FAIRsharing.bcjrnq; Last edited: June 23, 2021, 1:10 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

Other names: PMR

The Physiome Model Repository (PMR) is the main online repository for the IUPS Physiome Project, providing version and access controlled repositories, called workspaces, for users to store their data. PMR also provides a mechanism to create persistent access to specific revisions of a workspace, termed exposures. Exposure plugins are available for specific types of data (e.g., CellML or FieldML documents) which enable customizable views of the data when browsing the repository via a web browser, or an application accessing the repository’s content via web services.

Webpage:

https://models.physiomeproject.org

Publications: (6)

Publications
More detailed information about this field from each metasource.

The CellML Model Repository
PMID: 18658182
metasource: Fairsharing.org
version: FAIRsharing.org: PMR; Physiome Model Repository; DOI: https://doi.org/10.25504/FAIRsharing.bcjrnq; Last edited: June 23, 2021, 1:10 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

The Physiome Model Repository 2
PMID: 21216774
metasource: Fairsharing.org
version: FAIRsharing.org: PMR; Physiome Model Repository; DOI: https://doi.org/10.25504/FAIRsharing.bcjrnq; Last edited: June 23, 2021, 1:10 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

CellML metadata standards, associated tools and repositories
PMID: 19380315
metasource: Fairsharing.org
version: FAIRsharing.org: PMR; Physiome Model Repository; DOI: https://doi.org/10.25504/FAIRsharing.bcjrnq; Last edited: June 23, 2021, 1:10 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable
PMID: 27051515
metasource: Fairsharing.org
version: FAIRsharing.org: PMR; Physiome Model Repository; DOI: https://doi.org/10.25504/FAIRsharing.bcjrnq; Last edited: June 23, 2021, 1:10 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

Revision history aware repositories of computational models of biological systems
PMID: 21235804
metasource: Fairsharing.org
version: FAIRsharing.org: PMR; Physiome Model Repository; DOI: https://doi.org/10.25504/FAIRsharing.bcjrnq; Last edited: June 23, 2021, 1:10 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

Toward a curated CellML model repository
PMID: 17947072
metasource: Fairsharing.org
version: FAIRsharing.org: PMR; Physiome Model Repository; DOI: https://doi.org/10.25504/FAIRsharing.bcjrnq; Last edited: June 23, 2021, 1:10 p.m.; Last accessed: Jan 03 2022 7:07 p.m.

The CellML Model Repository PubMed citations: 90.

