Modeling samples from a graph perspective

Dagmar Waltemath | SEMS | University of Rostock, Germany

Biosamples Workshop, June 2015The University of Manchester

What does a modeling sample consist of?

Figures taken from Goldbeter (1991), http://www.ncbi.nlm.nih.gov/pubmed/1833774

What does a modeling sample consist of?

Figures taken from Goldbeter (1991), http://www.ncbi.nlm.nih.gov/pubmed/1833774

Model Simulation experiment

Simulation experiment

Simulation experiment

We are pretty good in terms of data formats for modeling samples.

Model Simulation experiment Simulation result

We are pretty good in terms of data formats for modeling samples.

Model Simulation experiment Simulation result

TM

We are pretty good in terms of data formats for modeling samples.

Model Simulation experiment Simulation result

TM

We are pretty good in terms of data formats for modeling samples.

Model Simulation experiment Simulation result

TM

NuML

NuML

NuML

We face problems with managing modeling samples.

How can we keep track of a model's / a system's evolution/provenance?

Figures courtesy Martin Scharm

We face problems with managing modeling samples.

How well does a model reproduce a desired behavior? (or set of behaviors)

Fig.: Cooper, Jonathan et al. "A call for virtual experiments: accelerating the scientific process." Progress in biophysics and molecular biology 117.1 (2015): 99-106.

Fig.: Cooper et al. https://travis.cs.ox.ac.uk/FunctionalCuration/

We face problems with managing modeling samples.

How can we ensure to provide all data necessary to reproduce a given study?

Integrating model-related data in a graph database.

Figure courtesy Fabienne Lambusch

Fig.: Henkel, Ron, Olaf Wolkenhauer, and Dagmar Waltemath. "Combining computational models, semantic annotations and simulation experiments in a graph database." Database 2015 (2015): bau130.

Integrating model-related data in a graph database.

Fig.: Henkel, Ron, Olaf Wolkenhauer, and Dagmar Waltemath. "Combining computational models, semantic annotations and simulation experiments in a graph database." Database 2015 (2015): bau130.

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http://sems.uni-rostock.de