Improving the Management of Computational Models -- Invited talk at the EBI
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Improving the Management of Computational Models: storage – retrieval & ranking – version control More information and slides to download at http://sems.uni-rostock.de/2013/12/martin-visits-the-ebi/
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Improving the Management of Computational Models -- Invited talk at the EBI
- 1. SYSTEMS BIOLOGY BIOINFORMATICS ROSTOCK SE S simulation experiment management system Improving the Management of Computational Models storage – retrieval & ranking – version control M AR TIN S CHARM1,2 , R ON H ENKEL1 , DAGMAR WALTEMATH1 , O LAF W OLKENHAUER1,3 1 2 3 Department of Systems Biology & Bioinformatics, University of Rostock Department of Computer Science, University of Oxford 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. 31 462 + 501 + x · 103 216 + 196 #models Introduction 2013-06-18 • • • Number of models is steadily increasing Models tend to get more complex Continuous development 2009-06-16 2005-04-11 time Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 2
- 3. Introduction ~288.91 ~27.06 reactions model 2013 noncurated • • • Number of models is steadily increasing Models tend to get more complex Continuous development curated Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 2
- 4. Introduction #Versions • • • Number of models is steadily increasing Models tend to get more complex Continuous development time Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 2
- 5. Introduction Tasks • Storage & Availability • Search & Retrieval • Version Control Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 3
- 6. Introduction Tasks • Storage & Availability • Search & Retrieval • Version Control Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 3
- 7. Introduction Tasks • Storage & Availability • Search & Retrieval • Version Control Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer ? 3
- 8. Introduction Tasks • Storage & Availability • Search & Retrieval version x-1 • version x version x+1 Version Control Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 3
- 9. Introduction Solutions Several projects develop methods to support the community Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer Model Repository 4
- 10. SE S SYSTEMS BIOLOGY BIOINFORMATICS ROSTOCK simulation experiment management system Retrieval is CP isVersion Pubm ed: 183127 0 envi ron men t Model refere nce Simul ation CP T ask Outpu t store Datag enera tor V aria ble Inte rpro : IPR 006 670 GO:0 0056 23 CP time time time CP V aria ble C2 Do cu me T ys nt on 19 91 Cel l Cy cle 6 var C2 CP 19 91 Cel l Cy cle 6 var Unipr ot:P0 4551 Unipr ot:P0 4551 is Pub med: Kegg 1831 Path 270 way sce04 111 Cel l ECCode: 3.1.3. 16 Unipr ot:P0 4551 Unipr ot:P0 4551 hasPart isVersion pM GO:0 0056 23 Inte rpro : IPR 006 670 Inte rpro : IPR 006 670 GO:0 0056 23 Doc ume nt isDescrib edBy is pM Pub med: Kegg 1831 Path 270 way sce04 111 T yso n_19 91 Cel l Inte rpro : IPR 006 670 isDescribedBy envi ron men t C2 ECCode: 3.1.3. 16 isDescrib edBy CP is C2 is Re act ion 3 Cel l isVersion Of isVersion Unipr ot:P0 4551 Do cu me T ys nt on Pub med: Kegg 1831 Path 270 way sce04 111 pM hasPart isVersion Of Unipr ot:P0 4551 isVersion Of C2 ECCode: 3.1.3. 16 Re act ion 3 is isVersion Of isDescribedBy Cel l pM Unipr ot:P0 4551 hasPart isVersion Of Unipr ot:P0 4551 retrieve SEDM L T yso n_19 91 C2 ECCode: 3.1.3. 