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Improving the management of computational models.

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Written by Martin Scharm (University of Rostock), Ron Henkel (University of Rostock), Dagmar Waltemath (University of Rostock), Olaf Wolkenhauer (University of Rostock, Stellenbosch University), and presented by Martin Scharm (University of Rostock) as part of the Reproducible and Citable Data and Models Workshop in Warnemünde, Germany. September 14th - 16th 2015.

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Improving the management of computational models.

  1. 1. SYSTEMS BIOLOGY BIOINFORMATICS ROSTOCK S E Ssimulation experiment management system Improving the Management of Computational Models storage – retrieval & ranking – version control MARTIN SCHARM 1,2 , RON HENKEL 1 , DAGMAR WALTEMATH 1 , OLAF WOLKENHAUER 1,3 1 Department of Systems Biology & Bioinformatics, University of Rostock 2 Department of Computer Science, University of Oxford 3 Stellenbosch Institute for Advanced Study, South Africa http://sems.uni-rostock.de European Bioinformatics Institute UK 2013 Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 1
  2. 2. Introduction time #models 2013-06-18 462+501+x·103 216+196 2009-06-16 31 2005-04-11 • Number of models is steadily increasing • Models tend to get more complex • Continuous development Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 2
  3. 3. Introduction reactions model ~27.06 curated ~288.91 noncurated 2013 • Number of models is steadily increasing • Models tend to get more complex • Continuous development Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 2
  4. 4. Introduction time #Versions • Number of models is steadily increasing • Models tend to get more complex • Continuous development Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 2
  5. 5. Introduction Tasks • Storage & Availability • Search & Retrieval • Version Control Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 3
  6. 6. Introduction Tasks • Storage & Availability • Search & Retrieval • Version Control Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 3
  7. 7. Introduction Tasks • Storage & Availability • Search & Retrieval • Version Control ? Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 3
  8. 8. Introduction Tasks • Storage & Availability • Search & Retrieval • Version Control version x-1 version x version x+1 Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 3
  9. 9. Introduction Solutions Several projects develop methods to support the community Model Repository Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 4
  10. 10. SYSTEMS BIOLOGY BIOINFORMATICS ROSTOCK S E Ssimulation experiment management system track development store retrieve rank Retrieval Ranking Δ Δ Version 1 Version 2 latest Version Control Do cu me ntTys on 19 91 Cel l Cy cle 6 var C2 pM Cel l Re act ion 3 CP Unipr ot:P0 4551 Unipr ot:P0 4551 GO:0 0056 23 Inte rpro : IPR 006 670 isVersion Of isVersion hasPart is Pub med: 1831 270 Kegg Path way sce04 111 isDescrib edBy is EC- Code: 3.1.3. 16 isVersion Of Docu ment SEDM L Model refere nce Outpu t Datag enera tor Simul ation Task Varia ble Varia ble Doc ume nt Tyso n_19 91 C2 CP time envi ron men t isDescribedBy Pubm ed: 183127 0 time timeCPC2 CP C2 Do cu me ntTys on 19 91 Cel l Cy cle 6 var C2 pM Cel l Re act ion 3 CP Unipr ot:P0 4551 Unipr ot:P0 4551 GO:0 0056 23 Inte rpro : IPR 006 670 isVersion Of isVersion hasPart is Pub med: 1831 270 Kegg Path way sce04 111 isDescrib edBy is EC- Code: 3.1.3. 16 isVersion Of Do cu me ntTys on 19 91 Cel l Cy cle 6 var C2 pM Cel l Re act ion 3 CP Unipr ot:P0 4551 Unipr ot:P0 4551 GO:0 0056 23 Inte rpro : IPR 006 670 isVersion Of isVersion hasPart is Pub med: 1831 270 Kegg Path way sce04 111 isDescrib edBy is EC- Code: 3.1.3. 16 isVersion Of Do cu me ntTys on 19 91 Cel l Cy cle 6 var C2 pM Cel l Re act ion 3 CP Unipr ot:P0 4551 Unipr ot:P0 4551 GO:0 0056 23 Inte rpro : IPR 006 670 isVersion Of isVersion hasPart is Pub med: 1831 270 Kegg Path way sce04 111 isDescrib edBy is EC- Code: 3.1.3. 16 isVersion Of Doc ume nt Tyso n_19 91 C2 CP time envi ron men t isDescribedBy Pubm ed: 183127 0 time timeCPC2 CP C2 Do cu me ntTys on 19 91 Cel l Cy cle 6 var C2 pM Cel l Re act ion 3 CP Unipr ot:P0 4551 Unipr ot:P0 4551 GO:0 0056 23 Inte rpro : IPR 006 670 isVersion Of isVersion hasPart is Pub med: 1831 270 Kegg Path way sce04 111 isDescrib edBy is EC- Code: 3.1.3. 16 isVersion Of Do cu me ntTys on 19 91 Cel l Cy cle 6 var C2 pM Cel l Re act ion 3 CP Unipr ot:P0 4551 Unipr ot:P0 4551 GO:0 0056 23 Inte rpro : IPR 006 670 isVersion Of isVersion hasPart is Pub med: 1831 270 Kegg Path way sce04 111 isDescrib edBy is EC- Code: 3.1.3. 16 isVersion Of Doc ume nt Tyso n_19 91 C2 CP time envi ron men t isDescribedBy Pubm ed: 183127 0 time timeCPC2 CP C2 Graph Database Docu ment SEDM L Model refere nce Outpu t Simul ation Task Docu ment SEDM L Model refere nce Outpu t Datag enera tor Simul ation Task Varia ble Varia ble Docu ment SEDM L Model refere nce Outpu t Datag enera tor Simul ation Task http://sems.uni-rostock.de/ Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 5
