the sems project: managing simulation models · systems biology bioinformatics rostock overview...

SYSTEMS BIOLOGY BIOINFORMATICS ROSTOCK Overview SEMS is a BMBF-funded e:Bio project dedicated to the development of methods and tools for improved management of computational models and associated simulation setups in standard formats. The SEMS-team is a group of young researchers who care for model storage and retrieval (Ron Henkel), model version control (Martin Scharm), the encoding of models and simulation setups (Martin Wolfien), and the development of software applications (Martin Peters). SE S simulation experiment management system Δ Δ retrieve rank track development store Version 1 Version 2 latest Linking models and simulation descriptions Sketch of links between different types of documents as represented in our graph database (Neo4j): simulation experiment descriptions and models (dashed line); defined observation variables and model entities (dotted line); annotated model entities and simulation experiment descriptions (dashed-dotted line); and model entities of different representation formats (double dotted-dashed line). (Figure taken from [3]) Feature extraction from model annotations Overview of concept distribution in SBO. The figure shows the distribution of concepts in the seven branches of the Systems Biology Ontology (SBO, Figure adapted from [2]). The size of the colored circles visualizes the number of concepts summarized by each branch. The bottom mirrored image visualizes the distribution of annotations from all models in the BioModels Database. (Figure originally published in [1]) Changes in model versions Novak 1993 12 updates 20 moves 80 inserts 20 deletes Statistics on model updates in the CellML Model Repository. The figure shows the updates in all versions of all models currently published in the CellML Model Repository. Each bar on the x-axis corresponds to a diff between two consecutive versions of the same model. Y-axis shows the total number of identified changes (yellow: update; blue: move; green: insert; red: delete). Data generated with BiVeS [4], Figure courtesy Martin Scharm. References [1] Rebekka Alm et al. Annotation-based feature extraction from sets of sbml models. In Databases in the life sciences (DILS), accepted for publication, 2014. [2] Mélanie Courtot et al. Controlled vocabularies and semantics in systems biology. Molec- ular systems biology, 7(1), 2011. [3] Ron Henkel et al. Combining computational models, semantic annotations, and associated simulation experiments in a graph database. in preparation, 2014. [4] Dagmar Waltemath et al. Improving the reuse of computational models through version control. Bioinformatics, 29(6):742–748, 2013. The SEMS Project: Managing Simulation Models Ron Henkel Martin Scharm Dagmar Waltemath Olaf Wolkenhauer

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SYSTEMS BIOLOGY

BIOINFORMATICS

ROSTOCK

Overview

SEMS is a BMBF-funded e:Bio project dedicated to the development of methods and tools for improved management of computational models and associated simulation setups in standardformats. The SEMS-team is a group of young researchers who care for model storage and retrieval (Ron Henkel), model version control (Martin Scharm), the encoding of models and simulationsetups (Martin Wolfien), and the development of software applications (Martin Peters).

S E Ssimulation experiment management system

∆ ∆

retrieve

rank

track development

store

Version 1

Version 2

latest

Linking models and simulation descriptions

Sketch of links between different types of documents as represented inour graph database (Neo4j): simulation experiment descriptions and models (dashed line);defined observation variables and model entities (dotted line); annotated model entitiesand simulation experiment descriptions (dashed-dotted line); and model entities of differentrepresentation formats (double dotted-dashed line). (Figure taken from [3])

Feature extraction from model annotations

Overview of concept distribution in SBO. The figure shows the distribution ofconcepts in the seven branches of the Systems Biology Ontology (SBO, Figure adaptedfrom [2]). The size of the colored circles visualizes the number of concepts summarized byeach branch. The bottom mirrored image visualizes the distribution of annotations from allmodels in the BioModels Database. (Figure originally published in [1])

Changes in model versions

Novak1993 12 updates 20 moves 80 inserts 20 deletes

Statistics on model updates in the CellML Model Repository. The figureshows the updates in all versions of all models currently published in the CellML ModelRepository. Each bar on the x-axis corresponds to a diff between two consecutive versionsof the same model. Y-axis shows the total number of identified changes (yellow: update;blue: move; green: insert; red: delete). Data generated with BiVeS [4], Figure courtesyMartin Scharm.

References

[1] Rebekka Alm et al. Annotation-based feature extraction from sets of sbml models. InDatabases in the life sciences (DILS), accepted for publication, 2014.

[2] Mélanie Courtot et al. Controlled vocabularies and semantics in systems biology. Molec-ular systems biology, 7(1), 2011.

[3] Ron Henkel et al. Combining computational models, semantic annotations, and associ-ated simulation experiments in a graph database. in preparation, 2014.

[4] Dagmar Waltemath et al. Improving the reuse of computational models through versioncontrol. Bioinformatics, 29(6):742–748, 2013.

The SEMS Project: Managing Simulation Models

Ron [email protected]

Martin [email protected]

Dagmar [email protected]

Olaf [email protected]

[email protected]