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 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 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 models 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 g. 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 g. 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 g. 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 g. 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

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 ssion 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 D r r diff construction C C E B s B Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer Di moves product of r: C deletes product of r: B inserts species: E product of r: E reaction s 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 Di moves product of r: C deletes product of r: B inserts species: E product of r: E reaction s A 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 < --> 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?

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: 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: Caffeine - 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 le 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 simplies exchange Proposal by Nicolas Le Novre, 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

improving the management of computational models -- invited talk at the ebi

Technology

time time

availability

ipr006670

cell cycle

compares models

bives mapping

gate isa sbo

ipr006670