  11. 11. Storage GraphDB Taken from: http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.174.8830&rep=rep1&type=pdf Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 6
  12. 12. Storage Available Data Model & Simulation Annotation & Ontologies A model’s network • Constituent names • XML encoded representation • Biochemical background • Synonyms • Model structure • Aggregation values • Model related data Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 7
  13. 13. Storage GraphDB Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Tyson 1991 - SBML Model Entities Annotations fig. courtesy R. Henkel Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 8
  14. 14. Storage GraphDB Document Model sodium channel sodium channel m gate time envmt has_annotation Pubmed: 12991237 time timevm v m is_connected is_connected is_mapped_to Tyson 1991 - CellML Model Component Variable fig. courtesy R. Henkel Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 9
  15. 15. Storage GraphDB Document SEDML Modelrefere nce Output Datagenera tor Simulation Task Variable Variable Tyson 1991 - SED-ML Simulation Entity Variable fig. courtesy R. Henkel Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 10
  16. 16. Storage GraphDB SBO: Ontology SBO:0000 SBO:544 SBO:236SBO:231 isA SBO:064 SBO:545SBO:004 SBO:003 Systems Biology Ontology Root 1. Level All Ontologies available in OWL can be added easily fig. courtesy R. Henkel Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 11
  17. 17. Storage GraphDB Models Model related data Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12
  18. 18. Storage GraphDB Models Model related data Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12
  19. 19. Storage GraphDB Models Model related data Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Document Model sodium channel sodium channel m gate time envmt has_annotation Pubmed: 12991237 time timevm v m is_connected is_connected is_mapped_to Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12
  20. 20. Storage GraphDB Models Model related data Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Document Model sodium channel sodium channel m gate time envmt has_annotation Pubmed: 12991237 time timevm v m is_connected is_connected is_mapped_to Document SEDML Modelrefere nce Output Datagenera tor Simulation Task Variable Variable Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12
  21. 21. Storage GraphDB Models Model related data Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Document Model sodium channel sodium channel m gate time envmt has_annotation Pubmed: 12991237 time timevm v m is_connected is_connected is_mapped_to Document SEDML Modelrefere nce Output Datagenera tor Simulation Task Variable Variable SBO: Ontology SBO:0000 SBO:544 SBO:236SBO:231 isA SBO:064 SBO:545SBO:004 SBO:003 Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12
  22. 22. Storage GraphDB Models Model related data Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Document Model sodium channel sodium channel m gate time envmt has_annotation Pubmed: 12991237 time timevm v m is_connected is_connected is_mapped_to Document SEDML Modelrefere nce Output Datagenera tor Simulation Task Variable Variable SBO: Ontology SBO:0000 SBO:544 SBO:236SBO:231 isA SBO:064 SBO:545SBO:004 SBO:003 Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12
  23. 23. Storage GraphDB Models Model related data Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Document Model sodium channel sodium channel m gate time envmt has_annotation Pubmed: 12991237 time timevm v m is_connected is_connected is_mapped_to Document SEDML Modelrefere nce Output Datagenera tor Simulation Task Variable Variable SBO: Ontology SBO:0000 SBO:544 SBO:236SBO:231 isA SBO:064 SBO:545SBO:004 SBO:003 Henkel et al. 2013, Graph-based storage of computational biology models and associated simulations, in preparation Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12
  24. 24. Storage GraphDB Models Model related data Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Document Model sodium channel sodium channel m gate time envmt has_annotation Pubmed: 12991237 time timevm v m is_connected is_connected is_mapped_to Document SEDML Modelrefere nce Output Datagenera tor Simulation Task Variable Variable SBO: Ontology SBO:0000 SBO:544 SBO:236SBO:231 isA SBO:064 SBO:545SBO:004 SBO:003 Index Model Id Name Component Variable Species Reaction Compartment Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12
