SED-ML Web Tools: Generate, modify and export standard-compliant simulation studies

Bergmann, Frank; Nickerson, David; Waltemath, Dagmar; Scharm, Martin

doi:10.7287/peerj.preprints.2515

Cited by 2 publications

(9 citation statements)

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“…150 Furthermore, COMBINE archives can contain important dynamical information about 151 the model, such as the influence of the parameter m that we explored in this study. In 152 order to demonstrate exchangeability of this study, we have exported it to the SED-ML 153 Web Tools [22] ( Fig S1) and iBioSim [35] (Fig S2). Reproducibility requires that a model implementation produces results consistent with 157 the original study, especially if a different authoring tool is used.…”

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confidence: 99%

“…In order to address the requirement of broad standards compliance, we tested Tellurium 256 against a set of tests provided by the SED-ML Web Tools [22]. These tests utilize The SBML Test Suite [45] is a collection of dynamical models along with expected 262 trajectories designed to test software tools for compliance with the SBML standard.…”

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confidence: 99%

“…Until then, we believe 431 that manually comparing results encoded as COMBINE archives as in the studies 432 presented here will provide immediate benefits to reproducibility. For moderate-size 433 models such as the Calzone study, we have shown that this approach is a practical Fig 2 was exported to a COMBINE archive from Tellurium, imported into the SED-ML Web Tools [22], and used to generate plots to verify that the simulation results were identical to Fig 2. The COMBINE archive used to create this example can be found online [78].…”

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confidence: 99%

“…21 Table S2. Advanced SED-ML Tests (Provided by SED-ML Web Tools [22]). The SBML test suite was converted into COMBINE archives using the provided notebook https://github.com/0u812/tellurium-combine-archive-testcases/blob/master/sbml-test-suite/convert-to-combine-arch.ipynb.…”

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confidence: 99%

“…In order to address the requirement of broad standards compliance, we tested Tellurium 256 against a set of tests provided by the SED-ML Web Tools [22]. These tests utilize expected trajectories encoded as a common-separated values (CSV) file, and graphical 265 plots for reference.…”

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Tellurium Notebooks - An Environment for Dynamical Model Development, Reproducibility, and Reuse

Medley

Choi

König

et al. 2017

Preprint

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The considerable difficulty encountered in reproducing the results of published dynamical models limits validation, exploration and reuse of this increasingly large biomedical research resource. To address this problem, we have developed Tellurium Notebook, a software system that facilitates building reproducible dynamical models and reusing models by 1) supporting the COMBINE archive format during model development for capturing model information in an exchangeable format and 2) enabling users to easily simulate and edit public COMBINE-compliant models from public repositories to facilitate studying model dynamics, variants and test cases. Tellurium Notebook, a Python-based Jupyter-like environment, is designed to seamlessly inter-operate with these community standards by automating conversion between COMBINE standards formulations and corresponding in-line, human-readable representations. Thus, Tellurium brings to systems biology the strategy used by other literate notebook systems such as Mathematica. These capabilities allow users to edit every aspect of the standards-compliant models and simulations, run the simulations in-line, and re-export to standard formats. We provide several use cases illustrating the advantages of our approach and how it allows development and reuse of models without requiring technical knowledge of standards. Adoption of Tellurium should accelerate model development, reproducibility and reuse. Author summaryThere is considerable value to systems and synthetic biology in creating reproducible models. An essential element of reproducibility is the use of community standards, an often challenging undertaking for modelers. This article describes Tellurium Notebook, a tool for developing dynamical models that provides an intuitive approach to building and reusing models built with community standards. Tellurium automates embedding human-readable representations of COMBINE archives in literate coding notebooks, bringing to systems biology this strategy central to other literate notebook systems such as Mathematica. We show that the ability to easily edit this human-readable representation enables users to test models under a variety of conditions, thereby providing a way to create, reuse, and modify standard-encoded models and simulations, regardless of the user's level of technical knowledge of said standards.

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confidence: 99%

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confidence: 99%

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confidence: 99%

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Tellurium Notebooks - An Environment for Dynamical Model Development, Reproducibility, and Reuse

Medley

Choi

König

et al. 2017

Preprint

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SED-ML Validator: tool for debugging simulation experiments

Shaikh,

Freiburger,

König

et al. 2021

Preprint

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More sophisticated models are needed to address problems in bioscience, synthetic biology, and precision medicine. To help facilitate the collaboration needed for such models, the community developed the Simulation Experiment Description Markup Language (SED-ML), a common format for describing simulations. However, the utility of SED-ML has been hampered by limited support for SED-ML among modeling software tools and by different interpretations of SED-ML among the tools that support the format. To help modelers debug their simulations and to push the community to use SED-ML consistently, we developed a tool for validating SED-ML files. We have used the validator to correct the official SED-ML example files. We plan to use the validator to correct the files in the BioModels database so that they can be simulated. We anticipate that the validator will be a valuable tool for developing more predictive simulations and that the validator will help increase the adoption and interoperability of SED-ML.

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SED-ML Web Tools: Generate, modify and export standard-compliant simulation studies

Cited by 2 publications

References 4 publications

Tellurium Notebooks - An Environment for Dynamical Model Development, Reproducibility, and Reuse

Tellurium Notebooks - An Environment for Dynamical Model Development, Reproducibility, and Reuse

SED-ML Validator: tool for debugging simulation experiments

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