16 isVersion Of Doc ume nt Pub med: Kegg 1831 Path 270 way sce04 111 is hasPart C2 Docu ment isDescrib edBy isVersion Re act ion 3 19 91 Cel l Cy cle 6 var isDescrib edBy CP isVersion Of Do cu me T ys nt on 19 91 Cel l Cy cle 6 var C2 isVersion Of Do cu me T ys nt on Re act ion 3 Pubm ed: 183127 0 CP is Graph Database C2 GO:0 0056 23 CP time time time CP C2 rank Do cu me T ys nt on T ask Outpu t Unipr ot:P0 4551 Unipr ot:P0 4551 Do cu me T ys nt on 19 91 Cel l Cy cle 6 var Docu ment Model refere nce SEDM L Re act ion 3 T ask Inte rpro : IPR 006 670 GO:0 0056 23 Outpu t isVersion Unipr ot:P0 4551 Unipr ot:P0 4551 Pub med: Kegg 1831 Path 270 way sce04 111 isDescrib edBy is Cel l pM Datag enera tor is isVersion Of T ask hasPart isVersion Of ECCode: 3.1.3. 16 Simul ation Simul ation CP Cel l pM Outpu t Docu ment SEDM L Model refere nce C2 is is ECCode: 3.1.3. 16 Datag enera tor Pub med: Kegg 1831 Path 270 way sce04 111 isDescrib edBy CP isVersion Δ Simul ation C2 isVersion Of track development SEDM L Model refere nce 19 91 Cel l Cy cle 6 var Re act ion 3 hasPart Δ Docu ment isVersion Of Version 2 Inte rpro : IPR 006 670 GO:0 0056 23 Doc ume nt V aria ble latest V aria ble T yso n_19 91 C2 Version Control CP isDescribedBy envi ron men t C2 Version 1 time time Pubm ed: 183127 0 CP time CP C2 Ranking http:/ /sems.uni-rostock.de/ Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 5
- 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. Storage Available Data Model & Simulation • • Dec 4, 2013 Constituent names XML encoded representation Annotation & Ontologies • • Biochemical background Synonyms SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer A model’s network • • • Model structure Aggregation values Model related data 7
- 13. Storage GraphDB Tyson 1991 - SBML Document Model Tyson1991 Cell Cycle 6 var isDescribedBy Entities Reaction3 C2 is CP Pubmed: 1831270 Kegg Pathway sce04111 pM Cell asProduct Annotations EC-Code: 3.1.3.16 Uniprot:P04551 Uniprot:P04551 Interpro: IPR006670 is hasPart isContainedIn isVersion isVersionOf isVersionOf asReactant GO:0005623 fig. courtesy R. Henkel Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 8
- 14. Storage GraphDB Tyson 1991 - CellML Document Model Model Component Variable sodium channel m v is_connected time envmt has_annotation is_connected time time Pubmed: 12991237 sodium channel m gate v m is_mapped_to fig. courtesy R. Henkel Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 9
- 15. Storage GraphDB Tyson 1991 - SED-ML Document Simulation Entity SEDML Modelrefere nce Simulation Task Output Datagenera tor Variable Variable Variable fig. courtesy R. Henkel Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 10
- 16. Storage GraphDB Systems Biology Ontology SBO: Ontology Root SBO:0000 isA 1. Level SBO:064 SBO:544 SBO:004 SBO:231 SBO:003 SBO:236 SBO:545 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. Storage GraphDB Models Dec 4, 2013 Model related data SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12
- 18. Storage GraphDB Models Model related data Document isDescribedBy Tyson1991 Cell Cycle 6 var Reaction3 C2 CP Pubmed: 1831270 Kegg Pathway sce04111 is pM Cell asProduct EC-Code: 3.1.3.16 Dec 4, 2013 Uniprot:P04551 Uniprot:P04551 Interpro: IPR006670 is hasPart isContainedIn isVersion isVersionOf isVersionOf asReactant GO:0005623 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12
- 19. Storage GraphDB Models Model related data Document isDescribedBy Tyson1991 Cell Cycle 6 var Reaction3 C2 CP Pubmed: 1831270 Kegg Pathway sce04111 is pM Cell asProduct asReactant Uniprot:P04551 Uniprot:P04551 is hasPart isVersion isVersionOf isVersionOf EC-Code: 3.1.3.16 isContainedIn Interpro: IPR006670 GO:0005623 Document Model sodium channel m v is_connected time envmt time has_annotation is_connected time Pubmed: 12991237 sodium channel m gate v m is_mapped_to Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12
