Simulation Experiment Description Markup Language
Names
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Simulation Experiment Description Markup Language
metasource: Fairsharing.org
version: FAIRsharing.org: SED-ML; Simulation Experiment Description Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.6f7m6j; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
SED-ML
metasource: Fairsharing.org
version: FAIRsharing.org: SED-ML; Simulation Experiment Description Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.6f7m6j; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
Names
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Simulation Experiment Description Markup Language
metasource: Fairsharing.orgversion: FAIRsharing.org: SED-ML; Simulation Experiment Description Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.6f7m6j; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
SED-ML
metasource: Fairsharing.orgversion: FAIRsharing.org: SED-ML; Simulation Experiment Description Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.6f7m6j; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
Names
More detailed information about this field from each metasource.
Simulation Experiment Description Markup Language
metasource: Fairsharing.orgversion: FAIRsharing.org: SED-ML; Simulation Experiment Description Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.6f7m6j; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
SED-ML
metasource: Fairsharing.orgversion: FAIRsharing.org: SED-ML; Simulation Experiment Description Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.6f7m6j; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
SED-ML is an XML-based format for encoding simulation setups, to ensure exchangeability and reproducibility of simulation experiments. It follows the requirements defined in the MIASE guidelines. 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.
Description
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SED-ML is an XML-based format for encoding simulation setups, to ensure exchangeability and reproducibility of simulation experiments. It follows the requirements defined in the MIASE guidelines. 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.
metasource: Fairsharing.orgversion: FAIRsharing.org: SED-ML; Simulation Experiment Description Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.6f7m6j; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
Webpage:
http://sed-ml.org/Webpage
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http://sed-ml.org/
metasource: Fairsharing.orgversion: FAIRsharing.org: SED-ML; Simulation Experiment Description Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.6f7m6j; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language
PMID: 22172142
metasource: Fairsharing.org
version: FAIRsharing.org: SED-ML; Simulation Experiment Description Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.6f7m6j; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2
PMID: 26528560
metasource: Fairsharing.org
version: FAIRsharing.org: SED-ML; Simulation Experiment Description Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.6f7m6j; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
Publications
More detailed information about this field from each metasource.
Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language
PMID: 22172142
metasource: Fairsharing.org
version: FAIRsharing.org: SED-ML; Simulation Experiment Description Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.6f7m6j; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2
PMID: 26528560
metasource: Fairsharing.org
version: FAIRsharing.org: SED-ML; Simulation Experiment Description Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.6f7m6j; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
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Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language
PubMed citations: 95.
95 articles citing: Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language
Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology. PMID:35671510
Specifications of standards in systems and synthetic biology: status and developments in 2021. PMID:34674411
Modular assembly of dynamic models in systems biology. PMID:34644304
The Systems Biology Simulation Core Library. PMID:34554191
RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats. PMID:34019658
Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1. PMID:33634751
Benchmarking of numerical integration methods for ODE models of biological systems. PMID:33514831
PEtab-Interoperable specification of parameter estimation problems in systems biology. PMID:33497393
Mathematical Modelling in Biomedicine: A Primer for the Curious and the Skeptic. PMID:33430432
Best Practices for Making Reproducible Biochemical Models. PMID:32853539
SBML Level 3: an extensible format for the exchange and reuse of biological models. PMID:32845085
Towards standardization guidelines for in silico approaches in personalized medicine. PMID:32827396
Publishing reproducible dynamic kinetic models. PMID:32793969
Editorial Reproducibility of Computational Models. PMID:32636531
Specifications of standards in systems and synthetic biology: status and developments in 2020. PMID:32598316
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). PMID:32598315
Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop. PMID:32313939
A combined experimental and modelling approach for the Weimberg pathway optimisation. PMID:32107375
Calibration of ionic and cellular cardiac electrophysiology models. PMID:32084308
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
ModelBricks-modules for reproducible modeling improving model annotation and provenance. PMID:31602314
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019. PMID:31301675
BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data. PMID:31131402
Recent advances in biomedical simulations: a manifesto for model engineering. PMID:30881691
A demonstration of modularity, reuse, reproducibility, portability and scalability for modeling and simulation of cardiac electrophysiology using Kepler Workflows. PMID:30849072
Benchmark problems for dynamic modeling of intracellular processes. PMID:30624608
Web-Based Interfaces for Virtual C. elegans Neuron Model Definition, Network Configuration, Behavioral Experiment Definition and Experiment Results Visualization. PMID:30483089
Harmonizing semantic annotations for computational models in biology. PMID:30462164
Code Generation in Computational Neuroscience: A Review of Tools and Techniques. PMID:30455637
Reproducible Research Using Biomodels. PMID:30191472
Tellurium: An extensible python-based modeling environment for systems and synthetic biology. PMID:30053414
FindSim: A Framework for Integrating Neuronal Data and Signaling Models. PMID:29997492
The CoLoMoTo Interactive Notebook: Accessible and Reproducible Computational Analyses for Qualitative Biological Networks. PMID:29971009
Tellurium notebooks-An environment for reproducible dynamical modeling in systems biology. PMID:29906293
Reproducible model development in the cardiac electrophysiology Web Lab. PMID:29842853
A blueprint for human whole-cell modeling. PMID:29806041
Challenges in Reproducibility, Replicability, and Comparability of Computational Models and Tools for Neuronal and Glial Networks, Cells, and Subcellular Structures. PMID:29765315
