Reproducibility, dissemination,  and management of modeling results
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Research Seminar BBT Braunschweig 2014

Research Seminar BBT Braunschweig 2014

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Reproducibility, dissemination, and management of modeling results Presentation Transcript

  • 1. Reproducibility, dissemination, and management of modeling results 17 February 2014, Braunschweig Dagmar Waltemath http://sems.uni-rostock.de
  • 2. Nature Blogs: Of Schemes and Dreams (2014) Nine Worrying Stats on the Effect of Poor Scientific Data Management http://sems.uni-rostock.de 2
  • 3. Nature Blogs: Of Schemes and Dreams (2014) Nine Worrying Stats on the Effect of Poor Scientific Data Management http://sems.uni-rostock.de 3
  • 4. “We’ve been hearing a common theme from the academic community – researchers are having difficulty managing and accessing their data. It seems to be an ongoing problem for research scientists, at any stage of their careers.” (Nature Blogs: Of Schemes and Dreams (2014) Nine Worrying Stats on the Effect of Poor Scientific Data Management) http://sems.uni-rostock.de 4
  • 5. Outline reproducibility dissemination http://sems.uni-rostock.de management 5
  • 6. Outline reproducibility dissemination management “People can’t share knowledge if they don’t speak a common language” Tom Davenport, Lawrence Prusak (2000) Working Knowledge http://sems.uni-rostock.de 6
  • 7. Reproducible modeling results :: Standards Model Entities, network of reactions, math Fig: Goldbeter (1991), http://www.ncbi.nlm.nih. gov/pubmed/1833774 Annotations Compartment: Cell GO:0005623 Publication: Goldbeter PMID:1833774 M = inactive CDCD2 Kinase: UniProt:CDK1a_XENIA Fig.: BioModels Database Behavior: Oscillation TEDDY_0000006 Algorithm: Gillespie KiSAO:000029 Protocols Fig.: BioModels Database http://sems.uni-rostock.de 7
  • 8. Reproducible modeling results :: Towards publication 1 3 2 + 4 5 Following: Waltemath et al (2013) Reproducibility of model-based results in systems biology. Springer http://sems.uni-rostock.de 8
  • 9. Outline reproducibility dissemination management [Quantitative] models will be only as useful as their access and reuse is easy for all scientists. Nicolas Le Novère (2006) Model storage, exchange and integration. BMC Neuroscience http://sems.uni-rostock.de 9
  • 10. Dissemination :: Model curation and annotation Fig.: Li et al (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Systems Biology http://sems.uni-rostock.de 10
  • 11. Dissemination :: Public model repositories 1. 2. 3. 4. Higher visibility of research Long-term availability Link to other resources Quality-checks Fig.: Piwowar and Vision (2013) Data reuse and the open data citation advantage. PeerJ http://sems.uni-rostock.de 11
  • 12. Dissemination :: Quality checks with functional curation Fig.: Example for functional curation on heart model, http://travis.cs.ox.ac.uk/FunctionalCuration/db.html Fig.: Cooper et al (under review) Through models to knowledge with virtual experiments http://sems.uni-rostock.de Martin Scharm 12
  • 13. Outline reproducibility dissemination management “And that’s why we need model Management.“ Following: http://www.indiana.edu/~hperp200/images/WhyWeNeedComputer_thumb.png http://sems.uni-rostock.de 13
