simulations using a wide range of models from the Physiome repository. The mathematics of the models are described in CellML, with units for all quantities. The primary idea is that the model is defined in one place (the CellML file), and all model code is auto-generated at compile or run time; it never has to be manually edited. We use ontological annotation to identify model variables describing certain biological quantities (membrane voltage, capacitance, etc.) to allow us to import any relevant CellML models into the Chaste framework in consistent units and to interact with them via consistent interfaces. This approach provides a great deal of flexibility for analysing different models of the same system. Chaste provides a wide choice of numerical methods for solving the ordinary differential equations that describe the models. Fixed-timestep explicit and implicit solvers are provided, as discussed in previous work. Here we introduce the Rush–Larsen and Generalized Rush–Larsen integration techniques, made available via symbolic manipulation of the model equations, which are automatically rearranged into the forms required by these approaches. We have also integrated the CVODE solvers, a ‘gold standard’ for stiff systems, and we have developed support for symbolic computation of the Jacobian matrix, yielding further increases in the performance and accuracy of CVODE. We discuss some of the technical details of this work and compare the performance of the available numerical methods. Finally, we discuss how this is generalized in our functional curation framework, which uses a domain-specific language for defining complex experiments as a basis for comparison of model behavior.
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Affiliation(s)
- Jonathan Cooper
- Computational Biology, Department of Computer Science, University of Oxford Oxford, UK
| | - Raymond J Spiteri
- Numerical Simulation Research Lab, Department of Computer Science, University of Saskatchewan Saskatoon, SK, Canada
| | - Gary R Mirams
- Computational Biology, Department of Computer Science, University of Oxford Oxford, UK
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13
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Nickerson DP, Ladd D, Hussan JR, Safaei S, Suresh V, Hunter PJ, Bradley CP. Using CellML with OpenCMISS to Simulate Multi-Scale Physiology. Front Bioeng Biotechnol 2015; 2:79. [PMID: 25601911 PMCID: PMC4283644 DOI: 10.3389/fbioe.2014.00079] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 12/11/2014] [Indexed: 11/13/2022] Open
Abstract
OpenCMISS is an open-source modeling environment aimed, in particular, at the solution of bioengineering problems. OpenCMISS consists of two main parts: a computational library (OpenCMISS-Iron) and a field manipulation and visualization library (OpenCMISS-Zinc). OpenCMISS is designed for the solution of coupled multi-scale, multi-physics problems in a general-purpose parallel environment. CellML is an XML format designed to encode biophysically based systems of ordinary differential equations and both linear and non-linear algebraic equations. A primary design goal of CellML is to allow mathematical models to be encoded in a modular and reusable format to aid reproducibility and interoperability of modeling studies. In OpenCMISS, we make use of CellML models to enable users to configure various aspects of their multi-scale physiological models. This avoids the need for users to be familiar with the OpenCMISS internal code in order to perform customized computational experiments. Examples of this are: cellular electrophysiology models embedded in tissue electrical propagation models; material constitutive relationships for mechanical growth and deformation simulations; time-varying boundary conditions for various problem domains; and fluid constitutive relationships and lumped-parameter models. In this paper, we provide implementation details describing how CellML models are integrated into multi-scale physiological models in OpenCMISS. The external interface OpenCMISS presents to users is also described, including specific examples exemplifying the extensibility and usability these tools provide the physiological modeling and simulation community. We conclude with some thoughts on future extension of OpenCMISS to make use of other community developed information standards, such as FieldML, SED-ML, and BioSignalML. Plans for the integration of accelerator code (graphical processing unit and field programmable gate array) generated from CellML models is also discussed.
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Affiliation(s)
- David P. Nickerson
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - David Ladd
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Jagir R. Hussan
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Soroush Safaei
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Vinod Suresh
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
- Department of Engineering Science, University of Auckland, Auckland, New Zealand
| | - Peter J. Hunter
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
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Gomez-Cabrero D, Lluch-Ariet M, Tegnér J, Cascante M, Miralles F, Roca J. Synergy-COPD: a systems approach for understanding and managing chronic diseases. J Transl Med 2014; 12 Suppl 2:S2. [PMID: 25472826 PMCID: PMC4255903 DOI: 10.1186/1479-5876-12-s2-s2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Chronic diseases (CD) are generating a dramatic societal burden worldwide that is expected to persist over the next decades. The challenges posed by the epidemics of CD have triggered a novel health paradigm with major consequences on the traditional concept of disease and with a profound impact on key aspects of healthcare systems. We hypothesized that the development of a systems approach to understand CD together with the generation of an ecosystem to transfer the acquired knowledge into the novel healthcare scenario may contribute to a cost-effective enhancement of health outcomes. To this end, we designed the Synergy-COPD project wherein the heterogeneity of chronic obstructive pulmonary disease (COPD) was addressed as a use case representative of CD. The current manuscript describes main features of the project design and the strategies put in place for its development, as well the expected outcomes during the project life-span. Moreover, the manuscript serves as introductory and unifying chapter of the different papers associated to the Supplement describing the characteristics, tools and the objectives of Synergy-COPD.