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017. PMID:29596055
Methods for enhancing the reproducibility of biomedical research findings using electronic health records. PMID:28912836
COPASI and its applications in biotechnology. PMID:28655634
PharmML in Action: an Interoperable Language for Modeling and Simulation. PMID:28575551
Reproducibility and Comparability of Computational Models for Astrocyte Calcium Excitability. PMID:28270761
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016. PMID:28187405
ASPASIA: A toolkit for evaluating the effects of biological interventions on SBML model behaviour. PMID:28158307
SED-ML web tools: generate, modify and export standard-compliant simulation studies. PMID:28049131
A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos. PMID:27830063
phraSED-ML: A paraphrased, human-readable adaptation of SED-ML. PMID:27774871
Notions of similarity for systems biology models. PMID:27742665
SpineCreator: a Graphical User Interface for the Creation of Layered Neural Models. PMID:27628934
Guidelines for Reproducibly Building and Simulating Systems Biology Models. PMID:27429432
Where next for the reproducibility agenda in computational biology? PMID:27422148
Modular modelling with Physiome standards. PMID:27353233
Toward Community Standards and Software for Whole-Cell Modeling. PMID:27305665
Logical Modeling and Dynamical Analysis of Cellular Networks. PMID:27303434
GESDB: a platform of simulation resources for genetic epidemiology studies. PMID:27242038
Using physiologically based models for clinical translation: predictive modelling, data interpretation or something in-between? PMID:27121495
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
MOCCASIN: converting MATLAB ODE models to SBML. PMID:26861819
The Cardiac Electrophysiology Web Lab. PMID:26789753
JigCell Run Manager (JC-RM): a tool for managing large sets of biochemical model parametrizations. PMID:26704692
Specifications of Standards in Systems and Synthetic Biology. PMID:26528556
NeuroManager: a workflow analysis based simulation management engine for computational neuroscience. PMID:26528175
An algorithm to detect and communicate the differences in computational models describing biological systems. PMID:26490504
Databases for multilevel biophysiology research available at Physiome.jp. PMID:26441671
Regulation of ERK-MAPK signaling in human epidermis. PMID:26209520
SEEK: a systems biology data and model management platform. PMID:26160520
MONALISA for stochastic simulations of Petri net models of biochemical systems. PMID:26156221
Evolutionary trends and functional anatomy of the human expanded autophagy network. PMID:26103419
JSBML 1.0: providing a smorgasbord of options to encode systems biology models. PMID:26079347
Automatising the analysis of stochastic biochemical time-series. PMID:26051821
The role of markup for enabling interoperability in health informatics. PMID:26042043
Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative. PMID:25759811
Combining computational models, semantic annotations and simulation experiments in a graph database. PMID:25754863
OpenCOR: a modular and interoperable approach to computational biology. PMID:25705192
Quantitative and logic modelling of molecular and gene networks. PMID:25645874
Ligand-dependent opening of the multiple AMPA receptor conductance states: a concerted model. PMID:25629405
Using CellML with OpenCMISS to Simulate Multi-Scale Physiology. PMID:25601911
Improving collaboration by standardization efforts in systems biology. PMID:25538939
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. PMID:25494900
Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data. PMID:25414366
LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2. PMID:25309419
WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions. PMID:25231498
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. PMID:24321545
From model specification to simulation of biologically constrained networks of spiking neurons. PMID:24253973
Function of dynamic models in systems biology: linking structure to behaviour. PMID:24103739
The systems biology simulation core algorithm. PMID:23826941
Chaste: an open source C++ library for computational physiology and biology. PMID:23516352
Programming biological models in Python using PySB. PMID:23423320
A CellML simulation compiler and code generator using ODE solving schemes. PMID:23083065
LibKiSAO: a Java library for Querying KiSAO. PMID:23006857
The Input Signal Step Function (ISSF), a standard method to encode input signals in SBML models with software support, applied to circadian clock models. PMID:22855577
Multiscale modeling and data integration in the virtual physiological rat project. PMID:22805979
Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE). PMID:22180826 -
Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2
PubMed citations: 6.
6 articles citing: Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2
A demonstration of modularity, reuse, reproducibility, portability and scalability for modeling and simulation of cardiac electrophysiology using Kepler Workflows. PMID:30849072
BioLQM: A Java Toolkit for the Manipulation and Conversion of Logical Qualitative Models of Biological Networks. PMID:30510517
Meeting the multiscale challenge: representing physiology processes over ApiNATOMY circuits using bond graphs. PMID:29285348
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016. PMID:28187405
SED-ML web tools: generate, modify and export standard-compliant simulation studies. PMID:28049131
FAIRDOMHub: a repository and collaboration environment for sharing systems biology research. PMID:27899646
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Tags
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enzymatic reaction
metasource: Fairsharing.org
version: FAIRsharing.org: SED-ML; Simulation Experiment Description Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.6f7m6j; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
mathematical model
metasource: Fairsharing.org
version: FAIRsharing.org: SED-ML; Simulation Experiment Description Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.6f7m6j; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
modeling and simulation
metasource: Fairsharing.org
version: FAIRsharing.org: SED-ML; Simulation Experiment Description Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.6f7m6j; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
Tags
More detailed information about this field from each metasource.
enzymatic reaction
metasource: Fairsharing.orgversion: FAIRsharing.org: SED-ML; Simulation Experiment Description Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.6f7m6j; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
mathematical model
metasource: Fairsharing.orgversion: FAIRsharing.org: SED-ML; Simulation Experiment Description Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.6f7m6j; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
modeling and simulation
metasource: Fairsharing.orgversion: FAIRsharing.org: SED-ML; Simulation Experiment Description Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.6f7m6j; Last edited: June 23, 2021, 1:09 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
enzymatic reaction mathematical model modeling and simulation
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