Towards semantic model composition via experiments

Peng, Danhua; Ewald, Roland; Uhrmacher, Adelinde M.

doi:10.1145/2601381.2601394

Cited by 14 publications

(23 citation statements)

References 45 publications

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“…We are looking at incorporating parameter estimation techniques into this framework, and further automated checking of experiment results could also be investigated (38). It would also be desirable to use a community agreed standard for protocols, rather than our own representation, and so we are proposing features of our new language for incorporation in future versions of the SED-ML standard being developed by the systems biology community (22).…”

Section: Discussionmentioning

confidence: 99%

The Cardiac Electrophysiology Web Lab

Cooper

Scharm

Mirams

2015

Preprint

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Computational modelling of cardiac cellular electrophysiology has a long history, with many models now available for different species, cell types, and experimental preparations. This success brings with it a challenge: how do we assess and compare the underlying hypotheses and emergent behaviours, in order to choose a model as a suitable basis for a new study, or characterize how a particular model behaves in different scenarios?We have created an online resource for the characterization and comparison of electrophysiological cell models under a wide range of experimental scenarios. The details of the mathematical model (quantitative assumptions and hypotheses formulated as ordinary differential equations) are separated from the experimental protocol being simulated. Each model and protocol is then encoded in computer-readable formats.A simulation tool runs virtual experiments on models, and a websitehttps://chaste.cs.ox.ac.uk/FunctionalCuration -provides a friendly interface, allowing users to store and compare results. The system currently contains a sample of 36 models and 23 protocols, including current-voltage curve generation, action potential properties under steady pacing at different rates, restitution properties, block of particular channels, and hypo-/hyper-kalaemia. This resource is publicly available, open source, and free; and we invite the community to use it and become involved in future developments. Those interested in comparing competing hypotheses using models can make a more informed decision; those developing new models can upload them for easy evaluation under the existing protocols, and even add their own protocols.

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Section: Discussionmentioning

confidence: 99%

The Cardiac Electrophysiology Web Lab

Cooper

Scharm

Mirams

2015

Preprint

View full text Add to dashboard Cite

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“…Other enhancements to the tools, and indeed the protocol language, may also be required as new ideas for protocols arise. We are looking at incorporating parameter estimation techniques into this framework, and further automated checking of experiment results could also be investigated (38). It would also be desirable to use a community agreed standard for protocols, rather than our own representation, and so we are proposing features of our new language for incorporation in future versions of the SED-ML standard being developed by the systems biology community (22).…”

Section: Discussionmentioning

confidence: 99%

The Cardiac Electrophysiology Web Lab

Cooper

Scharm

Mirams

2015

Preprint

View full text Add to dashboard Cite

Computational modelling of cardiac cellular electrophysiology has a long history, with many models now available for different species, cell types, and experimental preparations. This success brings with it a challenge: how do we assess and compare the underlying hypotheses and emergent behaviours, in order to choose a model as a suitable basis for a new study, or characterize how a particular model behaves in different scenarios? We have created an online resource for the characterization and comparison of electrophysiological cell models under a wide range of experimental scenarios. The details of the mathematical model (quantitative assumptions and hypotheses formulated as ordinary differential equations) are separated from the experimental protocol being simulated. Each model and protocol is then encoded in computer-readable formats. A simulation tool runs virtual experiments on models, and a website – https://chaste.cs.ox.ac.uk/FunctionalCuration – provides a friendly interface, allowing users to store and compare results. The system currently contains a sample of 36 models and 23 protocols, including current-voltage curve generation, action potential properties under steady pacing at different rates, restitution properties, block of particular channels, and hypo-/hyper-kalaemia. This resource is publicly available, open source, and free; and we invite the community to use it and become involved in future developments. Those interested in comparing competing hypotheses using models can make a more informed decision; those developing new models can upload them for easy evaluation under the existing protocols, and even add their own protocols.

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“…Based on adapted experiment specifications, experiments are executed with the composed model and results are checked, to test whether the specified behavioral properties, which have been successfully checked for the reuse model, still hold for the composed model, and whether this result meets the expectation, corresponding to step four in Figure 2. The goal, as presented in the work by Peng et al, 5 is to automatically provide information about behavioral properties to the user during model composition, which supports validating the composed model.…”

Section: Proposed Approachmentioning

confidence: 99%

Reusing simulation experiment specifications in developing models by successive composition — a case study of the Wnt/β-catenin signaling pathway

et al. 2017

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With the increasing size and complexity of models, developing models by composing existing ones becomes more important. We exploit the idea of reusing simulation experiments of individual models for composition to automatically generate experiments for the composed model. First, we illustrate the process of modeling based on composition and discuss the role simulation experiments can play in this process. Our focus is on semantic validation of the composed model. We explicitly specify simulation experiments in simulation experiment specification via a Scala layer, including the desired model behavioral properties and their required experiment setups. Models are annotated with experiment specifications, and upon composition, these specifications are adapted and automatically executed for the composed model. The approach is applied in a case study of developing a Wnt/b-catenin signaling pathway model by successively composing three individual models, where we exploit metric interval temporal logic to describe model behavioral properties and check averages of stochastic simulation results against these properties.

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Towards semantic model composition via experiments

Cited by 14 publications

References 45 publications

The Cardiac Electrophysiology Web Lab

The Cardiac Electrophysiology Web Lab

The Cardiac Electrophysiology Web Lab

Reusing simulation experiment specifications in developing models by successive composition — a case study of the Wnt/β-catenin signaling pathway

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