http://sems.uni-rostock.de

Dagmar WaltemathSeptember 2015 – GCB, Dortmund

Management of simulation studiesin computational biology

(e:Bio Junior Research Group SEMS)

The project goal is to improve the reproducibility of simulation studies in computational biology.

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The number of models in open repositories is steadily increasing, and so is their complexity.

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Fig.: Models in BioModels. Chelliah et al. Nucl. Acids Res. 2015;43:D542-D548

Open model repositories are rich resources of interlinked knowledge ready to be explored.

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Simulation studies comprise of several heterogeneous files.

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Many studies are not reproducible and thus not reusable.

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● The human factor● Lack of standards and tool interoperability● Lack of data availability● Lack of provenance information

Figs. (left to right): (A) The Economist, Trouble at the lab, 2013; (B) JISC, www.jisc.ac.uk, CC BY-NC-ND 2.0 UK; (C) Diego Delso, Wikimedia Commons, License CC-BY-SA 3.0; (D) C. Goble, Keynote ISMB/ECCB 2013 “Results may vary”, Slideshare

Waltemath and Wolkenhauer (2015) under review

SEMS: Model management for Computational Biology

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Martin Scharm Tom Gebhardt Mariam NassarMartin Peters Vasundra Touré Ron Henkel Fabienne Lambusch

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MASYMOSHow can we link model-related data?

● Publication

● Model

● Analysis (Simulation)

● Data (experimental and simulation)

● Results (Figures, data tables...)

Types of model-related data

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MASYMOSHow can we link model-related data?

● Data from open repositories (BioModels, PMR2, BioPortal)

Explicit linking

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MASYMOSIntegration of model-related data

● Data from open repositories (BioModels, PMR2, BioPortal)

● Links between data belonging to a simulation study

Henkel (2015) DATABASE

Explicit linking

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MASYMOSIntegration of model-related data

● Data from open repositories (BioModels, PMR2, BioPortal)

● Links between data belonging to a simulation study

● Graph database for integrated storage (Neo4J)

Explicit linking

Henkel (2015) DATABASE

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MASYMOS Can we improve model search?

Model

Publication

Annotation

Person

Simulation

Show me models by Tyson, dealing with the Cell Cycle and simulating concentration of cdc2!

Ron Henkel

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M2CATHow can we export search results?

internet

internet

internet

SEARCHubiquitin

internet

RESULTSEXPORT

EXPORT

EXPORT

EXPORT

Query database for annotations, persons, simulation descriptions

Retrieve information about models, simulations, figures, documentation

Export simulation study as COMBINE archive

Download archive and open the study with your favourite simulation tool

Open archive in CAT to modify its contents and to share it with others

internet

API Commincations enrich your studies with simulation results

Simulate a Study with just a single click

Fig.: Exporting COMBINE Archives from MASYMOS. Bergmann (2014), Scharm (2015)

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MASYMOSRanking, Comparison,Clustering

MASYMOSHenkel (2011) BMC SysBiol

Ran

k ing

Alm (2015) JBMS

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BioModels

Clu

ster

i ng

Sea

r ch

IIWhich models contain feedback loops?

How many modelscontain this specific submodule?

Which models have 'ATP' as product?

Lambusch, BA (2015),Henkel (2014) SWAT4LS

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BiVeSCan we describe a model's evolution?

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BiVeSCan we describe a model's evolution?

Fig.: Visualisation of the evolution of an early cell cyle model Scharm (2015)

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BiVeSDifference Detection

Fig.: BudHat – Detecting differences between model versions. Scharm (2015)

Martin Scharm

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BiVeSDifference Detection

Fig.: BiVeS algorithm and output format. Scharm (2015)

Martin Scharm

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COMODIHow can we characterise changes?

How do COmputational MOdels DIffer?

Fig.: Statistics on model versions in PMR2. Scharm (2015)

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COMODIHow can we characterise changes?

How do COmputational MOdels DIffer?

Fig.: Working draft of COMODI, slides presented at the 2015 e:Bio Meeting.

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COMODIHow can we characterise changes?

How do COmputational MOdels DIffer?

Fig.: Working draft of COMODI, slides presented at the 2015 e:Bio Meeting.

Standards are the basis of our work.

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Fig. : COMBINE standards today. Slide courtesy M. Hucka, Slideshare.

Special issue at JIBCOMBINE standards

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Summary

Methods

Ranked Retrieval

BiVeS

Model similarity

Tools StandardsTM

Archive

VANTEDVANTED

Reproducible Science

Thank you for your attention.

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HERMES-Forschungsförderung der Universität Rostock

Tom GebhardMariam NassarMartin Peters Martin Scharm Dagmar Waltemath

Ron Henkel (de.NBI-SYSBIO)Fabienne Lambusch

Vasundra Toure (SBGN-ED)

@SemsProject