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Affiliation(s)
- David Gomez-Cabrero
- Unit of Computational Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Magi Lluch-Ariet
- Department of eHealth, Barcelona Digital, 08017 Barcelona, Catalunya, Spain
| | - Jesper Tegnér
- Unit of Computational Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Marta Cascante
- Hospital Clinic - Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS). Universitat de Barcelona, 08036 Barcelona, Spain
- Departament de Bioquimica i Biologia Molecular i IBUB, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain
| | - Felip Miralles
- Department of eHealth, Barcelona Digital, 08017 Barcelona, Catalunya, Spain
| | - Josep Roca
- Hospital Clinic - Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS). Universitat de Barcelona, 08036 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Bunyola, Balearic Islands
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15
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Tieri P, Nardini C. Signalling pathway database usability: lessons learned. MOLECULAR BIOSYSTEMS 2014; 9:2401-7. [PMID: 23942525 DOI: 10.1039/c3mb70242a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND issues and limitations related to accessibility, understandability and ease of use of signalling pathway databases may hamper or divert research workflow, leading, in the worst case, to the generation of confusing reference frameworks and misinterpretation of experimental results. In an attempt to retrieve signalling pathway data related to a specific set of test genes, we queried and analysed the results from six of the major curated signalling pathway databases: Reactome, PathwayCommons, KEGG, InnateDB, PID, and Wikipathways. FINDINGS although we expected differences - often a desirable feature for the integration of each individual query, we observed variations of exceptional magnitude, with disproportionate quality and quantity of the results. Some of the more remarkable differences can be explained by the diverse conceptual designs and purposes of the databases, the types of data stored and the structure of the query, as well as by missing or erroneous descriptions of the search procedure. To go beyond the mere enumeration of these problems, we identified a number of operational features, in particular inner and cross coherence, which, once quantified, offer objective criteria to choose the best source of information. CONCLUSIONS in silico biology heavily relies on the information stored in databases. To ensure that computational biology mirrors biological reality and offers focused hypotheses to be experimentally validated, coherence of data codification is crucial and yet highly underestimated. We make practical recommendations for the end-user to cope with the current state of the databases as well as for the maintainers of those databases to contribute to the goal of the full enactment of the open data paradigm.
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Affiliation(s)
- Paolo Tieri
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Yue Yang Road 320, Shanghai, P. R. China
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16
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Britten RD, Christie GR, Little C, Miller AK, Bradley C, Wu A, Yu T, Hunter P, Nielsen P. FieldML, a proposed open standard for the Physiome project for mathematical model representation. Med Biol Eng Comput 2013; 51:1191-207. [PMID: 23900627 PMCID: PMC3825639 DOI: 10.1007/s11517-013-1097-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 07/02/2013] [Indexed: 11/28/2022]
Abstract
The FieldML project has made significant progress towards the goal of addressing the need to have open standards and open source software for representing finite element method (FEM) models and, more generally, multivariate field models, such as many of the models that are core to the euHeart project and the Physiome project. FieldML version 0.5 is the most recently released format from the FieldML project. It is an XML format that already has sufficient capability to represent the majority of euHeart’s explicit models such as the anatomical FEM models and simulation solution fields. The details of FieldML version 0.5 are presented, as well as its limitations and some discussion of the progress being made to address these limitations.
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17
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Winslow RL, Trayanova N, Geman D, Miller MI. Computational medicine: translating models to clinical care. Sci Transl Med 2013; 4:158rv11. [PMID: 23115356 DOI: 10.1126/scitranslmed.3003528] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Because of the inherent complexity of coupled nonlinear biological systems, the development of computational models is necessary for achieving a quantitative understanding of their structure and function in health and disease. Statistical learning is applied to high-dimensional biomolecular data to create models that describe relationships between molecules and networks. Multiscale modeling links networks to cells, organs, and organ systems. Computational approaches are used to characterize anatomic shape and its variations in health and disease. In each case, the purposes of modeling are to capture all that we know about disease and to develop improved therapies tailored to the needs of individuals. We discuss advances in computational medicine, with specific examples in the fields of cancer, diabetes, cardiology, and neurology. Advances in translating these computational methods to the clinic are described, as well as challenges in applying models for improving patient health.
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Affiliation(s)
- Raimond L Winslow
- The Institute for Computational Medicine, Center for Cardiovascular Bioinformatics and Modeling, and Department of Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA.
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18
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de Bono B, Hunter P. Integrating knowledge representation and quantitative modelling in physiology. Biotechnol J 2013; 7:958-72. [PMID: 22887885 DOI: 10.1002/biot.201100304] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A wealth of potentially shareable resources, such as data and models, is being generated through the study of physiology by computational means. Although in principle the resources generated are reusable, in practice, few can currently be shared. A key reason for this disparity stems from the lack of consistent cataloguing and annotation of these resources in a standardised manner. Here, we outline our vision for applying community-based modelling standards in support of an automated integration of models across physiological systems and scales. Two key initiatives, the Physiome Project and the European contribution - the Virtual Phsysiological Human Project, have emerged to support this multiscale model integration, and we focus on the role played by two key components of these frameworks, model encoding and semantic metadata annotation. We present examples of biomedical modelling scenarios (the endocrine effect of atrial natriuretic peptide, and the implications of alcohol and glucose toxicity) to illustrate the role that encoding standards and knowledge representation approaches, such as ontologies, could play in the management, searching and visualisation of physiology models, and thus in providing a rational basis for healthcare decisions and contributing towards realising the goal of of personalized medicine.
