short introduction to sed-ml
TRANSCRIPT
Reproducible virtual experiments with SED-ML
Dagmar Waltemath
dagmarwaltemath
m n
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On models and simulations
Figs: BioModels (top) and DOI: 10.1073/pnas.88.16.7328 (bottom)
Model Simulation
On models and simulations
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Model Simulation
On models and simulations
Model Simulation
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Figs left to right: Simulation in COPASI 4.16 (1s), COPASI 4.16 (100s), COPASI 4.16 (100s), selected species only
What information is contained in a SED-ML file?
Models used in analyses
● Links to published models● References to local models
● Instructions for pre-processing
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Types of experiments
● Time course analyses● Parameter scans● …
● Simulation algorithm and settings
Links to data
● Links to published data sets (DOI, URI)
● Experimental and simulation
Simulation output
● Observed model entities● Type of output (table, plot, …)
● Instructions for post-processing
NuML
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Good reasons to [use|implement] SED-ML export
● Reproduce another person's simulation results
● Document the development process and testing of a model
● Speed up curation of your data in open model repositories
● Make other people happy
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How to use SED-ML
Fig: Tool support for SED-ML (selection): Register your tool at http://sed-ml.org/→Showcase
Cell Designer SED-ML Script Editor SED-ML Web Tools SBW Simulation SED-ED
● Export SED-ML descriptions from your simulation tool
● Use SED-ML Web Tools for online creation & exploration→Frank
● Publish SED-ML files, e.g., through JWS Online
● Add SED-ML files to your COMBINE Archive →video
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How to support SED-ML development
● Offer export of SED-ML files in your simulation tools
● Provide curated SED-ML files in model repositories and model management tools (or COMBINE archives →video)
● Help us implement new features to turn the current proposal (SED-ML L1V3) into the next version of SED-ML (→HARMONY 2016)
● SED-ML library support ● Catch up with recent developments on the
web page● We also have a mailing list …
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Results must be reproducible to be trusted and reusable.
Ways outCurrent status Desired status
Blogs and databases
Detailed documentation
Open data
Standards
Reproducibility initiative
Sustainable Software
Infrastructure
Comprehensible, findable, available, correct models and simulation studies.
Many scientific studies in the life sciences are
not reproducible.
Waltemath and Wolkenhauer (2016) How modeling standards, software, and initiatives support reproducibility in systems biology and systems medicine. Accepted for publication, IEEE Transactions in Biomedical Engineering
Thank you for your attention.
David Nickerson
m n@SemsProject
http://co.mbine.org
SED-ML editorial board
http://sed-ml.org
Lucian Smith Brett Olivier
Ion Moraru
Sven Sahle