Management of simulation studies in computational biology
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Transcript of Management of simulation studies in computational biology
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http://sems.uni-rostock.de
Dagmar WaltemathSeptember 2015 – GCB, Dortmund
Management of simulation studiesin computational biology
(e:Bio Junior Research Group SEMS)
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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
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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
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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
x x x x
x x x x x x x
x x x
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x x x
x
x x x x
x x x xCellCycle Models
x x x x x x
x x x x x
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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.
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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
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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