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Affiliation(s)
- Bernard de Bono
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
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Waltemath D, Henkel R, Hälke R, Scharm M, Wolkenhauer O. Improving the reuse of computational models through version control. Bioinformatics 2013; 29:742-8. [PMID: 23335018 DOI: 10.1093/bioinformatics/btt018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Only models that are accessible to researchers can be reused. As computational models evolve over time, a number of different but related versions of a model exist. Consequently, tools are required to manage not only well-curated models but also their associated versions. RESULTS In this work, we discuss conceptual requirements for model version control. Focusing on XML formats such as Systems Biology Markup Language and CellML, we present methods for the identification and explanation of differences and for the justification of changes between model versions. In consequence, researchers can reflect on these changes, which in turn have considerable value for the development of new models. The implementation of model version control will therefore foster the exploration of published models and increase their reusability.
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Affiliation(s)
- Dagmar Waltemath
- Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany.
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20
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Frangi AF, Hose DR, Hunter PJ, Ayache N, Brooks D. Special issue on medical imaging and image computing in computational physiology. IEEE TRANSACTIONS ON MEDICAL IMAGING 2013; 32:1-7. [PMID: 23409282 DOI: 10.1109/tmi.2012.2234320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
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21
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Carusi A, Burrage K, Rodríguez B. Bridging experiments, models and simulations: an integrative approach to validation in computational cardiac electrophysiology. Am J Physiol Heart Circ Physiol 2012; 303:H144-55. [PMID: 22582088 DOI: 10.1152/ajpheart.01151.2011] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Computational models in physiology often integrate functional and structural information from a large range of spatiotemporal scales from the ionic to the whole organ level. Their sophistication raises both expectations and skepticism concerning how computational methods can improve our understanding of living organisms and also how they can reduce, replace, and refine animal experiments. A fundamental requirement to fulfill these expectations and achieve the full potential of computational physiology is a clear understanding of what models represent and how they can be validated. The present study aims at informing strategies for validation by elucidating the complex interrelations among experiments, models, and simulations in cardiac electrophysiology. We describe the processes, data, and knowledge involved in the construction of whole ventricular multiscale models of cardiac electrophysiology. Our analysis reveals that models, simulations, and experiments are intertwined, in an assemblage that is a system itself, namely the model-simulation-experiment (MSE) system. We argue that validation is part of the whole MSE system and is contingent upon 1) understanding and coping with sources of biovariability; 2) testing and developing robust techniques and tools as a prerequisite to conducting physiological investigations; 3) defining and adopting standards to facilitate the interoperability of experiments, models, and simulations; 4) and understanding physiological validation as an iterative process that contributes to defining the specific aspects of cardiac electrophysiology the MSE system targets, rather than being only an external test, and that this is driven by advances in experimental and computational methods and the combination of both.
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22
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Waltemath D, Adams R, Bergmann FT, Hucka M, Kolpakov F, Miller AK, Moraru II, Nickerson D, Sahle S, Snoep JL, Le Novère N. Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language. BMC SYSTEMS BIOLOGY 2011; 5:198. [PMID: 22172142 PMCID: PMC3292844 DOI: 10.1186/1752-0509-5-198] [Citation(s) in RCA: 139] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Accepted: 12/15/2011] [Indexed: 11/17/2022]
Abstract
BACKGROUND The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools. RESULTS In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions. CONCLUSIONS With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from different fields of research can be accurately described and combined.
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Affiliation(s)
- Dagmar Waltemath
- Department of Systems Biology & Bioinformatics, Institute of Computer Science, University of Rostock, D-18051 Rostock, Germany
| | - Richard Adams
- Centre for Systems Biology Edinburgh, CHWaddington Building, University of Edinburgh, Edinburgh EH9 3JD, UK
| | - Frank T Bergmann
- California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Michael Hucka
- California Institute of Technology, 1200 East California Blvd., Pasadena, CA 91125, USA
| | - Fedor Kolpakov
- Institute of Systems Biology Ltd., Detskiy proezd 15, Novosibirsk, 630090, Russia
| | - Andrew K Miller
- Auckland Bioengineering Institute, The University of Auckland, Auckland, New Zealand
| | - Ion I Moraru
- Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - David Nickerson
- Auckland Bioengineering Institute, The University of Auckland, Auckland, New Zealand
| | - Sven Sahle
- BIOQUANT, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg, Germany
| | - Jacky L Snoep
- Department of Biochemistry, Stellenbosch University, Privatebag X1, Matieland 7602, South Africa
- Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, the University of Manchester, 131 Princess Street Manchester, M1 7DN, UK
- Molecular Cell Physiology, VU University, Amsterdam, The Netherlands
| | - Nicolas Le Novère
- EBI, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
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Niederer SA, Kerfoot E, Benson AP, Bernabeu MO, Bernus O, Bradley C, Cherry EM, Clayton R, Fenton FH, Garny A, Heidenreich E, Land S, Maleckar M, Pathmanathan P, Plank G, Rodríguez JF, Roy I, Sachse FB, Seemann G, Skavhaug O, Smith NP. Verification of cardiac tissue electrophysiology simulators using an N-version benchmark. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2011; 369:4331-51. [PMID: 21969679 PMCID: PMC3263775 DOI: 10.1098/rsta.2011.0139] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Ongoing developments in cardiac modelling have resulted, in particular, in the development of advanced and increasingly complex computational frameworks for simulating cardiac tissue electrophysiology. The goal of these simulations is often to represent the detailed physiology and pathologies of the heart using codes that exploit the computational potential of high-performance computing architectures. These developments have rapidly progressed the simulation capacity of cardiac virtual physiological human style models; however, they have also made it increasingly challenging to verify that a given code provides a faithful representation of the purported governing equations and corresponding solution techniques. This study provides the first cardiac tissue electrophysiology simulation benchmark to allow these codes to be verified. The benchmark was successfully evaluated on 11 simulation platforms to generate a consensus gold-standard converged solution. The benchmark definition in combination with the gold-standard solution can now be used to verify new simulation codes and numerical methods in the future.