  25. 25. Storage GraphDB Models Model related data Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Document Model sodium channel sodium channel m gate time envmt has_annotation Pubmed: 12991237 time timevm v m is_connected is_connected is_mapped_to Document SEDML Modelrefere nce Output Datagenera tor Simulation Task Variable Variable SBO: Ontology SBO:0000 SBO:544 SBO:236SBO:231 isA SBO:064 SBO:545SBO:004 SBO:003 Index Model Publication Title Journal Abstract Authors Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12
  26. 26. Storage GraphDB Models Model related data Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Document Model sodium channel sodium channel m gate time envmt has_annotation Pubmed: 12991237 time timevm v m is_connected is_connected is_mapped_to Document SEDML Modelrefere nce Output Datagenera tor Simulation Task Variable Variable SBO: Ontology SBO:0000 SBO:544 SBO:236SBO:231 isA SBO:064 SBO:545SBO:004 SBO:003 Index Model Publication Person First name Last name Organization Email Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12
  27. 27. Storage GraphDB Models Model related data Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Document Model sodium channel sodium channel m gate time envmt has_annotation Pubmed: 12991237 time timevm v m is_connected is_connected is_mapped_to Document SEDML Modelrefere nce Output Datagenera tor Simulation Task Variable Variable SBO: Ontology SBO:0000 SBO:544 SBO:236SBO:231 isA SBO:064 SBO:545SBO:004 SBO:003 Index Model Publication Person Annotation URI Description Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12
  28. 28. Storage GraphDB Models Model related data Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Document Model sodium channel sodium channel m gate time envmt has_annotation Pubmed: 12991237 time timevm v m is_connected is_connected is_mapped_to Document SEDML Modelrefere nce Output Datagenera tor Simulation Task Variable Variable SBO: Ontology SBO:0000 SBO:544 SBO:236SBO:231 isA SBO:064 SBO:545SBO:004 SBO:003 Index Model Publication Person Annotation Simulation Id Name Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12
  29. 29. retrieval & ranking Example Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Show me models by Tyson describing the cell cycle and have cdc2! Person Annotation Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 13
  30. 30. retrieval & ranking Example Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Show me models by Tyson describing the cell cycle and have cdc2! Person Annotation Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 13
  31. 31. retrieval & ranking Example Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Show me models by Tyson describing the cell cycle and have cdc2! Person Annotation Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 13
  32. 32. retrieval & ranking Example Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Show me models by Tyson describing the cell cycle and have cdc2! Person Annotation Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 13
  33. 33. retrieval & ranking Example Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Show me models by Tyson describing the cell cycle and have cdc2! Person Annotation Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 13
  34. 34. retrieval & ranking Example Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Show me models by Tyson describing the cell cycle and have cdc2! Person Annotation Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 13
  35. 35. retrieval & ranking Example Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Thank you! Person Annotation 1. (0.859) Tyson1991 - Cell Cycle 6 var 2. (0.854) Tyson2001_Cell_Cycle_Regulation 3. (0.477) Chen2004 - Cell Cycle Regulation Henkel et al. 2010: Ranked retrieval of Computational Biology models Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 13
  36. 36. Version Control version x-1 version x version x+1 what happened ? track versions Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 14
  37. 37. Version Control version x-1 version x version x+1 track versions what happened ? Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 14
  38. 38. Model Evolution Example: Cell Cycle Cyclin Cdc2 P Cyclin Cdc2 P Modeling the cell division... John J Tyson, 1991 Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 15
  39. 39. Model Evolution Example: Cell Cycle Cyclin Cdc2 P Cyclin Cdc2 P Cdc25Cdc25∗ Wee1 Wee1∗ Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte Bela Novak and John J Tyson, 1993 Cyclin Cdc2 P Cyclin Cdc2 P Modeling the cell division... John J Tyson, 1991 Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 15
  40. 40. Model Evolution Example: Cell Cycle Cyclin Cdc2 P Cyclin Cdc2 P Cdc25Cdc25∗ Wee1 Wee1∗ Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte Bela Novak and John J Tyson, 1993 Cyclin Cdc2 P Cyclin Cdc2 P Cdc25Cdc25∗ Mik1 Mik1∗ Wee1 Wee1∗ Quantitative analysis of a molecular model of mitotic control in Fission yeast Bela Novak and John J Tyson, 1995 Cyclin Cdc2 P Cyclin Cdc2 P Modeling the cell division... John J Tyson, 1991 Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 15
