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2019 07-04-model reuse-bonn

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University Medicine Greifswald

This document discusses the transition from traditional paper-based models to interactive simulations for studying disease progression, emphasizing the importance of reproducibility and data integration in systems biology. It highlights advancements in simulation models, the necessity of standardized metadata, and the role of community-driven repositories for sharing and improving computational models. The future aims at linking experimental data with disease models to enhance biomedical research and treatment strategies.

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from paper-based model description to interactive simulation of disease progression PROF. DR.-ING. DIPL.-INF. DAGMAR WALTEMATH MEDICAL INFORMATICS | INSTITUTE FOR COMMUNITY MEDICINE UNIVERSITY MEDICINE GREIFSWALD (GERMANY) MODELREUSEWITHJOY
About me SEMS@University of Rostock, Germany (2015) 7/4/2019 DAGMAR WALTEMATH | MODEL REUSE WITH JOY 2 Projects. SEMS | de.NBI:SYSBIO | SBGN-ED+ | INCOME | MIRACUM Community work. Standard development | COMBINE coordinator | SED-ML editor Research interests. Data integration | Semantics | Reproducibility of scientific results | Sustainability of scientific outcomes Further interests. Education of young scientists | Open Access & open data | Gender equality in science @dagmarwaltemath 0000-0002-5886-5563
How this talk is organised THE HISTORY THE SCIENCE Disclaimer: All comic-style graphics in this presentation were done either by Anna Zhukova or by Martin Peters. Thank you very much! Images downloaded from pixabay. DAGMAR WALTEMATH | MODEL REUSE WITH JOY 37/4/2019
Systems Biology is… Systems biology is the science that studies how biological function emerges from the interactions between the components of living systems. … and how these emergent properties enable or constrain the behavior of these components. (Slide adapted from: Olaf Wolkenhauer) DAGMAR WALTEMATH | MODEL REUSE WITH JOY 47/4/2019
Simulation models can take many forms. MATHEMATICAL MODELS FURTHER APPROACHES Fig.s: https://doi.org/10.1371/journal.pcbi.1002815, https://doi.org/10.1371/journal.pcbi.1004591 DAGMAR WALTEMATH | MODEL REUSE WITH JOY 57/4/2019
Simulation models can be complex. First in silico Whole Cell Model Genome (525 genes), transcriptome, proteome and metabolome incorporated Describes whole life cycle of a single cell on molecular level, and predicts a wide range of cellular behaviors, and accounts for the specific function of every annotated gene product  Based on 900 publications Consists of 116 MATLAB files Incorporates over 1.900 experimentally observed parameters WHOLE-CELL MODEL KEY FIGURES Fig.: Karr et al. (2012), https://doi.org/10.1016/j.cell.2012.05.044 DAGMAR WALTEMATH | MODEL REUSE WITH JOY 67/4/2019
Early simulation models Tyson‘s Cell Cycle Model (1991) (BIOM5 und BIOM6) history
Publishing the model PAPER AVAILABLE INFORMATION 1) (textual) description of work and related efforts (referencing other papers) 2) (textual and visual) description of (biochemical) network 3) (printed) model parameters 4) (printed) mathematical equations 5) resulting plots DAGMAR WALTEMATH | MODEL REUSE WITH JOY 8 Fig.: http://doi.org/10.1073/pnas.88.16.7328 7/4/2019
What can you do with this model? STUDY THE PAPER, BELIEVE RE-IMPLEMENT BASED ON THE PAPER DAGMAR WALTEMATH | MODEL REUSE WITH JOY 97/4/2019
The year 2000 Novak‘s Cell Cycle model (1997) (BIOM7) history