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Affiliation(s)
- Steven A Niederer
- Department of Biomedical Engineering, Division of Imaging Sciences and Biomedical Engineering, King's College London, UK.
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Cooper J, Mirams GR, Niederer SA. High-throughput functional curation of cellular electrophysiology models. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2011; 107:11-20. [PMID: 21704062 DOI: 10.1016/j.pbiomolbio.2011.06.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 06/06/2011] [Indexed: 10/18/2022]
Abstract
Effective reuse of a quantitative mathematical model requires not just access to curated versions of the model equations, but also an understanding of the functional capabilities of the model, and the advisable scope of its application. To enable this "functional curation" we have developed a simulation environment that provides high-throughput evaluation of a mathematical model's functional response to an arbitrary user-defined protocol, and optionally compares the results against experimental data. In this study we demonstrate the efficacy of this simulation environment on 31 cardiac electrophysiology cell models using two test cases. The S1-S2 response is evaluated to characterise the models' restitution curves, and their L-type calcium channel current-voltage curves are evaluated. The significant variation in the response of these models, even when the models represent the same species and temperature, demonstrates the importance of knowing the functional characteristics of a model prior to its reuse. We also discuss the wider implications for this approach, in improving the selection of models for reuse, enabling the identification of models that exhibit particular experimentally observed phenomena, and making the incremental development of models more robust.
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Affiliation(s)
- Jonathan Cooper
- Oxford University Computing Laboratory, University of Oxford, Wolfson Building, Parks Road, Oxford OX13QD, UK.
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25
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Cooper J, Corrias A, Gavaghan D, Noble D. Considerations for the use of cellular electrophysiology models within cardiac tissue simulations. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2011; 107:74-80. [PMID: 21703295 DOI: 10.1016/j.pbiomolbio.2011.06.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 06/06/2011] [Indexed: 11/26/2022]
Abstract
The use of mathematical models to study cardiac electrophysiology has a long history, and numerous cellular scale models are now available, covering a range of species and cell types. Their use to study emergent properties in tissue is also widespread, typically using the monodomain or bidomain equations coupled to one or more cell models. Despite the relative maturity of this field, little has been written looking in detail at the interface between the cellular and tissue-level models. Mathematically this is relatively straightforward and well-defined. There are however many details and potential inconsistencies that need to be addressed, in order to ensure correct operation of a cellular model within a tissue simulation. This paper will describe these issues and how to address them. Simply having models available in a common format such as CellML is still of limited utility, with significant manual effort being required to integrate these models within a tissue simulation. We will thus also discuss the facilities available for automating this in a consistent fashion within Chaste, our robust and high-performance cardiac electrophysiology simulator. It will be seen that a common theme arising is the need to go beyond a representation of the model mathematics in a standard language, to include additional semantic information required in determining the model's interface, and hence to enhance interoperability. Such information can be added as metadata, but agreement is needed on the terms to use, including development of appropriate ontologies, if reliable automated use of CellML models is to become common.
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Affiliation(s)
- Jonathan Cooper
- Oxford University Computing Laboratory, University of Oxford, Wolfson Building, Parks Road, Oxford OX13QD, UK.
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26
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Orlowski P, Chappell M, Park CS, Grau V, Payne S. Modelling of pH dynamics in brain cells after stroke. Interface Focus 2011; 1:408-16. [PMID: 22419985 PMCID: PMC3262437 DOI: 10.1098/rsfs.2010.0025] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Accepted: 03/01/2011] [Indexed: 12/29/2022] Open
Abstract
The identification of salvageable brain tissue is a major challenge at stroke presentation. Standard techniques used in this context, such as the perfusion-diffusion mismatch, remain controversial. There is thus a need for new methods to help guide treatment. The potential role of pH imaging in this context is currently being investigated. Intracellular pH varies as a function of local perfusion, intracellular energy stores and time. Low pH triggers the production of free radicals and affects the calcium balance of the cells, which may lead to apoptosis and cell death. Thus, the characterization of pH dynamics may have predictive value for cell death after stroke, particularly when combined with novel imaging techniques. Therefore, we have extended an existing model of brain cellular metabolism to simulate the pH response of cells to ischaemia. Simulation results for conditions of reduced cerebral blood flow show good agreement for the evolution of intracellular pH with previously reported measurements and encourage the development of quantitative pH imaging to validate the predictive value of pH.