- 20. Storage GraphDB Models Model related data Document Document isDescribedBy Tyson1991 Cell Cycle 6 var Reaction3 C2 CP Pubmed: 1831270 SEDML Kegg Pathway sce04111 is pM Cell Modelrefere nce Simulation Task Output Datagenera tor asProduct asReactant isContainedIn EC-Code: 3.1.3.16 Uniprot:P04551 Uniprot:P04551 is hasPart isVersionOf isVersionOf isVersion Variable Interpro: IPR006670 GO:0005623 Variable Document Model sodium channel m v is_connected time envmt time has_annotation is_connected time Pubmed: 12991237 sodium channel m gate v m is_mapped_to Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12
- 21. Storage GraphDB Models Model related data Document Document isDescribedBy Tyson1991 Cell Cycle 6 var Reaction3 C2 CP Pubmed: 1831270 SEDML Kegg Pathway sce04111 is pM Cell Modelrefere nce Simulation Task Datagenera tor Output asProduct asReactant isContainedIn EC-Code: 3.1.3.16 Uniprot:P04551 Uniprot:P04551 is hasPart isVersionOf isVersionOf isVersion Variable Interpro: IPR006670 Variable GO:0005623 Document Model has_annotation SBO: Ontology Pubmed: 12991237 SBO:0000 sodium channel is_connected envmt is_connected sodium channel m gate isA SBO:064 m v time time time v SBO:544 SBO:004 SBO:231 SBO:003 SBO:236 SBO:545 m is_mapped_to Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12
- 22. Storage GraphDB Models Model related data Document Document isDescribedBy Tyson1991 Cell Cycle 6 var Reaction3 C2 CP Pubmed: 1831270 SEDML Kegg Pathway sce04111 is pM Cell Modelrefere nce Simulation Task Datagenera tor Output asProduct asReactant isContainedIn EC-Code: 3.1.3.16 Uniprot:P04551 Uniprot:P04551 is hasPart isVersionOf isVersionOf isVersion Variable Interpro: IPR006670 Variable GO:0005623 Document Model has_annotation SBO: Ontology Pubmed: 12991237 SBO:0000 sodium channel is_connected envmt is_connected sodium channel m gate isA SBO:064 m v time time time v SBO:544 SBO:004 SBO:231 SBO:003 SBO:236 SBO:545 m is_mapped_to Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12
- 23. Storage GraphDB Models Model related data Document Document isDescribedBy Tyson1991 Cell Cycle 6 var Reaction3 C2 CP Pubmed: 1831270 SEDML Kegg Pathway sce04111 is pM Modelrefere nce Cell Simulation Task Datagenera tor Output asProduct asReactant isContainedIn EC-Code: 3.1.3.16 Uniprot:P04551 Uniprot:P04551 is hasPart isVersionOf isVersionOf isVersion Variable Interpro: IPR006670 Variable GO:0005623 Document Model has_annotation SBO: Ontology Pubmed: 12991237 SBO:0000 sodium channel is_connected envmt is_connected sodium channel m gate isA SBO:064 m v time time time v SBO:544 SBO:004 SBO:231 SBO:003 SBO:236 SBO:545 m is_mapped_to 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. Storage GraphDB Models Index Model related data Document Document Model isDescribedBy Tyson1991 Cell Cycle 6 var Reaction3 C2 CP Pubmed: 1831270 SEDML Kegg Pathway sce04111 is pM Cell asProduct asReactant Uniprot:P04551 Uniprot:P04551 is hasPart isVersion isVersionOf isVersionOf EC-Code: 3.1.3.16 isContainedIn Interpro: IPR006670 GO:0005623 Document Model has_annotation Id Name Component Variable Species Reaction Compartment Modelrefere nce Simulation Task Datagenera tor Output Variable Variable SBO: Ontology Pubmed: 12991237 SBO:0000 sodium channel is_connected envmt is_connected sodium channel m gate isA SBO:064 m v time time time v SBO:544 SBO:004 SBO:231 SBO:003 SBO:236 SBO:545 m is_mapped_to Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12