  41. 41. Model Evolution Example: Cell Cycle Cyclin Cdc2 P Cyclin Cdc2 P Cdc25Cdc25∗ Wee1 Wee1∗ Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte Bela Novak and John J Tyson, 1993 Cyclin Cdc2 P Cyclin Cdc2 P Cdc25Cdc25∗ Mik1 Mik1∗ Wee1 Wee1∗ Quantitative analysis of a molecular model of mitotic control in Fission yeast Bela Novak and John J Tyson, 1995 Cyclin Cdc2 P Cyclin Cdc2 P Modeling the cell division... John J Tyson, 1991 Cyclin Cdc2 P Cyclin Cdc2 P Cdc25Cdc25∗ Mik1 Mik1∗ Wee1 Wee1∗ Cyclin Cdc2 P Rum1 Modeling the control of DNA replication in fission yeast Bela Novak and John J Tyson, 1997 Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 15
  42. 42. Version Control good news A r C B D cycE/cdk2 RB/E2F RB-Hypo free E2F A r B C D E s RB/E2F RB-Hypo free E2F cycE/cdk2 RB-Phos new insights Waltemath et al.: Improving the reuse of computational models through version control. Bioinformatics (2013) 29(6): 742-728; Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 16
  43. 43. BiVeS Difference Detection A r C B D cycE/cdk2 RB/E2F RB-Hypo free E2F A r B C D E s RB/E2F RB-Hypo free E2F cycE/cdk2 RB-Phos A r B C D A r B C D E s Biochemical Model Version Control System • compares models encoded in standadized formats (currently: and ) • maps hierarchically structured content mapping Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 17
  44. 44. BiVeS Difference Detection A r C B D cycE/cdk2 RB/E2F RB-Hypo free E2F A r B C D E s RB/E2F RB-Hypo free E2F cycE/cdk2 RB-Phos A r B C D A r B C D E s Biochemical Model Version Control System • compares models encoded in standadized formats (currently: and ) • maps hierarchically structured content • constructs a diff (in XML format) • is able to interprete this diff <XML> Diff moves product of r: C deletes product of r: B inserts species: E product of r: E reaction s </XML> mapping diff construction Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 18
  45. 45. BudHat Diff Visualization A r C B D cycE/cdk2 RB/E2F RB-Hypo free E2F A r B C D E s RB/E2F RB-Hypo free E2F cycE/cdk2 RB-Phos A r B C D A r B C D E s <XML> Diff moves product of r: C deletes product of r: B inserts species: E product of r: E reaction s </XML> • calls BiVeS to construct the diff • displays the result in various formats • the XML diff • a reaction network highlighting the changes using • a human readable report A r B C D E s Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 19
  46. 46. Applications Communicating Changes Novak & Tyson ’93: Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte extracts and intact embryos Biomodels Database BIOMD0000000107: Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 20
  47. 47. Applications Communicating Changes Fixed the model → How to communicate the changes? Unix diff? 1c1 < <?xml version=’1.0’ encoding=’UTF-8’ standalone=’no’?> --- > <?xml version="1.0" encoding="UTF-8" standalone="no"?> 287 lines... Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 21
  48. 48. Applications Communicating Changes Fixed the model → How to communicate the changes? BiVeS Diff? <?xml version="1.0" encoding="UTF-8" standalone="no"?> <bives type="fullDiff"> <update/> <delete> <node id="1" oldChildNo="1" oldParent="/listOfReactions[1]/reaction[ <attribute id="2" name="rdf:resource" oldPath="/listOfReactions[1]/r <node id="5" oldChildNo="4" oldParent="/listOfReactions[1]/reaction[ <node id="6" oldChildNo="1" oldParent="/listOfReactions[1]/reaction[ <attribute id="7" name="species" oldPath="/listOfReactions[1]/reacti </delete> <insert> <attribute id="3" name="metaid" newPath="/listOfReactions[1]/reactio <attribute id="4" name="metaid" newPath="/listOfReactions[1]/reactio <attribute id="9" name="metaid" newPath="/listOfReactions[1]/reactio <node id="10" newChildNo="1" newParent="/listOfReactions[1]/reaction much smarter, but still 24 lines.. Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 21
  49. 49. Applications Communicating Changes Fixed the model → How to communicate the changes? BiVeS Diff: Highlighted chemical reaction network Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 21
  50. 50. Applications Communicating Changes Fixed the model → How to communicate the changes? BiVeS Diff: Report Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 21
  51. 51. Applications BiomodelsDatabase / PMR2 Biomodels Database CellML Model Repository 963 # Models 1589 10193 # Versions 12878 9148 # prod. Diffs 12936 BiVeS Unix’ Diff BiVeS Unix’ Diff 2233 1890 # empty Diffs 10113 10043 434.825 1977.210 ∅ #ops 349.5282 480.249 6915 non-empty diffs following 2823 non-empty diffs Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 22