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Affiliation(s)
| | | | | | | | - Stephen Payne
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, UK
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27
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Overgaard M, Mogensen J. A framework for the study of multiple realizations: the importance of levels of analysis. Front Physiol 2011. [PMID: 21772823 PMCID: PMC3222887 DOI: 10.3389/fphys.2011.00079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The brain may undergo functional reorganizations. Selective loss of sensory input or training within a restricted part of a modality cause "shifts" within for instance somatotopic or tonotopic maps. Cross-modal plasticity occurs when input within a modality is absent - e.g., in the congenitally blind. Reorganizations are also found in functional recovery after brain injury. Focusing on such reorganizations, it may be studied whether a cognitive or conscious process can exclusively be mediated by one neural substrate - or may be associated with multiple neural representations. This is typically known as the problem of multiple realization - an essentially empirical issue with wide theoretical implications. This issue may appear to have a simple solution. When, for instance, the symptoms associated with brain injury disappear and the recovery is associated with increased activities within spared regions of the brain, it is tempting to conclude that the processes originally associated with the injured part of the brain are now mediated by an alternative neural substrate. Such a conclusion is, however, not a simple matter. Without a more thorough analysis, it cannot be concluded that a functional recovery of for instance language or attention is necessarily associated with a novel representation of the processes lost to injury. Alternatively, for instance, the recovery may reflect that apparently similar surface phenomena are obtained via dissimilar cognitive mechanisms. In this paper we propose a theoretical framework, which we believe can guide the design and interpretations of studies of post-traumatic recovery. It is essential to distinguish between a number of levels of analysis - including a differentiation between the surface phenomena and the underlying information processing - when addressing, for instance, whether a pre-traumatic and post-traumatically recovered cognitive or conscious process are actually the same. We propose a (somewhat preliminary) system of levels of analysis, which can be applied to such studies.
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Affiliation(s)
- Morten Overgaard
- CNRU, Department of Psychology and Communication, Aalborg University Aalborg, Denmark
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28
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Winslow RL. A framework for the study of multiple realizations: the importance of levels of analysis. Front Physiol 2011; 2:79. [PMID: 21772823 PMCID: PMC3222887 DOI: 10.3389/fpsyg.2011.00079] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Accepted: 04/13/2011] [Indexed: 12/12/2022] Open
Abstract
The brain may undergo functional reorganizations. Selective loss of sensory input or training within a restricted part of a modality cause "shifts" within for instance somatotopic or tonotopic maps. Cross-modal plasticity occurs when input within a modality is absent - e.g., in the congenitally blind. Reorganizations are also found in functional recovery after brain injury. Focusing on such reorganizations, it may be studied whether a cognitive or conscious process can exclusively be mediated by one neural substrate - or may be associated with multiple neural representations. This is typically known as the problem of multiple realization - an essentially empirical issue with wide theoretical implications. This issue may appear to have a simple solution. When, for instance, the symptoms associated with brain injury disappear and the recovery is associated with increased activities within spared regions of the brain, it is tempting to conclude that the processes originally associated with the injured part of the brain are now mediated by an alternative neural substrate. Such a conclusion is, however, not a simple matter. Without a more thorough analysis, it cannot be concluded that a functional recovery of for instance language or attention is necessarily associated with a novel representation of the processes lost to injury. Alternatively, for instance, the recovery may reflect that apparently similar surface phenomena are obtained via dissimilar cognitive mechanisms. In this paper we propose a theoretical framework, which we believe can guide the design and interpretations of studies of post-traumatic recovery. It is essential to distinguish between a number of levels of analysis - including a differentiation between the surface phenomena and the underlying information processing - when addressing, for instance, whether a pre-traumatic and post-traumatically recovered cognitive or conscious process are actually the same. We propose a (somewhat preliminary) system of levels of analysis, which can be applied to such studies.
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Affiliation(s)
- Raimond L. Winslow
- Department of Biomedical Engineering, Institute for Computational Medicine, The Johns Hopkins University School of Medicine and Whiting School of EngineeringBaltimore, MD, USA
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Liu G, Qutub AA, Vempati P, Mac Gabhann F, Popel AS. Module-based multiscale simulation of angiogenesis in skeletal muscle. Theor Biol Med Model 2011; 8:6. [PMID: 21463529 PMCID: PMC3079676 DOI: 10.1186/1742-4682-8-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Accepted: 04/04/2011] [Indexed: 12/21/2022] Open
Abstract
Background Mathematical modeling of angiogenesis has been gaining momentum as a means to shed new light on the biological complexity underlying blood vessel growth. A variety of computational models have been developed, each focusing on different aspects of the angiogenesis process and occurring at different biological scales, ranging from the molecular to the tissue levels. Integration of models at different scales is a challenging and currently unsolved problem. Results We present an object-oriented module-based computational integration strategy to build a multiscale model of angiogenesis that links currently available models. As an example case, we use this approach to integrate modules representing microvascular blood flow, oxygen transport, vascular endothelial growth factor transport and endothelial cell behavior (sensing, migration and proliferation). Modeling methodologies in these modules include algebraic equations, partial differential equations and agent-based models with complex logical rules. We apply this integrated model to simulate exercise-induced angiogenesis in skeletal muscle. The simulation results compare capillary growth patterns between different exercise conditions for a single bout of exercise. Results demonstrate how the computational infrastructure can effectively integrate multiple modules by coordinating their connectivity and data exchange. Model parameterization offers simulation flexibility and a platform for performing sensitivity analysis. Conclusions This systems biology strategy can be applied to larger scale integration of computational models of angiogenesis in skeletal muscle, or other complex processes in other tissues under physiological and pathological conditions.