- 25. Storage GraphDB Models Index Model related data Document Document Model isDescribedBy Tyson1991 Cell Cycle 6 var Reaction3 C2 CP Pubmed: 1831270 SEDML Kegg Pathway sce04111 is pM Cell Publication Modelrefere nce Simulation Task Datagenera tor Output asProduct asReactant isContainedIn EC-Code: 3.1.3.16 Uniprot:P04551 Uniprot:P04551 is hasPart isVersionOf isVersionOf isVersion Variable Interpro: IPR006670 GO:0005623 Document Model has_annotation Title Journal Abstract Authors Variable SBO: Ontology Pubmed: 12991237 SBO:0000 sodium channel is_connected envmt is_connected sodium channel m gate isA SBO:064 m v time time time v SBO:544 SBO:004 SBO:231 SBO:003 SBO:236 SBO:545 m is_mapped_to Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12
- 26. Storage GraphDB Models Index Model related data Document Document Model isDescribedBy Tyson1991 Cell Cycle 6 var Reaction3 C2 CP Pubmed: 1831270 SEDML Kegg Pathway sce04111 is pM Cell Publication Modelrefere nce Simulation Task Datagenera tor Output asProduct asReactant isContainedIn EC-Code: 3.1.3.16 Uniprot:P04551 Uniprot:P04551 is hasPart isVersionOf isVersionOf isVersion Variable Interpro: IPR006670 Person Variable GO:0005623 Document Model sodium channel is_connected envmt has_annotation is_connected First name Last name Organization Email Pubmed: 12991237 sodium channel m gate SBO: Ontology SBO:0000 isA SBO:064 m v time time time v SBO:544 SBO:004 SBO:231 SBO:003 SBO:236 SBO:545 m is_mapped_to Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12
- 27. Storage GraphDB Models Index Model related data Document Document Model isDescribedBy Tyson1991 Cell Cycle 6 var Reaction3 C2 CP Pubmed: 1831270 SEDML Kegg Pathway sce04111 is pM Cell Publication Modelrefere nce Simulation Task Datagenera tor Output asProduct asReactant isContainedIn EC-Code: 3.1.3.16 Uniprot:P04551 Uniprot:P04551 is hasPart isVersionOf isVersionOf isVersion Variable Interpro: IPR006670 Person Variable GO:0005623 Document Annotation Model has_annotation SBO: Ontology Pubmed: 12991237 SBO:0000 sodium channel is_connected envmt is_connected sodium channel m gate URI Description isA SBO:064 m v time time time v SBO:544 SBO:004 SBO:231 SBO:003 SBO:236 SBO:545 m is_mapped_to Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12
- 28. Storage GraphDB Models Index Model related data Document Document Model isDescribedBy Tyson1991 Cell Cycle 6 var Reaction3 C2 CP Pubmed: 1831270 SEDML Kegg Pathway sce04111 is pM Cell Publication Modelrefere nce Simulation Task Datagenera tor Output asProduct asReactant isContainedIn EC-Code: 3.1.3.16 Uniprot:P04551 Uniprot:P04551 is hasPart isVersionOf isVersionOf isVersion Variable Interpro: IPR006670 Person Variable GO:0005623 Document Annotation Model sodium channel is_connected envmt has_annotation is_connected SBO: Ontology Pubmed: 12991237 SBO:0000 Simulation sodium channel m gate isA SBO:064 m v time time is_mapped_to Dec 4, 2013 time v m SBO:544 SBO:004 SBO:231 SBO:003 SBO:236 SBO:545 Id Name SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12
- 29. retrieval & ranking Example Show me models by Tyson describing the cell cycle and have cdc2! Document isDescribedBy Tyson1991 Cell Cycle 6 var Reaction3 C2 CP Pubmed: 1831270 Kegg Pathway sce04111 is pM Cell asProduct asReactant isContainedIn is hasPart isVersionOf isVersionOf EC-Code: 3.1.3.16 isVersion Person Annotation Uniprot:P04551 Dec 4, 2013 Uniprot:P04551 Interpro: IPR006670 GO:0005623 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 13