Publishing the model PAPER AVAILABLE INFORMATION 1) (textual) description of work and related efforts (referencing other papers) 2) (textual and visual) description of (biochemical) network 3) (printed) model parameters 4) (printed) mathematical equations 5) resulting plots DAGMAR WALTEMATH | MODEL REUSE WITH JOY 11 Fig.: http://doi.org/10.1073/pnas.94.17.9147 7/4/2019
Publishing the model code SIMULATION MODEL AVAILABLE INFORMATION 1) Description of (biochemical) network in computer-readable format (SBML) 2) Mathematical equations in computer- readable format (MathML) 3) Model parameters inside model code DAGMAR WALTEMATH | MODEL REUSE WITH JOY 127/4/2019
What can you do with this data? CHECK THE MODEL (REPRODUCIBILITY) RE-USE THE CODE IN ANOTHER SOFTWARE (INTEROPERABILITY) Fig. (left) JWS Online, http://jjj.mib.ac.uk/models. Fig. (right) courtesy M.Hucka (2016), https://www.slideshare.net/thehuck/recent-software-and-services-to-support-the-sbml-community DAGMAR WALTEMATH | MODEL REUSE WITH JOY 137/4/2019
State-of-the-art (in theory) Calzone‘s Cell Cycle model (BIOM144) history
Publishing the model & code PAPER SIMULATION MODEL DAGMAR WALTEMATH | MODEL REUSE WITH JOY 15 Fig.: https://doi.org/10.1038/msb4100171 7/4/2019
Publishing the meta-data on repository – model – and entity level DAGMAR WALTEMATH | MODEL REUSE WITH JOY 16 Harmonised meta-data for simulation models in computational biology: Neal et al. (2018), Briefings in Bioinformatics (https://doi.org/10.1093/bib/bby087) 7/4/2019
Publishing the simulation setups COMBINE ARCHIVE manifest.xml Omex Skeleton, automatically generated by WebCAT metadata.rdf Omex Skeleton, automatically generated by WebCAT README.md Markdown Human readable information for users stumbling upon the archive model/ BIOMD0000000144.xml SBML L2V1 origin: www.ebi.ac.uk/biomodels-main/download?mid=BIOMD0000000144 calzone_2007.svg SVG origin: models.cellml.org/workspace/calzone_thieffry_tyson_novak_2007 calzone_2007.ai Illustrator origin: models.cellml.org/workspace/calzone_thieffry_tyson_novak_2007 calzone_2007.png PNG origin: models.cellml.org/workspace/calzone_thieffry_tyson_novak_2007 calzone_thieffry_tyson_novak_2007.cellml CellML 1.0 origin: models.cellml.org/workspace/calzone_thieffry_tyson_novak_2007 sbgn/Calzone2007.gml GML SBGN compliant figure generated using SBGN-ED sbgn/Calzone2007.graphml GraphML SBGN compliant figure generated using SBGN-ED sbgn/Calzone2007.pdf PDF SBGN compliant figure generated using SBGN-ED sbgn/Calzone2007.png PNG SBGN compliant figure generated using SBGN-ED sbgn/Calzone2007.sbgn SBGN-ML SBGN-ML encoded figure generated using SBGN-ED experiment/ Calzone2007-default-simulation.xml SED-ML L1V1 Simulation description generated using SED-ML Web Tools Calzone2007-simulation-figure-1B.xml SED-ML L1V1 Simulation description generated using SED-ML Web Tools based on Calzone2007-default-simulation.xml documentation/ Calzone2007.pdf PDF Scientific publication “Dynamical modeling of syncytial mitotic cycles in Drosophila embryos”obtained from msb.embopress.org/content/3/1/131 Calzone2007-supplementary-material.pdf PDF Supplementary information for the publication obtained from msb.embopress.org/content/3/1/131 result/ Fig1B-bottom-COPASI.svg SVG Imagegenerated by executing Calzone2007-simulation-figure-1B.xml on BIOMD0000000144.xml in COPASI Fig1B-top-COPASI.svg SVG Imagegenerated by executing Calzone2007-simulation-figure-1B.xml on BIOMD0000000144.xml in COPASI Fig1B-bottom-webtools.png PNG Imagegenerated by executing Calzone2007-simulation-figure-1B.xml on BIOMD0000000144.xml in SED-ML Web Tools Fig1B-top-webtools.png PNG Imagegenerated by executing Calzone2007-simulation-figure-1B.xml on BIOMD0000000144.xml in SED-ML Web Tools AVAILABLE INFORMATION 1) Paper and additional information 2) Meta-data 3) Graphical representation of model (SBGN) 4) Alternative parametrisations (SED-ML) 5) Model versions 6) Simulation experiments (SED-ML) Example archive available from: https://github.com/SemsProject/CombineArchiveShowCase/ DAGMAR WALTEMATH | MODEL REUSE WITH JOY 177/4/2019