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Affiliation(s)
- Gang Liu
- Systems Biology Laboratory, Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
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Nickerson DP, Terkildsen JR, Hamilton KL, Hunter PJ. A tool for multi-scale modelling of the renal nephron. Interface Focus 2011; 1:417-25. [PMID: 22670210 DOI: 10.1098/rsfs.2010.0032] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Accepted: 03/07/2011] [Indexed: 11/12/2022] Open
Abstract
We present the development of a tool, which provides users with the ability to visualize and interact with a comprehensive description of a multi-scale model of the renal nephron. A one-dimensional anatomical model of the nephron has been created and is used for visualization and modelling of tubule transport in various nephron anatomical segments. Mathematical models of nephron segments are embedded in the one-dimensional model. At the cellular level, these segment models use models encoded in CellML to describe cellular and subcellular transport kinetics. A web-based presentation environment has been developed that allows the user to visualize and navigate through the multi-scale nephron model, including simulation results, at the different spatial scales encompassed by the model description. The Zinc extension to Firefox is used to provide an interactive three-dimensional view of the tubule model and the native Firefox rendering of scalable vector graphics is used to present schematic diagrams for cellular and subcellular scale models. The model viewer is embedded in a web page that dynamically presents content based on user input. For example, when viewing the whole nephron model, the user might be presented with information on the various embedded segment models as they select them in the three-dimensional model view. Alternatively, the user chooses to focus the model viewer on a cellular model located in a particular nephron segment in order to view the various membrane transport proteins. Selecting a specific protein may then present the user with a description of the mathematical model governing the behaviour of that protein-including the mathematical model itself and various simulation experiments used to validate the model against the literature.
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Affiliation(s)
- David P Nickerson
- Auckland Bioengineering Institute , The University of Auckland , Auckland , New Zealand
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Safránek D, Cervený J, Klement M, Pospíšilová J, Brim L, Lazár D, Nedbal L. E-photosynthesis: web-based platform for modeling of complex photosynthetic processes. Biosystems 2010; 103:115-24. [PMID: 21073914 DOI: 10.1016/j.biosystems.2010.10.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 10/22/2010] [Accepted: 10/23/2010] [Indexed: 10/18/2022]
Abstract
E-photosynthesis framework is a web-based platform for modeling and analysis of photosynthetic processes. Compared to its earlier version, the present platform employs advanced software methods and technologies to support an effective implementation of vastly diverse kinetic models of photosynthesis. We report on the first phase implementation of the tool new version and demonstrate the functionalities of model visualization, presentation of model components, rate constants, initial conditions and of model annotation. The demonstration also includes export of a model to the Systems Biology Markup Language format and remote numerical simulation of the model.
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Affiliation(s)
- David Safránek
- Systems Biology Laboratory, Faculty of Informatics Masaryk University, Botanická 68a, CZ-60200 Brno, Czech Republic
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Miller AK, Marsh J, Reeve A, Garny A, Britten R, Halstead M, Cooper J, Nickerson DP, Nielsen PF. An overview of the CellML API and its implementation. BMC Bioinformatics 2010; 11:178. [PMID: 20377909 PMCID: PMC2858041 DOI: 10.1186/1471-2105-11-178] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2009] [Accepted: 04/08/2010] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND CellML is an XML based language for representing mathematical models, in a machine-independent form which is suitable for their exchange between different authors, and for archival in a model repository. Allowing for the exchange and archival of models in a computer readable form is a key strategic goal in bioinformatics, because of the associated improvements in scientific record accuracy, the faster iterative process of scientific development, and the ability to combine models into large integrative models.However, for CellML models to be useful, tools which can process them correctly are needed. Due to some of the more complex features present in CellML models, such as imports, developing code ab initio to correctly process models can be an onerous task. For this reason, there is a clear and pressing need for an application programming interface (API), and a good implementation of that API, upon which tools can base their support for CellML. RESULTS We developed an API which allows the information in CellML models to be retrieved and/or modified. We also developed a series of optional extension APIs, for tasks such as simplifying the handling of connections between variables, dealing with physical units, validating models, and translating models into different procedural languages.We have also provided a Free/Open Source implementation of this application programming interface, optimised to achieve good performance. CONCLUSIONS Tools have been developed using the API which are mature enough for widespread use. The API has the potential to accelerate the development of additional tools capable of processing CellML, and ultimately lead to an increased level of sharing of mathematical model descriptions.
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Affiliation(s)
- Andrew K Miller
- Auckland Bioengineering Institute, The University of Auckland, Auckland, NZ
| | - Justin Marsh
- Auckland Bioengineering Institute, The University of Auckland, Auckland, NZ
| | - Adam Reeve
- Auckland Bioengineering Institute, The University of Auckland, Auckland, NZ
| | - Alan Garny
- Department of Physiology, Anatomy and Genetics, Sherrington Building, Parks Road, Oxford OX1 3PT, UK
| | - Randall Britten
- Auckland Bioengineering Institute, The University of Auckland, Auckland, NZ
| | - Matt Halstead
- Auckland Bioengineering Institute, The University of Auckland, Auckland, NZ
| | - Jonathan Cooper
- Oxford University Computing Laboratory, Wolfson Building, Parks Road, Oxford OX1 3QD, UK
| | - David P Nickerson
- Auckland Bioengineering Institute, The University of Auckland, Auckland, NZ
| | - Poul F Nielsen
- Auckland Bioengineering Institute, The University of Auckland, Auckland, NZ
- Department of Engineering Science, The University of Auckland, Auckland, NZ
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Cooling MT, Rouilly V, Misirli G, Lawson J, Yu T, Hallinan J, Wipat A. Standard virtual biological parts: a repository of modular modeling components for synthetic biology. Bioinformatics 2010; 26:925-31. [DOI: 10.1093/bioinformatics/btq063] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Alterovitz G, Muso T, Ramoni MF. The challenges of informatics in synthetic biology: from biomolecular networks to artificial organisms. Brief Bioinform 2009; 11:80-95. [PMID: 19906839 DOI: 10.1093/bib/bbp054] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The field of synthetic biology holds an inspiring vision for the future; it integrates computational analysis, biological data and the systems engineering paradigm in the design of new biological machines and systems. These biological machines are built from basic biomolecular components analogous to electrical devices, and the information flow among these components requires the augmentation of biological insight with the power of a formal approach to information management. Here we review the informatics challenges in synthetic biology along three dimensions: in silico, in vitro and in vivo. First, we describe state of the art of the in silico support of synthetic biology, from the specific data exchange formats, to the most popular software platforms and algorithms. Next, we cast in vitro synthetic biology in terms of information flow, and discuss genetic fidelity in DNA manipulation, development strategies of biological parts and the regulation of biomolecular networks. Finally, we explore how the engineering chassis can manipulate biological circuitries in vivo to give rise to future artificial organisms.