- 30. retrieval & ranking Example Show me models by Tyson describing the cell cycle and have cdc2! Document isDescribedBy Tyson1991 Cell Cycle 6 var Reaction3 C2 CP Pubmed: 1831270 Kegg Pathway sce04111 is pM Cell asProduct asReactant isContainedIn is hasPart isVersionOf isVersionOf EC-Code: 3.1.3.16 isVersion Person Annotation Uniprot:P04551 Dec 4, 2013 Uniprot:P04551 Interpro: IPR006670 GO:0005623 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 13
- 31. retrieval & ranking Example Show me models by Tyson describing the cell cycle and have cdc2! Document isDescribedBy Tyson1991 Cell Cycle 6 var Reaction3 C2 CP Pubmed: 1831270 Kegg Pathway sce04111 is pM Cell asProduct asReactant isContainedIn is hasPart isVersionOf isVersionOf EC-Code: 3.1.3.16 isVersion Person Annotation Uniprot:P04551 Dec 4, 2013 Uniprot:P04551 Interpro: IPR006670 GO:0005623 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 13
- 32. retrieval & ranking Example Show me models by Tyson describing the cell cycle and have cdc2! Document isDescribedBy Tyson1991 Cell Cycle 6 var Reaction3 C2 CP Pubmed: 1831270 Kegg Pathway sce04111 is pM Cell asProduct asReactant isContainedIn is hasPart isVersionOf isVersionOf EC-Code: 3.1.3.16 isVersion Person Annotation Uniprot:P04551 Dec 4, 2013 Uniprot:P04551 Interpro: IPR006670 GO:0005623 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 13
- 33. retrieval & ranking Example Show me models by Tyson describing the cell cycle and have cdc2! Document isDescribedBy Tyson1991 Cell Cycle 6 var Reaction3 C2 CP Pubmed: 1831270 Kegg Pathway sce04111 is pM Cell asProduct asReactant isContainedIn is hasPart isVersionOf isVersionOf EC-Code: 3.1.3.16 isVersion Person Annotation Uniprot:P04551 Dec 4, 2013 Uniprot:P04551 Interpro: IPR006670 GO:0005623 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 13
- 34. retrieval & ranking Example Show me models by Tyson describing the cell cycle and have cdc2! Document isDescribedBy Tyson1991 Cell Cycle 6 var Reaction3 C2 CP Pubmed: 1831270 Kegg Pathway sce04111 is pM Cell asProduct asReactant isContainedIn is hasPart isVersionOf isVersionOf EC-Code: 3.1.3.16 isVersion Person Annotation Uniprot:P04551 Dec 4, 2013 Uniprot:P04551 Interpro: IPR006670 GO:0005623 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 13
- 35. retrieval & ranking Example Document Thank you! isDescribedBy Tyson1991 Cell Cycle 6 var Reaction3 C2 CP Pubmed: 1831270 Kegg Pathway sce04111 is pM Cell asProduct asReactant Person is hasPart isVersion 1. (0.859) Tyson1991 - Cell Cycle 6 var 2. (0.854) Tyson2001_Cell_Cycle_Regulation 3. (0.477) Chen2004 - Cell Cycle Regulation isVersionOf isVersionOf EC-Code: 3.1.3.16 isContainedIn Annotation Uniprot:P04551 Uniprot:P04551 Interpro: IPR006670 GO:0005623 Henkel et al. 2010: Ranked retrieval of Computational Biology models Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 13
- 36. Version Control track versions version x-1 version x version x+1 what happened ? Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 14
- 37. Version Control track versions version x-1 version x version x+1 what happened ? Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 14
- 38. Model Evolution Example: Cell Cycle Modeling the cell division... Cyclin Cdc2 P Cyclin Cdc2 P John J Tyson, 1991 Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 15
- 39. Model Evolution Example: Cell Cycle Modeling the cell division... Cyclin Cdc2 P Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte Cyclin Cyclin Cdc2 Cdc2 P P John J Tyson, 1991 Cdc25∗ Wee1 Cdc25 Wee1∗ Cyclin Cdc2 P Bela Novak and John J Tyson, 1993 Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 15