  • 14. Management :: Integration of model-related data “Which models are annotated with ‘Adenosine tri-phosphate’?” Document ”Which models contain reactions with ATP as reactant and ADP as product?“ C2 CP Pubmed: 1831270 Kegg Pathway sce04111 is pM Cell asProduct asReactant EC-Code: 3.1.3.16 Uniprot:P04551 Uniprot:P04551 Interpro: IPR006670 is hasPart isContainedIn isVersion isVersionOf • Relations between entities • Links to concepts in bio-ontologies Reaction3 isVersionOf • Graph store (Neo4J database) isDescribedBy Tyson1991 Cell Cycle 6 var GO:0005623 Fig.: Henkel et al (2012) Considerations of graph-based concepts to manage of computational biology models and associated simulations INFORMATIK2012, Braunschweig Ron Henkel http://sems.uni-rostock.de 14
  • 15. Management :: Integration of model-related data Document Document SEDML Pubmed: 1831270 isDescribedBy Tyson_1991 Modelreference C2 is_connected is_connected environment Simulation Task Datagenerator Output CP Variable is_connected Variable C2 CP time time time CP KISAO: Ontology C2 KISAO:097 is_mapped_to KISAO:000 KISAO:201 isA Document isDescribedBy KISAO:433 Tyson1991 Cell Cycle 6 var Reaction3 C2 CP pM KISAO:352 KISAO:20 KISAO:019 Kegg Pathway sce04111 is KISAO:273 KISAO:447 SBO: Ontology Cell asProduct isContainedIn is hasPart isA ha f nO sP art isVersionOf SBO:0000 is sio er EC-Code: 3.1.3.16 isV isVersionOf asReactant SBO:064 Uniprot:P04551 Interpro: IPR006670 GO:0005623 SBO:544 SBO:004 SBO:231 SBO:003 SBO:236 SBO:545 SBO:000064 Fig.: Henkel et al (in preparation) http://sems.uni-rostock.de 15
  • 16. Management :: Combination of methods Keywords describing a model of interest. Rank isVersion Of CP Unipr ot:P0 4551 is pM 3. Maex‘98 SEDM L Tyso n_19 91 Inte rpro : IPR 006 670 Pubm isDescribedBy Cel l envi ron men t ed: Pubm 183127 0 ed: 183127 0 Model refere nce CP Simul ation Task Outpu t Datag enera tor Varia ble GO:0 0056 23 C2 CP time time time CP C2 Varia ble ID: BIOMD000000005 Authors: Tyson JJ. Date: 13 Sep 2005 12:31:08 Publication: pubmed:1831270 Species: cdc2k, cyclin … Reaction: cyclin_cdc2k_dissociation, … Tyson‘91 Tyson‘91 ODE plot simulate Tyson‘91 Doc ume nt Pub med: Kegg 1831 Path 270 way sce04 111 is hasPart isVersion Unipr ot:P0 4551 Novak‘97 Docu ment isDescrib edBy C2 ECCode: 3.1.3. 16 Format retrieve select simulation description compare with paper search C2 isVersion Of 19 91 Cel l Cy cle 6 var 1. 2. Do cu me Tys nt on Re act ion 3 Name Tyson’91 ODE plot Model: BIOMD000000005 add simulation Algorithm: ODE solver description to Type: time course simulation software Output: plot Fig.: Following Waltemath et al (2013) Reproducibility of model-based results in systems biology. Springer. Henkel et al (2010) Ranked retrieval of Computational Biology models. BMC bioinformatics http://sems.uni-rostock.de Ron Henkel 16
  • 17. Management :: Provenance “Give me the best matching model published on the Cell Cycle and considering cdk1.” Lucene: species:cdk1, compartment:cell, … Fig.: Waltemath et al (2013) Improving the reuse of computational models through version control.Bioinformatics http://sems.uni-rostock.de 17
  • 18. Management :: Model version control Fig.: courtesy Martin Scharm, BudHat, http://sems.uni-rostock.de/budhat http://sems.uni-rostock.de Martin Scharm 18
  • 19. Summary :: SEMS projects & Contributions foster dissemination improve management 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 http://sems.uni-rostock.de Uniprot:P04551 Uniprot:P04551 Interpro: IPR006670 is hasPart isContainedIn isVersion isVersionOf asReactant isVersionOf ensure reproducibility GO:0005623 19
  • 20. Thank you for your attention. Collaborators Nicolas Le Novère Christian Rosenke David Nickerson Wolfgang Müller Jonathan Cooper Falk Schreiber Jon Olav Vik SED-ML Editorial Board Tommy Yu SBML Editorial Board HARMONY 2015 Wittenberg HERMESForschungsförderung HERMES-Forschungsförderung der der Universität RostockUniversität Rostock http://sems.uni-rostock.de @SemsProject 20