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Affiliation(s)
- Gil Alterovitz
- Children's Hospital Informatics Program, Harvard/MITDivision of Health Sciences and Technology, USA
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Wimalaratne SM, Halstead MDB, Lloyd CM, Cooling MT, Crampin EJ, Nielsen PF. A method for visualizing CellML models. ACTA ACUST UNITED AC 2009; 25:3012-9. [PMID: 19703920 DOI: 10.1093/bioinformatics/btp495] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION The Physiome Project was established in 1997 to develop tools to facilitate international collaboration in the physiological sciences and the sharing of biological models and experimental data. The CellML language was developed to represent and exchange mathematical models of biological processes. CellML models can be very complicated, making it difficult to interpret the underlying physical and biological concepts and relationships captured/described in the mathematical model. RESULTS To address this issue a set of ontologies was developed to explicitly annotate the biophysical concepts represented in the CellML models. This article presents a framework that combines a visual language, together with CellML ontologies, to support the visualization of the underlying physical and biological concepts described by the mathematical model and also their relationships with the CellML model. Automated CellML model visualization assists in the interpretation of model concepts and facilitates model communication and exchange between different communities.
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Affiliation(s)
- S M Wimalaratne
- Auckland Bioengineering Institute and Department of Engineering Science, The University of Auckland, 70 Symonds St, Auckland, New Zealand.
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Nordlie E, Gewaltig MO, Plesser HE. Towards reproducible descriptions of neuronal network models. PLoS Comput Biol 2009; 5:e1000456. [PMID: 19662159 PMCID: PMC2713426 DOI: 10.1371/journal.pcbi.1000456] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Accepted: 07/01/2009] [Indexed: 11/19/2022] Open
Abstract
Progress in science depends on the effective exchange of ideas among scientists. New ideas can be assessed and criticized in a meaningful manner only if they are formulated precisely. This applies to simulation studies as well as to experiments and theories. But after more than 50 years of neuronal network simulations, we still lack a clear and common understanding of the role of computational models in neuroscience as well as established practices for describing network models in publications. This hinders the critical evaluation of network models as well as their re-use. We analyze here 14 research papers proposing neuronal network models of different complexity and find widely varying approaches to model descriptions, with regard to both the means of description and the ordering and placement of material. We further observe great variation in the graphical representation of networks and the notation used in equations. Based on our observations, we propose a good model description practice, composed of guidelines for the organization of publications, a checklist for model descriptions, templates for tables presenting model structure, and guidelines for diagrams of networks. The main purpose of this good practice is to trigger a debate about the communication of neuronal network models in a manner comprehensible to humans, as opposed to machine-readable model description languages. We believe that the good model description practice proposed here, together with a number of other recent initiatives on data-, model-, and software-sharing, may lead to a deeper and more fruitful exchange of ideas among computational neuroscientists in years to come. We further hope that work on standardized ways of describing—and thinking about—complex neuronal networks will lead the scientific community to a clearer understanding of high-level concepts in network dynamics, and will thus lead to deeper insights into the function of the brain. Scientists make precise, testable statements about their observations and models of nature. Other scientists can then evaluate these statements and attempt to reproduce or extend them. Results that cannot be reproduced will be duly criticized to arrive at better interpretations of experimental results or better models. Over time, this discourse develops our joint scientific knowledge. A crucial condition for this process is that scientists can describe their own models in a manner that is precise and comprehensible to others. We analyze in this paper how well models of neuronal networks are described in the scientific literature and conclude that the wide variety of manners in which network models are described makes it difficult to communicate models successfully. We propose a good model description practice to improve the communication of neuronal network models.