  52. 52. Applications BiomodelsDatabase / PMR2 Biomodels Database CellML Model Repository 963 # Models 1589 10193 # Versions 12878 9148 # prod. Diffs 12936 BiVeS Unix’ Diff BiVeS Unix’ Diff 2233 1890 # empty Diffs 10113 10043 434.825 1977.210 ∅ #ops 349.5282 480.249 6915 non-empty diffs following 2823 non-empty diffs Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 22
  53. 53. Applications BiomodelsDatabase / PMR2 Biomodels Database CellML Model Repository 963 # Models 1589 10193 # Versions 12878 9148 # prod. Diffs 12936 BiVeS Unix’ Diff BiVeS Unix’ Diff 2233 1890 # empty Diffs 10113 10043 434.825 1977.210 ∅ #ops 349.5282 480.249 6915 non-empty diffs following 2823 non-empty diffs Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 22
  54. 54. Applications BiomodelsDB / PMR2 Biomodels Database q qqq q qq q qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq q qqqqqqqqqqqqqqqqqqqqq q qqqqqqqqqq q qqqqqqqqq qq qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq qqqqqqqqqqqq qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq q qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq q qq q qq q qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq q q q qqqqqqqqqqqqq q qqqqqq q qqqqqqqqqqqqqqqqqqqqqq q qqqqqqqqqqqqqqqqqqqqqqqq q qqqqqqqqqqqqqqqqqq q q q qqqqqqq q q q qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq q qqq q qq q qqqqqqq q qqqqqqqqqq q qqqqqqqqqqqqqqqq q qqqqqqq q qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq q qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq q qqqqqqqqqqqqqq q qqqqqq q qqqqqq q qqqqq q qqqqqqqqqqqqqq q qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq q q q qqqqqqqqqqqqqqqqqqqqqqqqqqqqqq q q q qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq q qqq q qq qq q qqqq qqqqqqqqqqqqqqq q qq q qqq q qqqqqqqqq qqqqqqqqqqqqqqqqqqqqqqqqqqq q qqqqqqqqqqqqqqqqqqqqq qq q qqq q qq q qqqqqqq q q q qqqqqqqqqqqqq q qqqqqq q qqqqq q qqqqqqqqqqq q qqq q q q qqqqqqqqqqqqqqqqqqqqqqqqq q qqqqq q qqqqqq q qqqqqqqqqqqqqqqqqq q qqqqqqqqqqqqqqqqqqqqq q qqqqqqqqqqqqqqqqqqqqqqqqqqqq q qqq q q q qq q qqqqqqqqqqqqqqqq q qqq q q q qqqqqq q qqqqqq q qqqqqqqqqqqqqqqqqqqqqqqqqq q qq q qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq q qqqqqqqqqqqqqqqqqqqqqqqqq q q q qqqqqqqqqqqqqqqqqqqqq q qqqqq q qqq q q q qq q qqq q qqqqqqqqqq q qqq q q q qqqqqqq q qqqqqqqqqqqqqqqqqqqqqqqqqq q qqqqq q qq q qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq q qq q qqqqq q qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq q qqqqqqqqqqqqqq q qqq q q q qq q qqqqq q qqq q qqqqqqqqqqqqqqqqq q qqqqqqqqqqqqqqqq q qqqqqqqqqqqqqqqqq q qq q qqqqqqqq q q qqq q qq q qq q qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq q qqqqqqqqqqqq q qq q qqqqqqqqqq q qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq q qqqq q qqqqqqqqqqqqqqqqqq q 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050000100000150000200000250000300000 #operations needed by BiVeS #operationsneededbyUnix'diff #operations Unix' diff == #operations BiVeS CellML Model Repository q qqqq q q q q q qq q qq q q q q q q q qqqq q qqqq q q q q q q q q q qqq q q qqq q q q qqqqq q q q q q q qqq q qqqqqqqq q qqq qq q qq q qq q qqqqq q q q qqqqqq qqq q qqqqqqqqq qqqqqqqqq q qqq q qqqq q qqq q qqqq q qqqqqqqqqqqqqqqqqqqqqq q qqqqqq q qqq q q q qqqq q qqq q q q qqqqq qq qqqq q qq q q q q q q qqq q qq q q q q q q q qqqqqq q qqq q qq q qq qq q q q qqqqq q qqqqqqqqqqqq q q q qq q q qqqq q qqqqqqqqqqqqq qq q qqqqqqqq q qq q q q q qq q qqqq q q q q q q q q qqq q q qq q q q qq q q qqqqqqqqqq q q q q q qq q qqqqqqq q qq q qqqqqqqqq q q q q qq q q qq q q qqqq q q q q q qqqqqqq q qqqqqq q q qqqqqqqqq q qqqqqq q qqqq q qqqqq q qqqqqq q qq q q qq q qqqqq q qqqqqqq q qqqqqq q q q q q qq q q q qqqqqq q q q q qqqq q q q qq qqqqqqqq q qqq q q q q q qqq qqq q q q qqqqqq q q q q qqqqq q q qq q q q qqq q qqqq q qq q qqq q 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qqqq q qqqqqqqqqq q qq q qqqqq q qqqqqqqqqq q qqq q qqqqqqq qq qqqqqqq q q q q q q qqqqqqqqqqq q q qq q q qqqqqqqqq q q q qq q q qqq q qqqqqqqqqq q qqqqq q qqq q qq qqqq qq qq q q q qqqqqqq q qq q qqq q qq q qqqq q q q q q q q q q qqqqq qq qq q qq q q q q q q q q q qq qqqqq q qqqqq q qq q qqq qq q q qqqqqqqqqqqqqqqqqqq qq q qq q q q q qqqqq q qq qq qq qqqqqqqq q qqqqq q qqqqqqqqqqqqqqqqqqqqqqqqqqqqqq q qqqqqqqqqqqqqqqqqqqqq q qqqq q qq q q q qqqq q q qq q q qq q q q q q q q q q qq q q qqq q qqq q q q qq q q qqq q qq q q q q qq q q qqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqqq q qqqq qq qq q q q qqqqq q q q qqqq q q q q qqq q qqqqqqqqqqqqqq qqqqq q qqq q q q qqqq qq qqqqqqqqqq q q qq q q qqq q qqq q q q q q q qq qq q q qq q q qqqqqq q q qqqq q qqqqqqqqqq q qqq q qqq q qq qqqqqqqqqqq qqq q q qqqqq q q qqqqqq q q qq qqq qqq q qqqqqq q qq qq q q q qqqqqq q qq q qqqq q qqq q qq q qq qqqqqqqqq q qqqqq q qqqq q q qqq q qqq q qqqqqqq q qqqqqqqq q qqqqq q qqqqqqqqqqqqqqqqqqqqqq q qqqqqqq q q q qqqqqqq qqq q qqqqq q qqqq q q qqq q q q q qqqqq q q qqq q q qq q q q q q q q qqq 0 5000 10000 15000 20000 25000 0500010000150002000025000 #operations needed by BiVeS #operationsneededbyUnix'diff #operations Unix' diff == #operations BiVeS Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 23
