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Minimum Information About a Simulation Experiment (MIASE)

Dagmar Waltemath, Richard Adams, Daniel A. Beard, Frank T. Bergmann, Upinder S. Bhalla, Randall Britten, Vijayalakshmi Chelliah, Michael T. Cooling, Jonathan Cooper, Edmund J. Crampin, Alan Garny, Stefan Hoops (+17 others)
2011 PLoS Computational Biology  
The Minimum Information About a Simulation Experiment (MIASE, Glossary in Box 1) describes the minimal set of information that must be provided to make the description of a simulation experiment available  ...  MIASE allows for the reproduction of any simulation experiment.  ...  Glossary MIASE Minimum Information About a Simulation Experiment.  ... 
doi:10.1371/journal.pcbi.1001122 pmid:21552546 pmcid:PMC3084216 fatcat:6ihq7usih5fu7gpdmob25pcwaa

Extending libSedML to support CellML models

David Nickerson, David Nickerson, Dongxue Amy You
2011 Nature Precedings  
MIASE ...is a community effort to identify the Minimum Information About a Simulation Experiment, to help enabling the reproducible description of simulation experiments. • The common set of information  ...  tools to exchange their simulation settings. • Information about the models to use; the simulation steps; and the output.  ...  Time course experiment wizard  ... 
doi:10.1038/npre.2011.5897 fatcat:ptl6pihr5veftptrd7otmdfese

Extending libSedML to support CellML models

David Nickerson, David Nickerson, Dongxue Amy You
2011 Nature Precedings  
MIASE ...is a community effort to identify the Minimum Information About a Simulation Experiment, to help enabling the reproducible description of simulation experiments. • The common set of information  ...  tools to exchange their simulation settings. • Information about the models to use; the simulation steps; and the output.  ...  Time course experiment wizard  ... 
doi:10.1038/npre.2011.5897.1 fatcat:qomlrhpwzfao5jarglx4xnx36m

Towards a web-based simulation experiment description repository

Michael Guravage, Michael Guravage
2011 Nature Precedings  
A set of guidelines specifying the Minimum Information About a Simulation Experiment(MIASE) [1] proposes a common set of information necessary to reproduce simulation experiments that incorporate quantitative  ...  Waltemath et al.Minimum information about a simulation experiment (miase) (unpublished,2010). biomodels.net/miase/.  ...  A set of guidelines specifying the Minimum Information About a Simulation Experiment(MIASE) [1] proposes a common set of information necessary to reproduce simulation experiments that incorporate quantitative  ... 
doi:10.1038/npre.2011.6346.1 fatcat:22j5sr55fbelpdtxb7qhx3qpda

Data Integration and Semantic Enrichment of Systems Biology Models and Simulations [chapter]

Vijayalakshmi Chelliah, Lukas Endler, Nick Juty, Camille Laibe, Chen Li, Nicolas Rodriguez, Nicolas Le Novère
2009 Lecture Notes in Computer Science  
Minimum Information About a Simulation Experiment (MIASE; http://www.ebi.ac.uk/compneur srv/miase/), describes the information needed to run and repeat a numerical simulation experiment derived from a  ...  MIRIAM and MIASE are now, part of the Minimum Information for Biological and Biomedical Investigations project (MIBBI;http://www.mibbi.org/) [6] .  ...  This led to the development of the Minimum Information About a Simulation Experiment (MIASE; http://www.ebi.ac.uk/ compneur-srv/miase) project.  ... 
doi:10.1007/978-3-642-02879-3_2 fatcat:2d7yaf2q5jbchoa5yqfspd6l2y

Function of dynamic models in systems biology: linking structure to behaviour

Christian Knüpfer, Clemens Beckstein
2013 Journal of Biomedical Semantics  
A simulation experiment always refers to a specific situation and a state of the model and the modelled system (conditional function).  ...  In order to fulfil this role a model has to be used in simulation experiments (pragmatical function).  ...  Acknowledgements We acknowledge Johannes Kretzschmar, Uwe Krüger and Christian Schäufler for valuable discussions about the topic.  ... 
doi:10.1186/2041-1480-4-24 pmid:24103739 pmcid:PMC3853929 fatcat:wg555nfpvra4jny6iwr5c5u4na

Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language

Dagmar Waltemath, Richard Adams, Frank T Bergmann, Michael Hucka, Fedor Kolpakov, Andrew K Miller, Ion I Moraru, David Nickerson, Sven Sahle, Jacky L Snoep, Nicolas Le Novère
2011 BMC Systems Biology  
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  ...  SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments.  ...  The Minimum Information About a Simulation Experiment (MIASE, [1] ) is a reporting guideline describing the minimal set of information that must be provided to make the description of a simulation experiment  ... 
doi:10.1186/1752-0509-5-198 pmid:22172142 pmcid:PMC3292844 fatcat:lct3n2evrzdpvftrhiajn4isdq

One file to share them all: Using the COMBINE Archive and the OMEX format to share all information about a modeling project [article]

Frank T. Bergmann, Richard Adams, Stuart Moodie, Jonathan Cooper, Mihai Glont, Martin Golebiewski, Michael Hucka, Camille Laibe, Andrew K. Miller, David P. Nickerson, Brett G. Olivier, Nicolas Rodriguez, Herbert M. Sauro (+4 others)
2014 arXiv   pre-print
information necessary for a modeling and simulation experiment in biology.  ...  An OMEX file is a ZIP container that includes a manifest file, listing the content of the archive, an optional metadata file adding information about the archive and its content, and the files describing  ...  org VCell Ion Moraru Java http :// www . nrcam . uchc . edu / COMBINE Computational Modeling in Biology Network MIASE Minimum Information About a Simulation Experiment MIRIAM Minimum Information  ... 
arXiv:1407.4992v2 fatcat:x2pn25x6rvdznfzgc7hlhip7aq