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Affiliation(s)
- Eilen Nordlie
- Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Aas, Norway
| | | | - Hans Ekkehard Plesser
- Department of Mathematical Sciences and Technology, Norwegian University of Life Sciences, Aas, Norway
- Center for Biomedical Computing, Simula Research Laboratory, Lysaker, Norway
- RIKEN Brain Science Institute, Wako-shi, Saitama, Japan
- * E-mail:
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Matsuoka Y, Ghosh S, Kitano H. Consistent design schematics for biological systems: standardization of representation in biological engineering. J R Soc Interface 2009; 6 Suppl 4:S393-404. [PMID: 19493898 PMCID: PMC2843967 DOI: 10.1098/rsif.2009.0046.focus] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2009] [Accepted: 05/05/2009] [Indexed: 11/12/2022] Open
Abstract
The discovery by design paradigm driving research in synthetic biology entails the engineering of de novo biological constructs with well-characterized input-output behaviours and interfaces. The construction of biological circuits requires iterative phases of design, simulation and assembly, leading to the fabrication of a biological device. In order to represent engineered models in a consistent visual format and further simulating them in silico, standardization of representation and model formalism is imperative. In this article, we review different efforts for standardization, particularly standards for graphical visualization and simulation/annotation schemata adopted in systems biology. We identify the importance of integrating the different standardization efforts and provide insights into potential avenues for developing a common framework for model visualization, simulation and sharing across various tools. We envision that such a synergistic approach would lead to the development of global, standardized schemata in biology, empowering deeper understanding of molecular mechanisms as well as engineering of novel biological systems.
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Lee J, Niederer S, Nordsletten D, Le Grice I, Smaill B, Kay D, Smith N. Coupling contraction, excitation, ventricular and coronary blood flow across scale and physics in the heart. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2009; 367:2311-2331. [PMID: 19414457 DOI: 10.1098/rsta.2008.0311] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In this study, we review the development and application of multi-physics and multi-scale coupling in the construction of whole-heart physiological models. Through an examination of recent computational modelling developments, we analyse the significance of coupling mechanisms for the increased understanding of cardiac function in the areas of excitation-contraction, coronary blood flow and ventricular fluid mechanical coupling. Within these physiological domains, we demonstrate and discuss the importance of model parametrization, imaging-based model anatomy and computational implementation.
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Affiliation(s)
- Jack Lee
- Oxford University Computing Laboratory, University of Oxford, Wolfson Building, Parks Road, Oxford OX1 3QD, UK
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Nickerson DP, Buist ML. A physiome standards-based model publication paradigm. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2009; 367:1823-44. [PMID: 19380314 DOI: 10.1098/rsta.2008.0296] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
In this era of widespread broadband Internet penetration and powerful Web browsers on most desktops, a shift in the publication paradigm for physiome-style models is envisaged. No longer will model authors simply submit an essentially textural description of the development and behaviour of their model. Rather, they will submit a complete working implementation of the model encoded and annotated according to the various standards adopted by the physiome project, accompanied by a traditional human-readable summary of the key scientific goals and outcomes of the work. While the final published, peer-reviewed article will look little different to the reader, in this new paradigm, both reviewers and readers will be able to interact with, use and extend the models in ways that are not currently possible. Here, we review recent developments that are laying the foundations for this new model publication paradigm. Initial developments have focused on the publication of mathematical models of cellular electrophysiology, using technology based on a CellML- or Systems Biology Markup Language (SBML)-encoded implementation of the mathematical models. Here, we review the current state of the art and what needs to be done before such a model publication becomes commonplace.
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Affiliation(s)
- David P Nickerson
- Division of Bioengineering, National University of Singapore, Singapore 117574, Republic of Singapore
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Gavaghan D, Coveney PV, Kohl P. The virtual physiological human: tools and applications I. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2009; 367:1817-1821. [PMID: 19380313 DOI: 10.1098/rsta.2009.0070] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
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Garny A, Noble D, Hunter PJ, Kohl P. CELLULAR OPEN RESOURCE (COR): current status and future directions. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2009; 367:1885-905. [PMID: 19380317 DOI: 10.1098/rsta.2008.0289] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The need for tools to aid the description and sharing of biological models was highlighted at the launch of the International Union of Physiological Sciences Physiome Project in 1997. This has resulted in the release, in 2001, of the CellML specifications (http://www.cellml.org/specifications/). CELLULAR OPEN RESOURCE (COR) was among the early adopters of this standard, eventually forming the first publicly available CellML-based modelling and collaboration environment. From the onset, COR was designed to provide an environment that could not only be used by experienced modellers, but also by experimentalists, teachers and students. It therefore tries to combine a user-friendly interface with a computationally efficient numerical engine. In this paper, we introduce the philosophy behind COR, explain its user interface and current functionality, including the editing and running of CellML files, highlight lessons learned from user feedback and problems experienced during the development of COR and conclude by exploring future development potential.
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Affiliation(s)
- Alan Garny
- Department of Physiology, Anatomy and Genetics, University of Oxford, Sherrington Building, Parks Road, Oxford OX1 3PT, UK.
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Vanlier J, Wu F, Qi F, Vinnakota KC, Han Y, Dash RK, Yang F, Beard DA. BISEN: Biochemical Simulation Environment. ACTA ACUST UNITED AC 2009; 25:836-7. [PMID: 19244386 DOI: 10.1093/bioinformatics/btp069] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
SUMMARY The Biochemical Simulation Environment (BISEN) is a suite of tools for generating equations and associated computer programs for simulating biochemical systems in the MATLAB computing environment. This is the first package that can generate appropriate systems of differential equations for user-specified multi-compartment systems of enzymes and transporters accounting for detailed biochemical thermodynamics, rapid equilibria of multiple biochemical species and dynamic proton and metal ion buffering. AVAILABILITY The software and a user manual (including several tutorial examples) are available at bbc.mcw.edu/BISEN.
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Affiliation(s)
- J Vanlier
- BioModeling and Bioinformatics, BioMedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
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