  55. 55. Applications BiomodelsDB / PMR2 qq q q qq qq q qq qq qqqq qq q qq qq q qqqq qq qq qqq qqqqq q qq qq qq q qq qq qqq qq q qqq q qqq qq qqq q qq qq q qq qqqqq qq q q qq q qqq qqq qqqqqq qqq qq qq q qq qqqq q q qq qq qq q q qq qqq qq qq qq q q qq q q qq qq qq q q qqqq qqq q qqqq q qqqq q q qq qq qq qqq qqqq qq qq qq qqq qqq qq q q qq qqqq qqq q qqqq qqqqq qqq qqqq q q qqqqq q q qqqq q qq qqqqq q qqq qqq qq q qq q qqqq qqq qqqq qqqq q q qq qqq q q q qqqqqq qq q qqq q qqqqqqq qqqq qqq qqq q q q qqq qqq qq qqq qq qq qq qq qq q qqq qq qqqq q q qqq qq qq qq qqq q qqq qq qq qqqq qqq q qq qqq q qqq qq qqqq qq qq q qqq qq qq qqqqqq qqqqqq q qqqq q qq q qqq qqq q qqq qq qqqqqqq qqqqqq qq qqq q qqqqq qq qqqq q qqq qqq q qqqqqq q q q qq qqq q qqq qqqq q q q qqq qqq qqq qqq qqq q q qqq qqqqqq qq qqqq q qqq q qq qq qq qqq qqqq qqq qqq qqq q q qqq qqqq q qq q qq q qq qq qqqq qq qq q qqq qqqq q qqq qqq q qq q q qqq qq qqq q q qq qqq qqq qqqq qqqqq qq qqqqqq q qqqqqq q q qq q qq qq qq qq qq qqqqqq qq q qqqq qqq qqq q qqqq qqqqqqqq qq q qqq qqq qq qq qqqqqq q q qq qqqqqq qq qqqqq qq q qqqqq qq qq qqqq qqq qqqqq q qq qq qq qq qq qqqq qqq qq qqqq qqq q qqq qq qqqqq qqqq q qq qq qqqqqqq q qqq qqq qq q qqqqqq qqq qqq qq qqqq qq qqq q qqqqq q qq qqq qqq qqq qqq q qqqqqqqq qqq q q q qqq q q q qqq qqqq q qqq qqq qqqq qq q qqq qq q qq q qq qq q qqq qq q q qq qq qq qqqq q qq qq q qqqq qqqqq qq qq qqq qq qq q qqqq qq qqq qqqqqqqq q qqq q qq q qqqq qq qq qqq qq q qq qqq q qq qq qqq qq qqqqq qqq qq qqq qq qqqqqq qqqq q qq qqqq qq qqq q qqq q qq q q qqqq q qqqqq qqq qq qq qq q qq qqq qqq qq qq q qqqqq qqqqq qq qqqqq q qqq qqq q q qqqqqq qqq qq qqq q qq q qq qq q qqqqq q qq q qqq qqq q qq qq qq q qq q qq qq qqqqq qq qq qqqq qqqq qq qq q qqq qqq qq qq qqq qqqq qqq qq q qq qqq qq qqq q qq qqq q q qq q qqq qq qqq qq qq qq q q qqqqqq qqqq qqqqq qqq qqq q qqqqqq qqq qq qq qqq qq qqq qqq qq qq qq qqq q qqqq q qqqq q qqqqq qq qq qqq qq qqqq qqq q qqq qqq qq qqqqq qqq q qqqqq qq qqq qqq qqqq qqqq qq qqq q qqq qq q q qqqq qqqq qqq q qq qq qqq qq qqq qqqq qq qq qqq qqq qqqqq qq qqq q qq qq qq qqqq qqqq q qq qq qqq q q qqq qq qq q qqq qqqqqq qqq qqqq qq q qqq qqq q qqq qqqq qqqq qqqq q qq qqqq q qqq qqqqq qqq qq qqqqq qq qq q qqq q qqq qq qq q qq qq qq qq qq q qqqq q qq qqq q q qqqq qq qqqqq qq qqqq qqq q q qq qqq q q qqqq qq qqqqq qqq q qqq q q qqqq qq qqqq q qq qq qqq qqq q qq qq qqq qqqqqqqqq q qqq qq qq qq qqq qqqqq qq qq qq qq qqq q q qq qq q qq qqqq qqq qq qq qq qqq q qqq qqqqqq qq qqqq qqq q q qqqqq qqqq qqq qqq q qq qqqq q qq qq qq qq qq qq qqqq q qqqq qqqq qqq qq qqqq qq qqq qqq qq q qq qqqqq qqq qqqq qqq q q q qq qq qqqqq q qqq qqq qqq qqq qqqqq q qq qqq q qqqqq qqqqqq qqq qqq qqqqq q qqq qq qqq qqq qqq qqq qq qqq qqqq qq qqqqq q qq q q qqq q qqq qq q qq q qq qqqq qq qq qqqq qqqqq qq q qqq qqqq q qqq q qqqqq qq qq qq qqqqq q qq qq qqqq qqq qq qq q q qqqqq q q q qq qqq qqq q qq qq q qq qq qqqq q qq qqqq qq qqqq q q q qqq qqq qq qq qqqq q qq qqq qq qq qq qqqqqq q qqq q qq qq q qq q qqq q qq qqq qq q qq qqq q qqqq q q qqq q q qqq qqq qqqq qqqq qqq q qq qqq qq qqq qqq qq qqqqqqq qqq qqqq qq qqq qq qqq q qqq qq qqqq q qq q qqq qq qqq qq qq qqqqq qqq q qq q q qqq qq qq q q qq qq q q qqq qqqq qq q qqqq qq qqq qq q qq qq qq q qqq qqq qq qq qqqq q qqq qqqqq qqqq qqq qq qq qqq q qq qq q qq qqq q qqq qqqqq q q qq qqq q qqq qq qq q qqqqq qq qqq qqq qqqq qqqqq q qq qqqq qqqq q q qqqq q qq qqq qq q q q qq q qqqq q qqq q q updatesinserts 1 5 10 50 100 500 1000 qqq q qqq q qq q qqqqq qq q qq qq qqq qq qqq q qq qq qq qqq q q qqqqqqqqqq qq qqq q q qqqqq q qqq qqq qq q q qqq qqqqqq qq qqqq qqqqqqq qqq qq qq qqq qqqq qq qqq qqq q qqq qq qqqq q q qq qqq q qqqqqq qq qqqq qqq q qq qq qq q qqq q qqq qqq qq qqq qqq qq qq qq qq qq q qqqqq qqqqq q qqq qqqq qq qqqqq qq q qq qq qqq qq qqqq qqq qqq qqqq q qq qq qqq q q qq qq qq q qq qq q qq qqq q qq q qqq q qq qqq qq qq qqq qq qqq q q qq qq qq qq qq qq qqq qqq qqq qqq qqq qqq qq q q qq q qqqq qq qq q qq q qq qq qq q qqqq qqq q qq qqq qq qq qq qqqqq qq q qq qq qqq qq qq qqq q qqqq qqqq q q q qq qq q qqqq q qqq qq qqq qqq qqq qqqqqqqq qqqq qqqqq qqq qq qqq qqq qqq qq qqq qqqq qqqqq q qqq qqqq qqqqq qqqqq q qqq qqq qqq qq qq q qq qq qq qqqq qq qq qqq qq qqqq qq qqqq q qqq q q qq qq qq qqqq qqq q qq qq q q qq q qqqqq qq q q qq qqq qqq qq q qq q qqq q qqq qqqq qqq qqqq qq q qq qq qq qqqqq qq qq qq q qq qq q qqq qqqqqq qqq q qqqqq q qqq qqq qqqq qqq qq qqqqq q qqq qq qqqq qqqqqqqq qq qq q q qqqqq q qqqq qq q q qqq qqq qq qqq qqq q qq qqq qqq qqq qqqqqq qq q qqqqq q qq qq qqq qqqqq q qqqq qqqq qq qqq qqqq qqq q qq qqq qqq qqqq q q qqqq qq q qq q qqq q q qqq qq qqq qqq qq qq qqqqqq qq qq qqq qqqqqqqqqq qqq qqqqq qqq qqqqqqq qqq qqq qq qqq qqqqqq q updatesinserts 1 5 10 50 100 500 1000 Biomodels Database CellML Model Repository move insert delete update move insert delete update Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 24
