e:Bio Kick-Off Meeting, SEMS
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The document presents work from the Department of Systems Biology and Bioinformatics at the University of Rostock on improving reproducibility in systems biology simulations. It discusses developing standards for representing simulations (SED-ML) and modeling provenance to better reproduce published results and enable model reuse. The goals are to specify simulation experiments, develop simulation management methods focusing on model provenance, establish links between model data, and promote reproducible science.
![Reproduce published results.
“[..] in Biomodels database the model BIOMD0000000139 and
BIOMD0000000140 are two different models and they are supposed to show
different results. Unfortunately simulating them [..] gives same result for
both the models. [..] “ (Quote: arvin mer on sbml-discuss)
(Figures produced in COPASI)
24.09.2013 e:Bio SEMS | sems.uni-rostock.de | Dagmar Waltemath 4](https://image.slidesharecdn.com/waltemathebio2013-130924070041-phpapp02/85/e-Bio-Kick-Off-Meeting-SEMS-4-320.jpg)
e:Bio Kick-Off Meeting, SEMS
- 1. Tools and Methods for Improved Result Reproducibility in Systems Biology (SEMS) Department of Systems Biology and Bioinformatics University of Rostock Dagmar Waltemath, Martin Scharm, Ron Henkel, Olaf Wolkenhauer e:Bio Kick-Off Meeting, 23-25 September 2013, Mainz 24.09.2013 e:Bio SEMS | sems.uni-rostock.de | Dagmar Waltemath 1
- 2. 24.09.2013 e:Bio SEMS | sems.uni-rostock.de | Dagmar Waltemath 2
- 3. Reuse existing models. 0 20000 40000 60000 80000 100000 120000 0 100 200 300 400 500 600 700 800 900 Apr-05 Jul-05 Oct-05 Jan-06 Apr-06 Jul-06 Oct-06 Jan-07 Apr-07 Jul-07 Oct-07 Jan-08 Apr-08 Jul-08 Oct-08 Jan-09 Apr-09 Jul-09 Oct-09 Jan-10 Apr-10 Jul-10 Oct-10 Jan-11 Apr-11 Jul-11 Oct-11 Jan-12 NumberofAnnotations NumberofModels Models Annotation + 140.811 derived models (Models in BioModels Database; Figure courtesy Ron Henkel) 24.09.2013 e:Bio SEMS | sems.uni-rostock.de | Dagmar Waltemath 3
- 4. Reproduce published results. “[..] in Biomodels database the model BIOMD0000000139 and BIOMD0000000140 are two different models and they are supposed to show different results. Unfortunately simulating them [..] gives same result for both the models. [..] “ (Quote: arvin mer on sbml-discuss) (Figures produced in COPASI) 24.09.2013 e:Bio SEMS | sems.uni-rostock.de | Dagmar Waltemath 4
- 5. SEMS – Improving result reproducibility 24.09.2013 e:Bio SEMS | sems.uni-rostock.de | Dagmar Waltemath 5 "Quantitative models will be only as useful as their access and reuse is easy for all scientists” (Nicolas Le Novère, 2006)
- 6. Standard representation formats (Fig. adapted from: Courtot, Waltemath et al. Nature MSB, 2011) 24.09.2013 e:Bio SEMS | sems.uni-rostock.de | Dagmar Waltemath 6
- 7. Standard representation formats NuML SBRML 24.09.2013 e:Bio SEMS | sems.uni-rostock.de | Dagmar Waltemath 7 (Fig. adapted from: Courtot, Waltemath et al. Nature MSB, 2011)
- 8. Standard representation formats MAMO NuML SBRML 24.09.2013 e:Bio SEMS | sems.uni-rostock.de | Dagmar Waltemath 8 (Fig. adapted from: Courtot, Waltemath et al. Nature MSB, 2011)
- 9. Data links MAMO NuML SBRML 24.09.2013 e:Bio SEMS | sems.uni-rostock.de | Dagmar Waltemath 9 (Fig. adapted from: Courtot, Waltemath et al. Nature MSB, 2011)
- 10. Data links MAMO NuML SBRML (Fig. adapted from: Courtot, Waltemath et al. Nature MSB, 2011) 24.09.2013 e:Bio SEMS | sems.uni-rostock.de | Dagmar Waltemath 10
- 11. Project goals 1. Specify and establish a standard for the description of simulation experiments (SED-ML) Waltemath et al. BMC Sys Biol (2011) 2. Develop methods for simulation management with focus on model provenance Waltemath et al. Bioinformatics (2013) 3. Establish links between model-related data on storage level Henkel et al. INFORMATIK2012 (2012) 4. Promote reproducible science 24.09.2013 e:Bio SEMS | sems.uni-rostock.de | Dagmar Waltemath 11
- 12. Standard representation of simulation experiments http://sed-ml.org/ 24.09.2013 e:Bio SEMS | sems.uni-rostock.de | Dagmar Waltemath 12
- 13. Model provenance (Figure courtesy Martin Scharm) 24.09.2013 e:Bio SEMS | sems.uni-rostock.de | Dagmar Waltemath 13
- 14. Model provenance: BiVeS & BudHat http://budhat.sems.uni-rostock.de VANTED 24.09.2013 e:Bio SEMS | sems.uni-rostock.de | Dagmar Waltemath 14
- 15. ModelGraphs:Linking model-related data (Fig.: Henkel et al. INFORMATIK2012 (2012)) (Figure courtesy Ron Henkel, COMBINE2013) 24.09.2013 e:Bio SEMS | sems.uni-rostock.de | Dagmar Waltemath 15 Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Document SEDML Modelrefere nce Output Datagenera tor Simulation Task Variable Variable Document Tyson_1991 C2 CP time environment isDescribedBy Pubmed: 1831270 time timeCPC2 CP C2 is_connected is_connected is_mapped_to is_connected SBO: Ontology SBO:0000 SBO:544 SBO:236SBO:231 isA SBO:064 SBO:545SBO:004 SBO:003 http://sems.uni-rostock.de/projects/morre/
- 16. ModelGraphs:Linking model-related data 24.09.2013 e:Bio SEMS | sems.uni-rostock.de | Dagmar Waltemath 16 Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670 isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Document SEDML Modelrefere nce Output Datagenera tor Simulation Task Variable Variable Document Tyson_1991 C2 CP time environment isDescribedBy Pubmed: 1831270 time timeCPC2 CP C2 is_connected is_connected is_mapped_to is_connected SBO: Ontology SBO:0000 SBO:544 SBO:236SBO:231 isA SBO:064 SBO:545SBO:004 SBO:003 Model Publication Annotation Person Simulation Show me models by Tyson, dealing with the Cell Cycle and simulating concentration of cdc2!