- 40. Model Evolution Example: Cell Cycle Modeling the cell division... Quantitative analysis of a molecular model of mitotic control in Fission yeast Cyclin Cdc2 Cyclin P Cdc2 P Mik1 Cdc25 ∗ Wee1 Cyclin Cdc2 Cdc2 P John J Tyson, 1991 Cdc25∗ Wee1∗ Cdc25 Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte Cyclin Mik1∗ Cyclin P Cdc2 P Bela Novak and John J Tyson, 1995 Wee1 Cdc25 Wee1∗ Cyclin Cdc2 P Bela Novak and John J Tyson, 1993 Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 15
- 41. Model Evolution Example: Cell Cycle Modeling the cell division... Quantitative analysis of a molecular model of mitotic control in Fission yeast Cyclin Cdc2 Cyclin Modeling the control of DNA replication in fission yeast P Cdc2 P Mik1∗ Cyclin Mik1 Cdc25 ∗ Cdc2 Cdc25 Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte Cyclin Cdc2 Cdc25∗ Cyclin Cdc2 P John J Tyson, 1991 Cdc25∗ Wee1 Cdc2 Mik1∗ Wee1∗ Cyclin Cdc2 Wee1∗ Cyclin Cdc2 Wee1 Wee1∗ P Bela Novak and John J Tyson, 1995 Wee1 Mik1 Cdc25 Cyclin P Cdc25 P P Cyclin P Cdc2 P Rum1 Bela Novak and John J Tyson, 1993 Bela Novak and John J Tyson, 1997 Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 15
- 42. Version Control good news A RB/E2F free E2F RB/E2F r A C RB-Phos r E s C B cycE/cdk2 D new insights RB-Hypo D cycE/cdk2 free E2F B RB-Hypo 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. BiVeS Difference Detection free E2F RB/E2F r A C RB/E2F RB-Phos r A E s C B cycE/cdk2 D D RB-Hypo free E2F cycE/cdk2 B RB-Hypo Biochemical Model Version Control System • • mapping A compares models encoded in standadized formats (currently: and ) maps hierarchically structured content A D D r r C C E B s B Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 17
- 44. BiVeS Difference Detection free E2F RB/E2F r A C RB/E2F Biochemical Model Version Control System RB-Phos r A E • s compares models encoded in standadized and ) formats (currently: • • • maps hierarchically structured content C B cycE/cdk2 D D RB-Hypo free E2F cycE/cdk2 RB-Hypo mapping A B constructs a diff (in XML format) is able to interprete this diff A D <XML> D r r diff construction C C E B s B Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer Diff moves product of r: C deletes product of r: B inserts species: E product of r: E reaction s </XML> 18
- 45. BudHat Diff Visualization r A RB/E2F free E2F RB/E2F A C RB-Phos r E s C B cycE/cdk2 D D RB-Hypo A free E2F B cycE/cdk2 D r r C C 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 D RB-Hypo • • E B s E B s <XML> Diff moves product of r: C deletes product of r: B inserts species: E product of r: E reaction s A </XML> Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer r B C D 19
- 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. 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. 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. 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. 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. Applications BiomodelsDatabase / PMR2 Biomodels Database CellML Model Repository 963 10193 9148 BiVeS 2233 434.825 # Models # Versions # prod. Diffs 1589 12878 12936 Unix’ Diff 1890 1977.210 # empty Diffs ∅ #ops BiVeS 10113 349.5282 6915 non-empty diffs Dec 4, 2013 following Unix’ Diff 10043 480.249 2823 non-empty diffs SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 22
- 52. Applications BiomodelsDatabase / PMR2 Biomodels Database CellML Model Repository 963 10193 9148 BiVeS 2233 434.825 # Models # Versions # prod. Diffs 1589 12878 12936 Unix’ Diff 1890 1977.210 # empty Diffs ∅ #ops BiVeS 10113 349.5282 6915 non-empty diffs Dec 4, 2013 following Unix’ Diff 10043 480.249 2823 non-empty diffs SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 22
