This document discusses SED-ML (Simulation Experiment Description Markup Language), a standard for describing computational simulations. SED-ML files contain information like the models, data, simulation settings and algorithms used in an experiment. Using SED-ML allows experiments to be reproduced and shared. The document encourages adopting SED-ML to make research more reproducible and help curation of models in repositories. It also provides an overview of tools that support SED-ML and ways to get involved in its development.

1. Reproducible virtual experiments with SED-ML
Dagmar Waltemath
dagmar.waltemath@uni-rostock.de
dagmarwaltemath
m n

2. 2
On models and simulations
Figs: BioModels (top) and DOI: 10.1073/pnas.88.16.7328 (bottom)
Model Simulation

3. On models and simulations
TM
Model Simulation

4. On models and simulations
Model Simulation
TM
Figs left to right: Simulation in COPASI 4.16 (1s), COPASI 4.16 (100s), COPASI 4.16 (100s), selected species only

5. 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
TM
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

6. 6
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

7. 7
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

8. 8
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 …

9. 9
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

10. 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