What can you do with an archive? Explore data and meta-data Identify Data set of interest Run model Online/ offline Safe new versions and documentation in archive Modify, merge, extend, combine... Re-publish DAGMAR WALTEMATH | MODEL REUSE WITH JOY 18 Download Archive 7/4/2019
What can you do with an archive? Example: Download archive from Github and run it in JWS Online DAGMAR WALTEMATH | MODEL REUSE WITH JOY 197/4/2019
What does the (near) future bring? DAGMAR WALTEMATH | MODEL REUSE WITH JOY 207/4/2019
Linking models and data simplifies verification of models, and experimental data sets. DAGMAR WALTEMATH | MODEL REUSE WITH JOY 21 Integrating Disease maps and Biomedical data (e.g., https://pdmap.uni.lu/minerva/) Linking models and experimental data sets (e.g., JWS Online) 7/4/2019
Connecting pathways, ontologies and datasets leads to new means of data exploration. DAGMAR WALTEMATH | MODEL REUSE WITH JOY 22 Comprehensive knowledge of cancer signaling networks and linked data, working with interactive Pathway Maps, https://acsn.curie.fr/ACSN2/ACSN2.html 7/4/2019
Easy access to patient-specific liver disease progression helps doctors choose a therapy. DAGMAR WALTEMATH | MODEL REUSE WITH JOY 23 Fig.: Koenig et al. (2016), ODLS, Halle (Saale), http://livermetabolism.com 7/4/2019
The pillars of success WHAT‘S THE SECRET? DAGMAR WALTEMATH | MODEL REUSE WITH JOY 247/4/2019
The research field develops and adheres to FAIR standards for modeling and simulation. Data formatsRecommendations Semantic / Ontologies DAGMAR WALTEMATH | MODEL REUSE WITH JOY 257/4/2019
Data formats are interoperable and are being developed collaboratively. Editorial Boards Specifications Software tool support http://co.mbine.org/standards Standard development Meetings Annual special issue with list of latest specifications and errata DAGMAR WALTEMATH | MODEL REUSE WITH JOY 267/4/2019
The community builds, feeds & uses open repositories for simulation studies. DAGMAR WALTEMATH | MODEL REUSE WITH JOY 277/4/2019
The community actively develops open, standard-compliant libraries & tools. MODELING AND SIMULATION SOFTWARE REPOSITORIES & MANAGEMENT TOOLS … Full list available at: http://sbml.org/SBML_Software_Guide/ DAGMAR WALTEMATH | MODEL REUSE WITH JOY 287/4/2019
The (data) Science DEVELOPMENT OF MODEL MANAGEMENT STRATEGIES BY SEMS & FRIENDS (2011-2019) DAGMAR WALTEMATH | MODEL REUSE WITH JOY 29
Characteristics of the data Heterogeneous Big Distributed Complex Highly connected But Good standards available to represent the data Agreed-upon semantic annotation schemes & ontologies to enrich the data Open data movement Community spirit DAGMAR WALTEMATH | MODEL REUSE WITH JOY 307/4/2019
Issues that SEMS investigated 2012-17 Handling the steadily increasing size & numbers of models and studies (database performance) Increasing the quality of published models (semantic annotations, reproducibility of results) Keeping track of model changes and relations (comprehensibility) Identifying and handling similarities in model representations (reuse) DAGMAR WALTEMATH | MODEL REUSE WITH JOY 31 ~ 300.000 models in BioModels Database, on average 5 versions per model. XML, RDF, OWL 7/4/2019
A graph-based approach keeps storage and retrieval efficient. DAGMAR WALTEMATH | MODEL REUSE WITH JOY 32 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 Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Example: Tyson 1991 (BIOM5), Source: Waltemath & Henkel, Neo4j Life & Health Sciences Day - Berlin, 21st June, 2017, adapted from Henkel et al. (2015) DATABASE (https://doi.org/10.1093/database/bau130) SBO: Ontology SBO:0000 SBO:544 SBO:236SBO:231 isA SBO:064 SBO:545SBO:004 SBO:003 Models Simulation Annotation 7/4/2019
