BiVeS & BudHat: Invited Talk @ IPK Gatersleben
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BiVeS & BudHat: Invited Talk @ IPK Gatersleben

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Talk at the IPK in Gatersleben to initiate collaborations with the VANTED/e!Dal crews. The slides are also available at our website ...

Talk at the IPK in Gatersleben to initiate collaborations with the VANTED/e!Dal crews. The slides are also available at our website http://sems.uni-rostock.de/2013/05/research-visit-at-the-ipk-gatersleben/

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    BiVeS & BudHat: Invited Talk @ IPK Gatersleben BiVeS & BudHat: Invited Talk @ IPK Gatersleben Presentation Transcript

    • SYSTEMS BIOLOGYBIOINFORMATICSROSTOCKS E Ssimulation experiment management systemBiVeS & BudHatVersion Control for Computational ModelsMARTIN SCHARMDepartment of Systems Biology & BioinformaticsFaculty of Computer Science & Electrical EngineeringUniversity of Rostockhttp://sems.uni-rostock.deGatersleben 2013June 11, 2013 Bives & Budhat | Martin Scharm 1 / 13
    • SYSTEMS BIOLOGYBIOINFORMATICSROSTOCKS E Ssimulation experiment management systemtrack developmentstore retrieverankManagementΔΔVersion 1Version 2latestFormat-independent,graph-based storageInformation Retrieval-basedsearch and rankingDiff-basedversion controlhttp://sems.uni-rostock.de/June 11, 2013 Bives & Budhat | Martin Scharm 2 / 13
    • Version ControlIntro• many models• multiple versions of each model• several repositoriestime#modelsJune 11, 2013 Bives & Budhat | Martin Scharm 3 / 13
    • Version ControlIntro• many models• multiple versions of each model• several repositoriesversion x-1 version x version x+1June 11, 2013 Bives & Budhat | Martin Scharm 3 / 13
    • Version ControlIntro• many models• multiple versions of each model• several repositoriesJune 11, 2013 Bives & Budhat | Martin Scharm 3 / 13
    • Version ControlIntro• many models• multiple versions of each model• several repositoriesversion x-1 version x version x+1track versionswhat happened ?June 11, 2013 Bives & Budhat | Martin Scharm 3 / 13
    • Version Controlgood newsA r CBDcycE/cdk2RB/E2FRB-Hypofree E2FA rBCDE sRB/E2FRB-Hypofree E2FcycE/cdk2RB-Phosnew insightsWaltemath et al.: Improving the reuse of computational models through versioncontrol. Bioinformatics (2013) 29(6): 742-728;June 11, 2013 Bives & Budhat | Martin Scharm 4 / 13
    • BiVeSDifference DetectionA r CBDcycE/cdk2RB/E2FRB-Hypofree E2FA rBCDE sRB/E2FRB-Hypofree E2FcycE/cdk2RB-PhosArBCDArBCDEsBiochemical Model Version Control System• compares models encoded in standadizedformats (currently: and )• maps hierarchically structured contentmappingJune 11, 2013 Bives & Budhat | Martin Scharm 5 / 13
    • BiVeSMapping• input: 2 XML documents• map unambiguosnodes/subtrees• propagate mapping up/down• exploit further knowledge ofbiological systemssame IDsamesubtreehash...... ...... ......... ...... ...June 11, 2013 Bives & Budhat | Martin Scharm 6 / 13
    • BiVeSMapping• input: 2 XML documents• map unambiguosnodes/subtrees• propagate mapping up/down• exploit further knowledge ofbiological systemseq. netw....... ...... ......... ...... ...June 11, 2013 Bives & Budhat | Martin Scharm 6 / 13
    • BiVeSMapping• input: 2 XML documents• map unambiguosnodes/subtrees• propagate mapping up/down• exploit further knowledge ofbiological systemsA BCD EA BCD EA BCD EJune 11, 2013 Bives & Budhat | Martin Scharm 6 / 13
    • BiVeSDifference DetectionA r CBDcycE/cdk2RB/E2FRB-Hypofree E2FA rBCDE sRB/E2FRB-Hypofree E2FcycE/cdk2RB-PhosArBCDArBCDEsBiochemical Model Version Control System• compares models encoded in standadizedformats (currently: and )• maps hierarchically structured content• constructs a diff (in XML format)• is able to interprete this diff<XML>Diffmovesproduct of r: Cdeletesproduct of r: Binsertsspecies: Eproduct of r: Ereaction s</XML>mappingdi constructionJune 11, 2013 Bives & Budhat | Martin Scharm 7 / 13
    • BudHatDiff VisualizationA r CBDcycE/cdk2RB/E2FRB-Hypofree E2FA rBCDE sRB/E2FRB-Hypofree E2FcycE/cdk2RB-PhosArBCDArBCDEs<XML>Diffmovesproduct of r: Cdeletesproduct of r: Binsertsspecies: Eproduct of r: Ereaction s</XML>• calls BiVeS to construct the diff• displays the result in various formats• the XML diff• a reaction network highlighting thechanges using• a human readable reportA r BCDE sJune 11, 2013 Bives & Budhat | Martin Scharm 8 / 13
    • BiVeS & BudHatDEMOThe Power of BudHat!http://budhat.sems.uni-rostock.deJune 11, 2013 Bives & Budhat | Martin Scharm 9 / 13
    • Rostock goes GaterslebenOur AimVANTED BiVeSJune 11, 2013 Bives & Budhat | Martin Scharm 10 / 13
    • Rostock goes GaterslebenOur AimVANTED BiVeSJune 11, 2013 Bives & Budhat | Martin Scharm 10 / 13
    • Rostock goes GaterslebenOur AimVANTED BiVeSlet’s collaborate!We VANT BiVeS!June 11, 2013 Bives & Budhat | Martin Scharm 10 / 13
    • BiVeSIntegrationjvm network cmdimport de.unirostock.sems.bives.api.SBMLDiff;[...]SBMLDiff differ = new SBMLDiff (sbmlFileA, sbmlFileB);differ.mapTrees ();String graph = differ.getGraphML ();[...]June 11, 2013 Bives & Budhat | Martin Scharm 11 / 13
    • BiVeSIntegrationjvm network cmdcurl -d "file1=http://some.server/model/version1"-d "file2=http://other.server/model/version2"-d "get=graphml" bives.server/apiJune 11, 2013 Bives & Budhat | Martin Scharm 11 / 13
    • BiVeSIntegrationjvm network cmdjava -jar BiVeS.jar path/to/version1 path/to/version2git diff 88fea1cddf b64477d742 model.fileJune 11, 2013 Bives & Budhat | Martin Scharm 11 / 13
    • BiVeS & BudHatSummary• BiVeS = Difference detection for hierarchically structured content• BudHat = Prototype to demonstrate the capabilities• Both tools are open source• Our goal is to extend existing models repositories with a valuable versioncontrol mechanismJune 11, 2013 Bives & Budhat | Martin Scharm 12 / 13
    • SYSTEMS BIOLOGYBIOINFORMATICSROSTOCKS E Ssimulation experiment management systemThat’s it! Stay tuned ;-)@SemsProjecthttp://sems.uni-rostock.dehttp://budhat.sems.uni-rostock.deQuestions? Suggestions? Recommendations? Drop me an email:<martin.scharm@uni-rostock.de>June 11, 2013 Bives & Budhat | Martin Scharm 13 / 13