  56. 56. Applications BiomodelsDB / PMR2 qqq qqq q q qqq qq q qq q qq qqqq q qq qq qq qq qq q qq qqq qq qq q qq q qq qq qqqqqqqq q qqq qqq qq qqq q q qqq q qq qq qq qq q qqq qq qqq qq qqq q qqq q qqqqq qq qq qqq qq qq q qq qq qq qqqq qq q qqqq qqq q qqq qq qq qqq qq q qqq qq qqq qqq qq qq qq q qq q qqq q qqqq qqq qq q q q qqq qq qq q qqq qqqq qq qq qqq q qq qq qq qqq qqq qq qqq qq q qqq qqq qq q q qqq q qq q q qqqqq q qq qqq q qq q qq qq qqq q qq q q qq qq qq qqq qqq qq q qqq qq qq q qq q qq qq q q qqq q qq q qq qqqq q qqqqqq qqq qq qq qq q q qq qqq qqq qq qqq qqq q q qqqq qq qq q qq qqq qqqq q qq qqqqq q qqq qq qqq qqq qq q qqqqqqqq q qq qq qq q qq qqq qqq qq qqq q qq qq qqq q q qq q qqqq qqq qq qqq qqq qq q qqq q qq qqq qq qqqq qq qq qq qqq q qq q qqq qq qq qq q qq qqq q qqq qq q q q qqqqqq qqqqqq q qq qq qq qq q qq qqq qq qq qqq qqqqqq q q qqqq qqq q q qqq q qqq qqq qqq qq q q q qqq qq qq qqq qqqq q qqqq qq qq q qq qq qq qqqq qq q qq qqqq q q qqq q qqq qq qq q qqq qqq qqq q qq qqq qq q qq qqqq q qq qqqq qqq qq qq q qqq qq qqq q q qq qq q qq qqq q qq qqq qq qqqq qqqq qq q qq qq qqqq q qq q q qqq q qqqq q qq qq q qqq q qq q q qq qqq qq qq q qq q qq qq qqq qqq qq q q qq qqq qqqqq q qq q q q qq qqq qq qqq q qqq qq qq qqqq qq qqq qq qq q qqqq qq q q q qq q qqq qq qq qqq q q qq q qqq qq q q qq qqq qq q qqq qqqqq qqqqqq qqq qq q qqq qqq qq q qq qq qqq q q qq qq q qqqqq qqq qqq q qqq qq qqqq q qq q q qq q qq qq q qq qq qqq qq q qq qqqq q qq qq qq q qq q q qqq qq q qq qqqq qq qqq qq qq qqqq qqq qqq qq q qqq qq q qqqq qq q q q qq q qqqq qq q q qqq qq qq qqqq q qq qqq qq qqqqq q q qqq q qq qq qqq qq q qq qq qqq qq qqq q qq qqq qqq q qq q qqqqq q qqq qq q qq qq qq q qq q qq qqq qq q qqqqq qq q qq qqqq qqq q qqq q q q q qq q qq qqqq q qq qqq qqqqq qq qqqq qq qq q qqq q qqq qq q q qq qq qqq qqq qqq qq qqq qqq q qqqq q qq qqq qq qq q qq q qq qqqq q q qq qqq qqq q qq q q qqq q q qqq qq q qq qq qq qq q q q qqq qqq qqq qqq qq q qq qqq qqq qqq qq q q qq qq qq q qqq qqq qq qq qq qq q qq qqq q qq qqqq qq q qq qq qq qq qq qqqq qqq qq q q qqq q qqq qq qqq q q qqqq qq qq qq qq qq q qqq qqq q qqq q qqq q qq qq q qq qq qq qqq q qqq qqqq qqqq qq qq qqq qqq qqq qqq q qqq q qq q qqqq q qq q q qq qq qq qq qq qq q qqq qqqq qq qq q qqq q q q qqq q qqq q q qq q qq qqq qqq q qqq qq qq attrnodetext 1 5 10 50 100 500 1000 q qq qq q q qq q qq q q q qqqqq qq qq q q qqq qqq q qq qq qqq q qq qqq qq qq qq qqqqq qqqqq q q qq qqqq q qq qqqq q q qqq q qqqq qq q q qqq qq qq qqq qqq qqq qqqq qq qqqqqq q q qqq qqq q qq qq qq qqq q qqq qq qqqq qqq q qqqqq qqq q q qqq qq qqq qqq qqqqq q q qq q qqq qqq qqq qq q qqq qq qqq q qq qq qqq qqqqq qqq qqq q qqq qq qqq q qqqqq q q qqq q qq qq q qqqqqq q qqqq qq qqqqqqqq qqqqqq qq qqq qqqqqqq q qqqq qqqq q qqq qq qqqqqqq qq qq q qqq qq qqqq qqqqq q qqqq qqq qq qq qq qqqq qq qqqq qqqq qq q q qqqqqq qqq qqqqqq qq qqqqqq q q qqqq q qq q qq qq qq q qqq qq qqqq qq qqq q q qq qq qq q qqq q q qqqqqq qq qqqq q qqq qqqq qqq qq qq qqqq qq qq qqq q qqqq qqq qqq qqq q qq qqq q qq qqq qq qqq qqq q qq qqqqqq qq qqq q qqq qq qqqqq qq qq qq qqq qqq qq qq qq qqq qq qqqq qqq q qq qqq qq qqqq qq qqq qqq q q q qqq qqqq q qqqq qq q qq qqqq qq q q qqqq qqq qq q qq qqq qq qqq q qq q qq qq q qq q qqq qq q qq q qq qq q q qq qqq q qqq qqq qqq q qq q q qqq qq q q q qqqq qq q qqqq qq qqqqq qq attrnodetext 1 5 10 50 100 500 1000 Biomodels Database CellML Model Repository Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 25
  57. 57. Summary • SEMS develops methods for improved model management • Storage • Retrieval & Ranking • Version Control • ... and implements these methods in tools that are • modularly designed • open source • easy to integrate Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 26
  58. 58. Future • Support for further standards • PharmML • CombineArchive • SBGN • respect further ontologies in storage/search • Improved version control • mapping w/ respect to biological meaning • scoring schemes for differences • filter for changes • Improved availability and analyzability of data Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 27
  59. 59. SYSTEMS BIOLOGY BIOINFORMATICS ROSTOCK S E Ssimulation experiment management system Thank you for your attention! SEMS group Dagmar Waltemath Ron Henkel Martin Peters Markus Wolfien Rebekka Alm Olaf Wolkenhauer @SemsProject http://sems.uni-rostock.de Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 28
  60. 60. BiVeS Integration jvm network cmd import de.unirostock.sems.bives.api.SBMLDiff; [...] SBMLDiff differ = new SBMLDiff (sbmlFileA, sbmlFileB); differ.mapTrees (); String graph = differ.getCRNGraphML (); [...] Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 29