- 53. Applications BiomodelsDatabase / PMR2 Biomodels Database CellML Model Repository 963 10193 9148 BiVeS 2233 434.825 # Models # Versions # prod. Diffs 1589 12878 12936 Unix’ Diff 1890 1977.210 # empty Diffs ∅ #ops BiVeS 10113 349.5282 6915 non-empty diffs Dec 4, 2013 following Unix’ Diff 10043 480.249 2823 non-empty diffs SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 22
- 54. Applications BiomodelsDB / PMR2 CellML Model Repository Biomodels Database 250000 q q q q 0 q q q q q qq q q q q q 20000 q q 40000 60000 80000 #operations needed by BiVeS Dec 4, 2013 q q SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer qq qq q q q q qq q q q qq q q q q q q q q q q q q q q q q qq q q q q q q q q q q q q qq q q q q q qqqq qq qq q q q q q q q q q qqq q q q qq q qq q q qqqq q q q q qq q q qqqq q q q qq qqq q qqq q q qqqqqqq q qq qq qqqqqqqqq qq q qq q qq qqqq qq q qqq q q q qqq qqqqq q qqq q qq qq q q qqq qqq qq qqq q qqqq q q q q qqq qqqqqq qqqqq qqqq qqq q q qqqqqq qqqq q q qq qqqqq qqq qqqqqq q qqqq q q qq qqqq qqqq qq q q qq qqq qqqq qqq qqq qq qq qq qq qqq q qq qqq q qq qq qq q q q qqqq qq qqqq q qq q q q qq q q q 5000 q q q q q q q q q qq q qq q q q q qq q q qq q qq q qq q q q q qq q qq q q qq q qqqq q qq q qq q q qq q qq q q qq q q q qq q q q qq qq q qq q qq qq q q q q q qq q q qqqq q qqq q q q qqqq q q qq q qq qq qqqq q q qq qq q qq 0 100000 q 20000 q q q q 15000 q q q 10000 150000 #operations needed by Unix' diff 200000 q q 0 #operations Unix' diff == #operations BiVeS q q 50000 #operations needed by Unix' diff 25000 300000 q #operations Unix' diff == #operations BiVeS q 0 5000 q q q q 10000 15000 20000 25000 #operations needed by BiVeS 23
- 55. Applications BiomodelsDB / PMR2 Biomodels Database move inserts qqqqqq q q q qqqqqq qq q qq qq qqqq q qqqqqq q q q qqqqqq qq qqqq qq q qqqq q qqq q qqq q q qq q q qqqq q qq q qq q qq qq q q q q qq q qq q q q q q insert q q q q qqqqqqqqqqqqqqqqqqqqqqqqqqqqqq qqqqqqqqq q qqqqq q qqqq q q qqqqqqqqqqqqqqqqqq qqqqqqqqq qq qqqqq qqqq qq qq qq q q q q q qqqqqqqqqqq qq qqqq qqqqqqq qq qq qq q q q q qq qqqqqqqqqqq qqqqqq q qqqqqqqq qq qq q qqqqq qqqq qqqq qqqq qq q qq qq q q qqq qq qq q q qq q q qq qqq q qq q q q q qq qq q q qq q q q delete updates qq qqqqqqqqqqqqqqqqqqqqqqqqqqq q qqqqqqq qq qq q qq qq qqqqqqqqqqqqq qqqqqqqqqqqqqqqq q qqqqqqqqqq q q qqq qq q q qq q q q qq qqqqqqqqqqqqqqqqqqqqqqqqqqq q q q qqqq q q q q qq qq qqqqqqqqq q q qqqqqqqqqq qq qq q q q q q qq qqqqqqqqq q q q q qqqqqq q q qq qq qq qqqq q qq qq qq qq qq q qqqqqq qqq q qq q q q q q qq q q qq update q q q q qqqqqq q q q qqqqqq qqqqqqq q q qq q qqq q q qqq qq qq q q q qq qqqq q q q qq q q q q qqq q q q q q q q q q q q q q qq qq q qq qq q q qq q qq q q q q 1 5 10 50 100 q q q 500 q q q q q q q q q q 1000 CellML Model Repository move inserts qqqqqqq qqqqqqqq qqqq q qq qq q qqqqqqqqqqq qqq qqqq q qq qqqqq q q q q qqq qq q q qqqqq qq q qq qqq q qq qqq qq qq qq q qq q qq q q qq q insert q qq qqqqqqqqq qqqqqqq qq q qqqq qqqq q qqqqqq qqq qqqqqqq qqq q q q qqq q qqqqqq qqq qqqqqqq qqq q q q qq qqqqqq q q qq qq q qqq qqq q qq qqq q q qq q q qq qq q q qq delete updates qqqqqqqqqqqqqqqqqqq q qqqqqqqqqqq q qq q qqqqqqqqqq qqqqqqqq qq qq q qq q qq qq q qqqqqqq qqqqqqqqqq q qq q q qq q qqq qqqqq qq q qqq q q qq q q qq q q qq qq q update qqqqqqqq qqqqqq qqqq qqq q q qqqqqqqq qqqq q qqqqqqq q qqqqqqqq qqq qq qqqq q qqqqqq q q q q q qq q 1 Dec 4, 2013 5 10 50 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 100 q q 500 1000 24