The linking of data sets on graph-level allows for complex queries. DAGMAR WALTEMATH | MODEL REUSE WITH JOY 33 2 experiments, 3 model versions, changes, meta-data Fig.: Martin Peters, SEMS Fig (right): Henkel et al. (2015) DATABASE, https://doi.org/10.1093/database/bau130 7/4/2019
Lucene-based indices incorporate all relevant information for later search & comparison. DAGMAR WALTEMATH | MODEL REUSE WITH JOY 34 Model Publication Annotation Person Simulation 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 • Id • Name • Title • Journal • Abstract • Authors • … • Id • Name • Component • Variable • Species • Reaction • Compartment • First name • Last name • Organization • Email • URI • Description Fig.: Henkel et al. (2015) DATABASE 7/4/2019
A weighted ranked-retrieval methods returns only most relevant models. DAGMAR WALTEMATH | MODEL REUSE WITH JOY 35 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 Annotation Person Show me models by Tyson describing the cell cycle and having cdc2 1. (0.859) Tyson1991 - Cell Cycle 6 var 2. (0.854) Tyson2001_Cell_Cycle_Regulation 3. (0.477) Chen2004 - Cell Cycle Regulation Which are the most frequently used GO annotations in my model set? Which models contain reactions with 'ATP' as reactant and 'ADP' as product? Find good candidates for features describing my model set. Which models are annotated with ‘Ubiquitin'’? Give me all the files I need to run this simulation study. Fig.: Henkel et al. (2015) DATABASE 7/4/2019
A method to detect and track differences in model versions ensures transparency. How did my model change between version x and X+1? DAGMAR WALTEMATH | MODEL REUSE WITH JOY 36 „Sophisticated“ XYDIFF & change ontology How often did this model change, when and wy?Give me all versions of this model.Figs.: Waltemath et al. (2015) Oxford Bioinformatics (https://doi.org/10.1093/bioinformatics/btt018); Implementation: M. Scharm, https://github.com/SemsProject/BiVeS 7/4/2019
Identification of frequent pattern in network graphs helps determine structural similarity. DAGMAR WALTEMATH | MODEL REUSE WITH JOY 37 Fig.: Size and number of reactions and participating species (left), and identified frequent patterns (right). Implementation: Fabienne Lambusch. Figure: Lambusch et al. (2018) DATABASE (https://doi.org/10.1093/database/bay051) 7/4/2019
Identification of frequent pattern in network graphs helps determine structural similarity. DAGMAR WALTEMATH | MODEL REUSE WITH JOY 38 Fig.: Tyson BIOM5 (left), and identified patterns based on the (right). Implementation: Fabienne Lambusch. Figure: Lambusch et al. (2018) DATABASE (https://doi.org/10.1093/database/bay051) How similar are these two models with respect to structure? Give me all models with this particular sub-structure. 7/4/2019
Example applications MODEL RETRIEVAL | MODEL VERSION CONTROL & PROVENANCE | DAGMAR WALTEMATH | MODEL REUSE WITH JOY 39
Implementing model version control in the FAIRDOMHub Internal use of BIVES difference detection for SBML models DAGMAR WALTEMATH | MODEL REUSE WITH JOY 407/4/2019
Change statistics for model versions Internal use of BIVES difference detection for SBML and CellML models, Change ontology COMODI, SBGN Visualisation tool DiViL; https://most.bio.informatik.uni-rostock.de, Scharm et al (2018), BMC SysBio (https://doi.org/10.1186/s12918-018-0553-2) DAGMAR WALTEMATH | MODEL REUSE WITH JOY 41 BIOM7 7/4/2019
Change statistics for model versions Internal use of BIVES difference detection for SBML and CellML models, Change ontology COMODI, SBGN Visualisation tool DiViL; https://most.bio.informatik.uni-rostock.de, Scharm et al (2018), BMC SysBio (https://doi.org/10.1186/s12918-018-0553-2) DAGMAR WALTEMATH | MODEL REUSE WITH JOY 42 BIOM7 7/4/2019