90 articles citing: The CellML Model Repository

Acetylcholine Reduces IKr and Prolongs Action Potentials in Human Ventricular Cardiomyocytes. PMID:35203454
Multiscale Modeling of Cardiovascular Function Predicts That the End-Systolic Pressure Volume Relationship Can Be Targeted via Multiple Therapeutic Strategies. PMID:32973561
Investigating cardiac stimulation limits of MRI gradient coils using electromagnetic and electrophysiological simulations in human and canine body models. PMID:32812280
Isolating structural errors in reaction networks in systems biology. PMID:32790862
ModelBricks-modules for reproducible modeling improving model annotation and provenance. PMID:31602314
Spontaneous termination of chaotic spiral wave dynamics in human cardiac ion channel models. PMID:31461472
Genetic variation in GNB5 causes bradycardia by augmenting the cholinergic response via increased acetylcholine-activated potassium current (I K,ACh). PMID:31208990
Best Practices to Maximize the Use and Reuse of Quantitative and Systems Pharmacology Models: Recommendations From the United Kingdom Quantitative and Systems Pharmacology Network. PMID:30667172
Cellular Mechanisms of Sinus Node Dysfunction in Carriers of the SCN5A-E161K Mutation and Role of the H558R Polymorphism. PMID:30618807
"Reproducible" Research in Mathematical Sciences Requires Changes in our Peer Review Culture and Modernization of our Current Publication Approach. PMID:30232583
BioModelKit - An Integrative Framework for Multi-Scale Biomodel-Engineering. PMID:30205646
Tellurium notebooks-An environment for reproducible dynamical modeling in systems biology. PMID:29906293
Information sensitivity functions to assess parameter information gain and identifiability of dynamical systems. PMID:29769407
Credibility, Replicability, and Reproducibility in Simulation for Biomedicine and Clinical Applications in Neuroscience. PMID:29713272
Confocal Microscopy-Based Estimation of Parameters for Computational Modeling of Electrical Conduction in the Normal and Infarcted Heart. PMID:29670532
Validation and Trustworthiness of Multiscale Models of Cardiac Electrophysiology. PMID:29497385
Sinus Bradycardia in Carriers of the SCN5A-1795insD Mutation: Unraveling the Mechanism through Computer Simulations. PMID:29473904
Comparing two sequential Monte Carlo samplers for exact and approximate Bayesian inference on biological models. PMID:28931636
Patch-Clamp Recording from Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes: Improving Action Potential Characteristics through Dynamic Clamp. PMID:28867785
Systems modelling ageing: from single senescent cells to simple multi-cellular models. PMID:28698310
Reproducibility and Comparability of Computational Models for Astrocyte Calcium Excitability. PMID:28270761
Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience. PMID:27629590
Guidelines for Reproducibly Building and Simulating Systems Biology Models. PMID:27429432
Using physiologically based models for clinical translation: predictive modelling, data interpretation or something in-between? PMID:27121495
Computational cardiology and risk stratification for sudden cardiac death: one of the grand challenges for cardiology in the 21st century. PMID:27060987
The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable. PMID:27051515
Reproducibility in Computational Neuroscience Models and Simulations. PMID:27046845
Hodgkin-Huxley revisited: reparametrization and identifiability analysis of the classic action potential model with approximate Bayesian methods. PMID:27019736
Effects of Amiodarone and N-desethylamiodarone on Cardiac Voltage-Gated Sodium Channels. PMID:26973526
Challenges in horizontal model integration. PMID:26968798
The Cardiac Electrophysiology Web Lab. PMID:26789753
Tracing regulatory routes in metabolism using generalised supply-demand analysis. PMID:26635009
Metabolomics, Standards, and Metabolic Modeling for Synthetic Biology in Plants. PMID:26557642
Databases for multilevel biophysiology research available at Physiome.jp. PMID:26441671
Reasoning over genetic variance information in cause-and-effect models of neurodegenerative diseases. PMID:26249223
BioModels: Content, Features, Functionality, and Use. PMID:26225232
A web portal for in-silico action potential predictions. PMID:25963830
Cellular cardiac electrophysiology modeling with Chaste and CellML. PMID:25610400
Closing the loop: modelling of heart failure progression from health to end-stage using a meta-analysis of left ventricular pressure-volume loops. PMID:25479594
Computational strategies for a system-level understanding of metabolism. PMID:25427076
Mechanistic modeling confronts the complexity of molecular cell biology. PMID:25368428
LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2. PMID:25309419
MOSBIE: a tool for comparison and analysis of rule-based biochemical models. PMID:25253680
WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions. PMID:25231498
Prediction of Thorough QT study results using action potential simulations based on ion channel screens. PMID:25087753
Bridging the gaps in systems biology. PMID:24728588
A vision and strategy for the virtual physiological human: 2012 update. PMID:24427536
Integrating multi-scale data to create a virtual physiological mouse heart. PMID:24427525
Enhanced currents through L-type calcium channels in cardiomyocytes disturb the electrophysiology of the dystrophic heart. PMID:24337461
Path2Models: large-scale generation of computational models from biochemical pathway maps. PMID:24180668
An online model composition tool for system biology models. PMID:24006914
FieldML, a proposed open standard for the Physiome project for mathematical model representation. PMID:23900627
The systems biology simulation core algorithm. PMID:23826941
Anti-addiction drug ibogaine inhibits voltage-gated ionic currents: a study to assess the drug's cardiac ion channel profile. PMID:23707769
A single compartment model of pacemaking in dissasociated substantia nigra neurons: stability and energy analysis. PMID:23686304
Variability in high-throughput ion-channel screening data and consequences for cardiac safety assessment. PMID:23651875
Evaluation of an in silico cardiac safety assay: using ion channel screening data to predict QT interval changes in the rabbit ventricular wedge. PMID:23624022
mRNA expression levels in failing human hearts predict cellular electrophysiological remodeling: a population-based simulation study. PMID:23437117
Computational medicine: translating models to clinical care. PMID:23115356
A physiologically based, multi-scale model of skeletal muscle structure and function. PMID:22993509
The Cell Collective: toward an open and collaborative approach to systems biology. PMID:22871178
Multi-way metamodelling facilitates insight into the complex input-output maps of nonlinear dynamic models. PMID:22818032
Understanding regulation of metabolism through feasibility analysis. PMID:22808034
Declarative representation of uncertainty in mathematical models. PMID:22802941
PathCase-SB: integrating data sources and providing tools for systems biology research. PMID:22697505
A tool for multi-scale modelling of the renal nephron. PMID:22670210
Application of cardiac electrophysiology simulations to pro-arrhythmic safety testing. PMID:22568589
Genotype-Phenotype Map Characteristics of an In silico Heart Cell. PMID:22232604
Analyzing the functional properties of the creatine kinase system with multiscale 'sloppy' modeling. PMID:21912519
Graphical approach to model reduction for nonlinear biochemical networks. PMID:21901136
A preliminary model of gastrointestinal electromechanical coupling. PMID:21878406
The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions. PMID:21878109
Integrating systems biology models and biomedical ontologies. PMID:21835028
Hierarchical cluster-based partial least squares regression (HC-PLSR) is an efficient tool for metamodelling of nonlinear dynamic models. PMID:21627852
Simulation of multiple ion channel block provides improved early prediction of compounds' clinical torsadogenic risk. PMID:21300721
Model annotation for synthetic biology: automating model to nucleotide sequence conversion. PMID:21296753
Revision history aware repositories of computational models of biological systems. PMID:21235804
Postsynaptic signal transduction models for long-term potentiation and depression. PMID:21188161
Ranked retrieval of Computational Biology models. PMID:20701772
Annotation of SBML models through rule-based semantic integration. PMID:20626923
Multiple ontologies in action: composite annotations for biosimulation models. PMID:20601121
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. PMID:20587024
An overview of the CellML API and its implementation. PMID:20377909
The challenges of informatics in synthetic biology: from biomolecular networks to artificial organisms. PMID:19906839
Saint: a lightweight integration environment for model annotation. PMID:19734151
Towards reproducible descriptions of neuronal network models. PMID:19662159
Consistent design schematics for biological systems: standardization of representation in biological engineering. PMID:19493898
CellML metadata standards, associated tools and repositories. PMID:19380315
Designing and encoding models for synthetic biology. PMID:19364720
A thermodynamic model of the cardiac sarcoplasmic/endoplasmic Ca(2+) (SERCA) pump. PMID:19254563
The Physiome Model Repository 2 PubMed citations: 57.

