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SYSTEMS BIOLOGYBIOINFORMATICSROSTOCKS E Ssimulation experiment management systemBiVeS & BudHatVersion Control for Computat...
SYSTEMS BIOLOGYBIOINFORMATICSROSTOCKS E Ssimulation experiment management systemtrack developmentstore retrieverankManagem...
Version ControlIntro• many models• multiple versions of each model• several repositoriestime#modelsJune 11, 2013 Bives & B...
Version ControlIntro• many models• multiple versions of each model• several repositoriesversion x-1 version x version x+1J...
Version ControlIntro• many models• multiple versions of each model• several repositoriesJune 11, 2013 Bives & Budhat | Mar...
Version ControlIntro• many models• multiple versions of each model• several repositoriesversion x-1 version x version x+1t...
Version Controlgood newsA r CBDcycE/cdk2RB/E2FRB-Hypofree E2FA rBCDE sRB/E2FRB-Hypofree E2FcycE/cdk2RB-Phosnew insightsWal...
BiVeSDifference DetectionA r CBDcycE/cdk2RB/E2FRB-Hypofree E2FA rBCDE sRB/E2FRB-Hypofree E2FcycE/cdk2RB-PhosArBCDArBCDEsBi...
BiVeSMapping• input: 2 XML documents• map unambiguosnodes/subtrees• propagate mapping up/down• exploit further knowledge o...
BiVeSMapping• input: 2 XML documents• map unambiguosnodes/subtrees• propagate mapping up/down• exploit further knowledge o...
BiVeSMapping• input: 2 XML documents• map unambiguosnodes/subtrees• propagate mapping up/down• exploit further knowledge o...
BiVeSDifference DetectionA r CBDcycE/cdk2RB/E2FRB-Hypofree E2FA rBCDE sRB/E2FRB-Hypofree E2FcycE/cdk2RB-PhosArBCDArBCDEsBi...
BudHatDiff VisualizationA r CBDcycE/cdk2RB/E2FRB-Hypofree E2FA rBCDE sRB/E2FRB-Hypofree E2FcycE/cdk2RB-PhosArBCDArBCDEsXML...
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 ...
BiVeSIntegrationjvm network cmdimport de.unirostock.sems.bives.api.SBMLDiff;[...]SBMLDiff differ = new SBMLDiff (sbmlFileA...
BiVeSIntegrationjvm network cmdcurl -d file1=http://some.server/model/version1-d file2=http://other.server/model/version2-...
BiVeSIntegrationjvm network cmdjava -jar BiVeS.jar path/to/version1 path/to/version2git diff 88fea1cddf b64477d742 model.f...
BiVeS  BudHatSummary• BiVeS = Difference detection for hierarchically structured content• BudHat = Prototype to demonstrat...
SYSTEMS BIOLOGYBIOINFORMATICSROSTOCKS E Ssimulation experiment management systemThat’s it! Stay tuned ;-)@SemsProjecthttp:...
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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 http://sems.uni-rostock.de/2013/05/research-visit-at-the-ipk-gatersleben/

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BiVeS & BudHat: Invited Talk @ IPK Gatersleben

  1. 1. 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
  2. 2. 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
  3. 3. Version ControlIntro• many models• multiple versions of each model• several repositoriestime#modelsJune 11, 2013 Bives & Budhat | Martin Scharm 3 / 13
  4. 4. 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
  5. 5. Version ControlIntro• many models• multiple versions of each model• several repositoriesJune 11, 2013 Bives & Budhat | Martin Scharm 3 / 13
  6. 6. 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
  7. 7. 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
  8. 8. 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
  9. 9. 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
  10. 10. 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
  11. 11. 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
  12. 12. 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
  13. 13. BudHatDiff VisualizationA r CBDcycE/cdk2RB/E2FRB-Hypofree E2FA rBCDE sRB/E2FRB-Hypofree E2FcycE/cdk2RB-PhosArBCDArBCDEsXMLDiffmovesproduct 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
  14. 14. BiVeS BudHatDEMOThe Power of BudHat!http://budhat.sems.uni-rostock.deJune 11, 2013 Bives Budhat | Martin Scharm 9 / 13
  15. 15. Rostock goes GaterslebenOur AimVANTED BiVeSJune 11, 2013 Bives Budhat | Martin Scharm 10 / 13
  16. 16. Rostock goes GaterslebenOur AimVANTED BiVeSJune 11, 2013 Bives Budhat | Martin Scharm 10 / 13
  17. 17. Rostock goes GaterslebenOur AimVANTED BiVeSlet’s collaborate!We VANT BiVeS!June 11, 2013 Bives Budhat | Martin Scharm 10 / 13
  18. 18. 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
  19. 19. 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
  20. 20. 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
  21. 21. 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
  22. 22. 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.deJune 11, 2013 Bives Budhat | Martin Scharm 13 / 13

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