  61. 61. BiVeS Integration jvm network cmd curl -d ’{ "get": [ "documentType", "xmlDiff" ], "files": { "versionA":"http://your.db/path/to/versionA.sbml", "versionB":"http://your.db/path/to/versionA.sbml" } }’ http://bives.server.tld Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 29
  62. 62. BiVeS Integration jvm network cmd java -jar BiVeS.jar path/to/versionA path/to/versionB git diff 88fea1cddf b64477d742 model.file Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 29
  63. 63. BiVeS -vs- Unix’ Diff Artifacts delete a single line in an XML: <variable name="T" units="kelvin" initial_value="295" public_interface="out"/> for Unix’ diff it is 1 operation. Bives detects 5 operations (delete node variable and 4 attributes). Worse if multiple nodes on the same line: <para><emphasis><ulink url="caffeine.zip">Caffeine</ulink></emphasis> - Caffeine-induced Ca2+ transients from 18 i And worst if whole document only 1 line → max. 2 operations for the Unix diff tool. Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 30
  64. 64. CombineArchive Single file containing models and model related data: • simulation experiment descriptions in SED-ML • graphical representations in SBGN-ML necessary for the description of a model and all associated data and procedures → simplifies exchange Proposal by Nicolas Le Novère, Frank Bergmann, and Richard Adams http://co.mbine.org/documents/archive We developed a JAVA library to create/read/manipulate CombineArchives http://sems.uni-rostock.de/projects/combinearchive/ → database import/export, difference detection between whole archives Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 31
  65. 65. BiVeS Mapping • input: 2 XML documents • map unambiguos nodes/subtrees • propagate mapping up/down • exploit further knowledge of biological systems same ID same subtree hash ... ... ...... ... ... ... ...... ... Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 32
  66. 66. BiVeS Mapping • input: 2 XML documents • map unambiguos nodes/subtrees • propagate mapping up/down • exploit further knowledge of biological systems eq. netw.... ... ...... ... ... ... ...... ... Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 32
  67. 67. BiVeS Mapping • input: 2 XML documents • map unambiguos nodes/subtrees • propagate mapping up/down • exploit further knowledge of biological systems A B C D E A B C D E A B C D E Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 32
  68. 68. Applications Investigating BiomodelsDB / PMR2 qqqq qq q q q qqq qq q q qqq qq qq qqq qqqq q q q qq qq qqq q qq qq qqq qq qq qq qq qqqq qqq q qqq qq qqq q qqqq qq qqq qq qqq qqqq qq qq qqq qqq qqqq qq qq qq qqq q qqqq qqqqq qq qqqq qqq q q qq q qqqq qqq q qqqqq q qqq qqqq qqqqq qq qq qqq qqq qqq q q qq qqq qqq qqq q qqqqq qqq qq qq qq qq q qqqq qqqq qqq qq q qqq qqqq qqq qq qqqq q qqqqq qq q qq qq qqqqq q qq qqq qqq qqqq q qqq qqq q qqq qq q qq qq qq qqq q qq qqqq q qq qq qqqq qqqq qqq qq qqq qqqq q q qq qqq q qq q qqqqq qq q q qq qq qq qq qq q qqq qq q qqq q qqqq qq qq qqq q qqq qq qq qqq qqqq qqq qqqq q qqqqq qqq qq qqq q qq qqqq qq qq qq qqq qq q q qq q qq q q qqq qq qqq qqq qqq qq qq qq qqqq qq q q q qq q qq qqq q qqq q qqqq qqqqq qqqq qqq qqqqq qq qq q qqq q qqqq q qq qq qq qq qqq q qqqqq q qqq qq q qq q qq qqqqq q qq qq qq qq qqq q qqqq qqq q q qqqqq qqqq qqq q qq q qqq qq qqqq qqqq q q q qqqq qqqq q qq qqq q q qqq q qq qq qq q qq qq q qq qqq qq qq qqq qq qqqq qq q bivesunix 0 500 1000 1500 qq qq q qq q qq qq q qqqq qqq q qqq q qq q qqqq qqq q qqq qq q qqq qqq qq q qqqq qqqq q q qq qqqq q q qq qqq q qqqq qq q qq qq qqq q qq qq q qqq qq qq qq qq q q qqqq qqq qq qq qq qqq qq qq qqqq q qq q q qqq q qq qqq qqq qqqq qq q qq q qqqqqq qqqqq qq qq qqq q q qq qqqqqq qq qqq qq qqqqqqqq qq qq q qq q q qqq qq qqqq q qq qqq q q qq qq qq qqq qq qqqq bivesunix 0 500 1000 1500 Biomodels Database CellML Model Repository Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 33
  69. 69. Applications Investigating BiomodelsDB / PMR2 q q qqqq q qqqq qq q qqq qqqq q q qqq qqq qq qq qqq qq q qqq q qqqq qq qqq qqqq qq qqqqq qqq qq q q qqq q q qqq qqq qq qq q qqq q qq qq qqq qqq qq qqq qqq qq qq q qq qqq q qq qqq q qq qq q qqq q qqq q qq qq qq qqq qq qq qq q qqqqq q qqqqq qq qq qqq q qqq qq q qqqqq qq q qqqqq qqq qqq qq qq q q qqq qqqq q q qqq qq qqq q qq qq q q qq qq q qq qq qqq q q qqqq q qq qq qq qq qq qq q qq qq q qqqq qqq q bivesunix 0 500 1000 1500 2000 2500 3000 3500 q qqqq qqqqq q qqq qq qqqq qqq qqq qq q qqq qq qqq q qq q qqqq qq q qq qqq q qqq qqq qqq q q qqq qq qq qq qq qq qq qqqq qq qqq qq qq qqq q qq qqq q qqqq qq qqq qq qq qq q qqq qq qqq q qqq q qqqqq q qq qqq q qq qq qq qqqqq q qq q q q q qq qqqq q qq q bivesunix 0 500 1000 1500 2000 2500 3000 3500 Biomodels Database CellML Model Repository Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 34

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