57 articles citing: The Physiome Model Repository 2

A semantics, energy-based approach to automate biomodel composition. PMID:35657966
A Parameter Representing Missing Charge Should Be Considered when Calibrating Action Potential Models. PMID:35557969
Pacemaking function of two simplified cell models. PMID:35404982
cellmlmanip and chaste_codegen: automatic CellML to C++ code generation with fixes for singularities and automatically generated Jacobians. PMID:35299708
NLIMED: Natural Language Interface for Model Entity Discovery in Biosimulation Model Repositories. PMID:35283794
Computational Models for Clinical Applications in Personalized Medicine-Guidelines and Recommendations for Data Integration and Model Validation. PMID:35207655
Modular assembly of dynamic models in systems biology. PMID:34644304
Relating simulation studies by provenance-Developing a family of Wnt signaling models. PMID:34351901
Countering reproducibility issues in mathematical models with software engineering techniques: A case study using a one-dimensional mathematical model of the atrioventricular node. PMID:34280231
libOmexMeta: Enabling semantic annotation of models to support FAIR principles. PMID:34132740
Immediate and Delayed Response of Simulated Human Atrial Myocytes to Clinically-Relevant Hypokalemia. PMID:34122128
Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: a software engineering perspective. PMID:34083542
Ca2+ Release via IP3 Receptors Shapes the Cardiac Ca2+ Transient for Hypertrophic Signaling. PMID:32871099
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). PMID:32598315
Self-restoration of cardiac excitation rhythm by anti-arrhythmic ion channel gating. PMID:32510321
Calibration of ionic and cellular cardiac electrophysiology models. PMID:32084308
Organizing genome engineering for the gigabase scale. PMID:32019919
BioModels-15 years of sharing computational models in life science. PMID:31701150
Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. PMID:31602618
Model annotation and discovery with the Physiome Model Repository. PMID:31492098
Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating, and Developing Standardized Models of Neurons and Circuits. PMID:31201122
Computational Modeling of Glucose Uptake in the Enterocyte. PMID:31031632
A demonstration of modularity, reuse, reproducibility, portability and scalability for modeling and simulation of cardiac electrophysiology using Kepler Workflows. PMID:30849072
Harmonizing semantic annotations for computational models in biology. PMID:30462164
Myocyte Remodeling Due to Fibro-Fatty Infiltrations Influences Arrhythmogenicity. PMID:30344493
SemGen: a tool for semantics-based annotation and composition of biosimulation models. PMID:30256901
Identifying frequent patterns in biochemical reaction networks: a workflow. PMID:29992320
Reproducible model development in the cardiac electrophysiology Web Lab. PMID:29842853
Evolution of computational models in BioModels Database and the Physiome Model Repository. PMID:29650016
Next-generation, personalised, model-based critical care medicine: a state-of-the art review of in silico virtual patient models, methods, and cohorts, and how to validation them. PMID:29463246
Tailoring Mathematical Models to Stem-Cell Derived Cardiomyocyte Lines Can Improve Predictions of Drug-Induced Changes to Their Electrophysiology. PMID:29311950
Meeting the multiscale challenge: representing physiology processes over ApiNATOMY circuits using bond graphs. PMID:29285348
Qualitative causal analyses of biosimulation models. PMID:28804276
A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos. PMID:27830063
Notions of similarity for systems biology models. PMID:27742665
COMODI: an ontology to characterise differences in versions of computational models in biology. PMID:27401413
Modular modelling with Physiome standards. PMID:27353233
The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable. PMID:27051515
Requirements for the formal representation of pathophysiology mechanisms by clinicians. PMID:27051514
Multiscale musculoskeletal modelling, data-model fusion and electromyography-informed modelling. PMID:27051510
Reproducibility in Computational Neuroscience Models and Simulations. PMID:27046845
Uncertainty and variability in models of the cardiac action potential: Can we build trustworthy models? PMID:26611884
Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization. PMID:26559508
An algorithm to detect and communicate the differences in computational models describing biological systems. PMID:26490504
Annotation-based feature extraction from sets of SBML models. PMID:25904997
Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative. PMID:25759811
The Open Physiology workflow: modeling processes over physiology circuitboards of interoperable tissue units. PMID:25759670
Combining computational models, semantic annotations and simulation experiments in a graph database. PMID:25754863
Cellular cardiac electrophysiology modeling with Chaste and CellML. PMID:25610400
Improving collaboration by standardization efforts in systems biology. PMID:25538939
Mechanistic modeling confronts the complexity of molecular cell biology. PMID:25368428
MOSBIE: a tool for comparison and analysis of rule-based biochemical models. PMID:25253680
Ontology of physics for biology: representing physical dependencies as a basis for biological processes. PMID:24295137
FieldML, a proposed open standard for the Physiome project for mathematical model representation. PMID:23900627
PathCase-SB: integrating data sources and providing tools for systems biology research. PMID:22697505
OREMPdb: a semantic dictionary of computational pathway models. PMID:22536973
Editorial: TBME Letters special issue on multiscale modeling and analysis in computational biology and medicine--part-2. PMID:22105190
CellML metadata standards, associated tools and repositories PubMed citations: 23.