GESDB: a platform of simulation resources for genetic epidemiology studies

Po-Ju Yao, Ren-Hua Chung
2016 Database: The Journal of Biological Databases and Curation  
The statistics will be informative for researchers to choose an appropriate simulation tool or select a common dataset for method comparisons. GESDB can be accessed at  ...  GESDB consists of a database for storing simulation scripts, simulated data and documentation from published articles as well as a discussion forum, which provides a platform for discussion of the simulated  ...  This work was funded by a grant from the National Health Research Institutes (PH-105-PP-10) in Taiwan. Conflict of interest. None declared.  ... 
doi:10.1093/database/baw082 pmid:27242038 pmcid:PMC4885602 fatcat:mvcbnkrrqjbmtbde5q5tixa6dq

LibKiSAO: a Java library for Querying KiSAO

Anna Zhukova, Richard Adams, Camille Laibe, Nicolas Le Novère
2012 BMC Research Notes  
Information about analogous methods having similar characteristics and about algorithm parameters incorporated into KiSAO is desirable for simulation tools.  ...  The Kinetic Simulation Algorithm Ontology (KiSAO) supplies information about existing algorithms available for the simulation of Systems Biology models, their characteristics, parameters and inter-relationships  ...  Equations; MIASE: Minimal Information About a Simulation Experiment; OWL: Web Ontology Language; SED-ML: Simulation Experiment Description Markup Language; URI: Uniform resource identifier.  ... 
doi:10.1186/1756-0500-5-520 pmid:23006857 pmcid:PMC3532180 fatcat:36flsimdlfaorhzfrz4532uifi

D5.5 - A workflow and checklist of key information needed from modelling tool owners to facilitate integration into KB

Anastasios Papadiamantis, Thomas Exner, Haralambos Sarimveis, Vladimir Lobaskin
2020 Zenodo  
For this process to be successful, a clearly defined modelling tools integration workflow needs to be developed and implemented.  ...  This will facilitate a linked data approach to integrate and exploit knowledge from publicly available sources and feed into the modelling tools for further studies.  ...  Minimum Information About a Simulation Experiment (MIASE) Guidelines One of the main requirements in scientific research is reproducibility of experimental work.  ... 
doi:10.5281/zenodo.3603087 fatcat:hqha7hguwze5zm635tnffhjnri

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project

Frank T Bergmann, Richard Adams, Stuart Moodie, Jonathan Cooper, Mihai Glont, Martin Golebiewski, Michael Hucka, Camille Laibe, Andrew K Miller, David P Nickerson, Brett G Olivier, Nicolas Rodriguez (+6 others)
2014 BMC Bioinformatics  
information necessary for a modeling and simulation experiment in biology.  ...  An OMEX file is a ZIP container that includes a manifest file, listing the content of the archive, an optional metadata file adding information about the archive and its content, and the files describing  ...  Several guidelines were developed to list this information, including the Minimum Information Requested in the Annotation of Models (MIRIAM) [6] and the Minimum Information About Simulation Experiments  ... 
doi:10.1186/s12859-014-0369-z pmid:25494900 pmcid:PMC4272562 fatcat:3dqofrgqz5f2dlivtikejgyonu

Domain-Specific Languages for Flexbily Experimenting with Stochastic Models

Danhua Peng, Tom Warnke, Adelinde M. Uhrmacher
2015 SNE Simulation Notes Europe  
Developing a model for simulation is a difficult task, in which simulation experiments play a critical role.  ...  Domain specific languages can be used to specify different tasks of simulation experiments, such as experiment configuration, observation, analysis, and evaluation of experimental results.  ...  Several work exists on identifying requirements in describing simulation experiments, such as Minimum Information About a Simulation Experiment (MIASE) [10] and Minimum Simulation Reporting Requirements  ... 
doi:10.11128/sne.25.tn.10299 fatcat:dbnraztdq5hmdc24phyvhh3o6u

Trends and Tools for Modeling in Modern Biology [chapter]

Michael Hucka, James Schaff
2009 Photosynthesis in silico  
project (Minimum Information About a Simulation Experiment; http://www.ebi.ac.uk/ compneur-srv/miase/) was initiated.  ...  simulation experiment; MIRIAM -minimum information requested in the annotation of biochemical models; SBGN -systems biology graphical notation; SBML -systems biology markup language; SBO -systems biology  ... 
doi:10.1007/978-1-4020-9237-4_1 fatcat:5xfr2qvwcrh45c7p5r2spte534

Where next for the reproducibility agenda in computational biology?

Joanna Lewis, Charles E. Breeze, Jane Charlesworth, Oliver J. Maclaren, Jonathan Cooper
2016 BMC Systems Biology  
Several fields have developed 'minimum information' checklists to support the full reporting of computational simulations, analyses and results, and standardised data formats and model description languages  ...  The concept of reproducibility is a foundation of the scientific method.  ...  ] and Minimum Information About a Simulation Experiment (MIASE) [44] guidelines.  ... 
doi:10.1186/s12918-016-0288-x pmid:27422148 pmcid:PMC4946111 fatcat:swap4ubuxna4pcoz7d4p33phg4
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