- 56. Applications BiomodelsDB / PMR2 text Biomodels Database node q q q q qqq qqq qqqqqqqq qqq q q q q qqq qqq qqqq q qq q q qqqq q q q q qq qq q q qq q q q q qq q q q q q q q q qq q q q q attr qqqqqqqqqqqqqqqqqqqqqqqqqqqq qqqqqqqq qq qq q qqq q q qq qqq q qqqqqqqqqqqqqqqqqqqqqqqqqqqq qqqqqqqqq q q q q q qq q q q q qqqqqqqqqqqqqqqqqqqqqqqqq qqqqqq qq qq q qq q q q q q q qqqqqqqqqqqq qq q qqqqqqqqqq q qq q qq qqqqq qqqqqq qqqqq qqq q q qq qq qq qq qq q q qqq qqqqq q q qq q q q q qq q q qqqqqqqqqqqqqqqqqqqqqqqqqq q qqqqqqqq q q q qqqqqqqqqqqqqqqqqqqqqqqqqq q qqqqq q q q q q qq qqqqqqqqqq qqqqqqqqqqqqq q qqq q q q q q q qq qqqqqqqqqq qqqqqq q qqqqq q qqq q qq qq qqq q qq qqqqqq qqqq q qqq q q qqq qqqq q qq q q q q q 1 5 10 50 100 500 1000 text qqqqqqq qqqq qqqq q qqq qqqqqqqq qqq qqqq q qq qqqqqqqq qqq qq qqq qqqqq q q q qq q q qq q q q q q q attr qqqqqq qqqqqqqq qqqq qqq q qq qq qq q q qqqqq q q q q qqqqqqqqqq qqqqqqq qq q qqq qqq q qq qq qq qq q q qq qqq qqqqqq q qq qq q q q qqqqq q q q qq q q q q q qq q q q qq qq q node CellML Model Repository qqqqqqqqqqq q qqqqq qqqq q qq q qqqqqqqqqqqq qqqqq qqqq qq q qq qqqqqqqqqqqq qq qq qq q q q qqqqqq qqq q qqq qqqq q qqq qqqq qq q q q qqqqq q qqq q q q q qq q 1 Dec 4, 2013 5 10 50 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 100 500 1000 25
- 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. 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. SYSTEMS BIOLOGY BIOINFORMATICS ROSTOCK SE S simulation 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. 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. BiVeS Integration network jvm 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. 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. 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. 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. 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. 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. BiVeS Mapping A • • • • input: 2 XML documents map unambiguos nodes/subtrees propagate mapping up/down exploit further knowledge of biological systems B A C D C E D A SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer E B C D Dec 4, 2013 B E 32
- 68. Applications Investigating BiomodelsDB / PMR2 unix Biomodels Database bives qqqqqq qqqq qqqqqqqq qqq qq qqq qqq qq qq qq qq q q q q q qq qqqqqqqqqqqqqqqqqqqqqqqqq qqq qq qq q q qqqq qqq qqq q q qq q qq qq qq qq q q qqqqqqqqqqqqqqqqqqqq qqqqq q q qq qq qq qqq q qqq qq q q q q q qq qqqq qqqqqqqqqqqqqq qq qq q qq q q q qq q q q q qq qqq q q qqqqqqqqqqq qq qq qqq qq q q qq q qq q q qq q qqqq q q qq q 0 500 1000 q q qq qq qq q q qq q q qq q qq q q q q 1500 unix CellML Model Repository bives qq q qqqq qqqqqq qq q q q qq qq qq qq q q q q q q qq q q qqq qqq qqqq q q q qqq qq qq qq q q q q qq q q q q qq q qq qqqq q qqqqq q qq qqqq q q q q q q qq qq qqq q qq qqq q q qq q qqqq q q qqqq q qq q q qqq q q qq q q q qqq q q q q q qq qq q q q q qq q qq q 0 Dec 4, 2013 500 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 1000 1500 33
- 69. Applications Investigating BiomodelsDB / PMR2 unix Biomodels Database bives qqqq qq qqqqqq q q qq q q q q qqq q qq q q q qq qqqqqq qq qqq qq qqqqqqq q q q q qq qq qqqqqqqqqqq qq q q qqq qqqq q q qq q q q qqq qqq qq qq q qqq q q q q q q qq q q q q q q q q qq q q q q q 0 500 1000 1500 q qqq qq qq q q qq q qqq q q q q qq q q q qq q q q q q q 2000 qq 2500 q qq q q qq 3000 q q q 3500 unix CellML Model Repository bives qq q qqq qq q qq q qq q q q qq q q q qqq qqq q q q qq q q q qq q q q q q q q q q qq qqqqqqq q qq qqqqqqq qqq q q q q q q q q qqqqqq q q q qq qq q q q q q q q q q qq q 0 Dec 4, 2013 500 1000 1500 2000 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer q qq q qq qq q q q 2500 qq q q q 3000 qq q q q qq q q qq q q qq q qq q qq q q q q q 3500 34