23 articles citing: CellML metadata standards, associated tools and repositories

Arterial Hypertension and Unusual Ascending Aortic Dilatation in a Neonate With Acute Kidney Injury: Mechanistic Computer Modeling. PMID:31780955
Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. PMID:31602618
ModelBricks-modules for reproducible modeling improving model annotation and provenance. PMID:31602314
Harmonizing semantic annotations for computational models in biology. PMID:30462164
FindSim: A Framework for Integrating Neuronal Data and Signaling Models. PMID:29997492
Towards the virtual artery: a multiscale model for vascular physiology at the physics-chemistry-biology interface. PMID:27698036
Multiscale musculoskeletal modelling, data-model fusion and electromyography-informed modelling. PMID:27051510
Cellular cardiac electrophysiology modeling with Chaste and CellML. PMID:25610400
Using CellML with OpenCMISS to Simulate Multi-Scale Physiology. PMID:25601911
Synergy-COPD: a systems approach for understanding and managing chronic diseases. PMID:25472826
FieldML, a proposed open standard for the Physiome project for mathematical model representation. PMID:23900627
Computational medicine: translating models to clinical care. PMID:23115356
A tool for multi-scale modelling of the renal nephron. PMID:22670210
Modelling of pH dynamics in brain cells after stroke. PMID:22419985
Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language. PMID:22172142
Verification of cardiac tissue electrophysiology simulators using an N-version benchmark. PMID:21969679
A framework for the study of multiple realizations: the importance of levels of analysis. PMID:21772823
Module-based multiscale simulation of angiogenesis in skeletal muscle. PMID:21463529
An overview of the CellML API and its implementation. PMID:20377909
The challenges of informatics in synthetic biology: from biomolecular networks to artificial organisms. PMID:19906839
Towards reproducible descriptions of neuronal network models. PMID:19662159
Consistent design schematics for biological systems: standardization of representation in biological engineering. PMID:19493898
BISEN: Biochemical Simulation Environment. PMID:19244386
The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable PubMed citations: 11.

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

Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology. PMID:35671510
The need for standardisation in life science research - an approach to excellence and trust. PMID:33604028
SBML Level 3: an extensible format for the exchange and reuse of biological models. PMID:32845085
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). PMID:32598315
Model annotation and discovery with the Physiome Model Repository. PMID:31492098
Assessing the Validity and Utility of the Guyton Model of Arterial Blood Pressure Control. PMID:30571241
Harmonizing semantic annotations for computational models in biology. PMID:30462164
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017. PMID:29596055
Next-generation, personalised, model-based critical care medicine: a state-of-the art review of in silico virtual patient models, methods, and cohorts, and how to validation them. PMID:29463246
Systems Medicine-Complexity Within, Simplicity Without. PMID:28713872
The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation. PMID:27538448
Revision history aware repositories of computational models of biological systems PubMed citations: 8.

8 articles citing: Revision history aware repositories of computational models of biological systems

Community-driven roadmap for integrated disease maps. PMID:29688273
Evolution of computational models in BioModels Database and the Physiome Model Repository. PMID:29650016
Notions of similarity for systems biology models. PMID:27742665
Modular modelling with Physiome standards. PMID:27353233
The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable. PMID:27051515
An algorithm to detect and communicate the differences in computational models describing biological systems. PMID:26490504
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. PMID:25494900
Synergy-COPD: a systems approach for understanding and managing chronic diseases. PMID:25472826