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Improving the Management of Computational Models -- Invited talk at the EBI

The document discusses the Simulation Experiment Management System (SEMS) developed for the management of computational models in systems biology and bioinformatics. It emphasizes the increasing complexity and quantity of models, highlighting essential tasks such as storage, retrieval, and version control. Various strategies and projects are being developed to support the community in managing these computational models efficiently.

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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
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
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
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
Introduction Tasks • Storage & Availability • Search & Retrieval • Version Control Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 3
Introduction Tasks • Storage & Availability • Search & Retrieval • Version Control Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 3
Introduction Tasks • Storage & Availability • Search & Retrieval • Version Control Dec 4, 2013 SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer ? 3
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
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
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
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
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
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
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
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
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
Storage GraphDB Models Dec 4, 2013 Model related data SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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

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Improving the Management of Computational Models -- Invited talk at the EBI

  • 1.
    SYSTEMS BIOLOGY BIOINFORMATICS ROSTOCK SE S simulationexperiment 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 modelsis 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 modelsis 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 methodsto 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 simulationexperiment 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 Dec4, 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 Modelrelated data SEMS | Martin Scharm, Ron Henkel, Dagmar Waltemath, Olaf Wolkenhauer 12
  • 18.
    Storage GraphDB Models Model related data Document isDescribedBy Tyson1991 CellCycle 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 CellCycle 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 CellCycle 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 CellCycle 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 CellCycle 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 CellCycle 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 CellCycle 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 CellCycle 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 CellCycle 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 CellCycle 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 CellCycle 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 Showme 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 Showme 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 Showme 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 Showme 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 Showme 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 Showme 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 Thankyou! 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 versionx-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 versionx-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: CellCycle 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: CellCycle 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: CellCycle 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: CellCycle 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 freeE2F 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 freeE2F 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 BiochemicalModel 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 freeE2F 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 themodel → 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 themodel → 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 themodel → 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 themodel → 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 BiomodelsDatabase 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 BiomodelsDatabase 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 BiomodelsDatabase 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 CellMLModel 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 BiomodelsDatabase 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 BiomodelsDatabase 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 methodsfor 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 furtherstandards • 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 simulationexperiment 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.
  • 62.
    BiVeS Integration jvm network cmd java -jar BiVeS.jarpath/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 containingmodels 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 XMLdocuments 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 XMLdocuments 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 XMLdocuments 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