- 17. Summary 24.09.2013 e:Bio SEMS | sems.uni-rostock.de | Dagmar Waltemath 17 track development store retrieve rank Retrieval Ranking Δ Δ Version 1 Version 2 latest Version Control Do cu me ntTys on 19 91 Cel l Cy cle 6 var C2 pM Cel l Re act ion 3 CP Unipr ot:P0 4551 Unipr ot:P0 4551 GO:0 0056 23 Inte rpro : IPR 006 670 isVersion Of isVersion hasPart is Pub med: 1831 270 Kegg Path way sce04 111 isDescrib edBy is EC- Code: 3.1.3. 16 isVersion Of Docu ment SEDM L Model refere nce Outpu t Datag enera tor Simul ation Task Varia ble Varia ble Doc ume nt Tyso n_19 91 C2 CP time envi ron men t isDescribedBy Pubm ed: 183127 0 Pubm ed: 183127 0 time timeCPC2 CP C2 Do cu me ntTys on 19 91 Cel l Cy cle 6 var C2 pM Cel l Re act ion 3 CP Unipr ot:P0 4551 Unipr ot:P0 4551 GO:0 0056 23 Inte rpro : IPR 006 670 isVersion Of isVersion hasPart is Pub med: 1831 270 Kegg Path way sce04 111 isDescrib edBy is EC- Code: 3.1.3. 16 isVersion Of Do cu me ntTys on 19 91 Cel l Cy cle 6 var C2 pM Cel l Re act ion 3 CP Unipr ot:P0 4551 Unipr ot:P0 4551 GO:0 0056 23 Inte rpro : IPR 006 670 isVersion Of isVersion hasPart is Pub med: 1831 270 Kegg Path way sce04 111 isDescrib edBy is EC- Code: 3.1.3. 16 isVersion Of Do cu me ntTys on 19 91 Cel l Cy cle 6 var C2 pM Cel l Re act ion 3 CP Unipr ot:P0 4551 Unipr ot:P0 4551 GO:0 0056 23 Inte rpro : IPR 006 670 isVersion Of isVersion hasPart is Pub med: 1831 270 Kegg Path way sce04 111 isDescrib edBy is EC- Code: 3.1.3. 16 isVersion Of Doc ume nt Tyso n_19 91 C2 CP time envi ron men t isDescribedBy Pubm ed: 183127 0 Pubm ed: 183127 0 time timeCPC2 CP C2 Do cu me ntTys on 19 91 Cel l Cy cle 6 var C2 pM Cel l Re act ion 3 CP Unipr ot:P0 4551 Unipr ot:P0 4551 GO:0 0056 23 Inte rpro : IPR 006 670 isVersion Of isVersion hasPart is Pub med: 1831 270 Kegg Path way sce04 111 isDescrib edBy is EC- Code: 3.1.3. 16 isVersion Of Do cu me ntTys on 19 91 Cel l Cy cle 6 var C2 pM Cel l Re act ion 3 CP Unipr ot:P0 4551 Unipr ot:P0 4551 GO:0 0056 23 Inte rpro : IPR 006 670 isVersion Of isVersion hasPart is Pub med: 1831 270 Kegg Path way sce04 111 isDescrib edBy is EC- Code: 3.1.3. 16 isVersion Of Doc ume nt Tyso n_19 91 C2 CP time envi ron men t isDescribedBy Pubm ed: 183127 0 time timeCPC2 CP C2 Storage Docu ment SEDM L Model refere nce Outpu t Simul ation Task Docu ment SEDM L Model refere nce Outpu t Datag enera tor Simul ation Task Varia ble Varia ble Docu ment SEDM L Model refere nce Outpu t Datag enera tor Simul ation Task http://sbml.org
- 18. Thank you for your attention! SEMS group Martin Scharm Martin Peters Markus Wolfien Rebekka Alm Olaf Wolkenhauer Associated member Ron Henkel Collaborators Falk Schreiber (IPK Gatersleben) Christian Rosenke (University of Rostock) Jon Olav Vik (UMB) Jonathan Cooper (University of Oxford) Tommy Yu (University of Auckland) COMBINE SED-ML Editors biomodels.net http://sems.uni-rostock.de/ @SemsProject HERMES- Forschungsförderung der Universität Rostock