Change statistics for model versions Internal use of BIVES difference detection for SBML and CellML models, Change ontology COMODI, SBGN Visualisation tool DiViL; https://most.bio.informatik.uni-rostock.de, Scharm et al (2018), BMC SysBio (https://doi.org/10.1186/s12918-018-0553-2) DAGMAR WALTEMATH | MODEL REUSE WITH JOY 43 BIOM7 7/4/2019
Ranked retrieval of reproducible simulation studies Internal use of the COMBINEArchive-library, MORRE, MASYMOS, http://cellml.org/models Internal use of the COMBINEArchive library, SEDMLlibrary, https://jjj.biochem.sun.ac.za/ DAGMAR WALTEMATH | MODEL REUSE WITH JOY 447/4/2019
…we can help you manage it, so it can be retrieved and reused by others. If your work is standardised, documented, and open DAGMAR WALTEMATH | MODEL REUSE WITH JOY 45
Summary DAGMAR WALTEMATH | MODEL REUSE WITH JOY 46
Standardisation and integration of data improved model accessibility and reusability. COPPIC FOREST (DECORTICATED) Matlab logo: By Jarekt (Own work) [Public domain], via Wikimedia Commons; Python logo: By www.python.org [GPL, via Wikimedia Commons]; Java logo: By Cguevara94 (Own work) [CC BY-SA 4.0], via Wikimedia Commons, modified. DAGMAR WALTEMATH | MODEL REUSE WITH JOY 47 PATH (ACCESSIBLE) 7/4/2019
Biological data is well-integrated with simulation models, but biomedical/clinical data lacks behind. DAGMAR WALTEMATH | MODEL REUSE WITH JOY 48
Thank you for your attention Dagmar Waltemath University Medicine Greifswald @dagmarwaltemath 0000-0002-5886-5563 Contact me to adopt a SEMS – work in Greifswald or clone a github repository!

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2019 07-04-model reuse-bonn

  • 1. from paper-based model description to interactive simulation of disease progression PROF. DR.-ING. DIPL.-INF. DAGMAR WALTEMATH MEDICAL INFORMATICS | INSTITUTE FOR COMMUNITY MEDICINE UNIVERSITY MEDICINE GREIFSWALD (GERMANY) MODELREUSEWITHJOY
  • 2. About me SEMS@University of Rostock, Germany (2015) 7/4/2019 DAGMAR WALTEMATH | MODEL REUSE WITH JOY 2 Projects. SEMS | de.NBI:SYSBIO | SBGN-ED+ | INCOME | MIRACUM Community work. Standard development | COMBINE coordinator | SED-ML editor Research interests. Data integration | Semantics | Reproducibility of scientific results | Sustainability of scientific outcomes Further interests. Education of young scientists | Open Access & open data | Gender equality in science @dagmarwaltemath 0000-0002-5886-5563
  • 3. How this talk is organised THE HISTORY THE SCIENCE Disclaimer: All comic-style graphics in this presentation were done either by Anna Zhukova or by Martin Peters. Thank you very much! Images downloaded from pixabay. DAGMAR WALTEMATH | MODEL REUSE WITH JOY 37/4/2019
  • 4. Systems Biology is… Systems biology is the science that studies how biological function emerges from the interactions between the components of living systems. … and how these emergent properties enable or constrain the behavior of these components. (Slide adapted from: Olaf Wolkenhauer) DAGMAR WALTEMATH | MODEL REUSE WITH JOY 47/4/2019
  • 5. Simulation models can take many forms. MATHEMATICAL MODELS FURTHER APPROACHES Fig.s: https://doi.org/10.1371/journal.pcbi.1002815, https://doi.org/10.1371/journal.pcbi.1004591 DAGMAR WALTEMATH | MODEL REUSE WITH JOY 57/4/2019
  • 6. Simulation models can be complex. First in silico Whole Cell Model Genome (525 genes), transcriptome, proteome and metabolome incorporated Describes whole life cycle of a single cell on molecular level, and predicts a wide range of cellular behaviors, and accounts for the specific function of every annotated gene product  Based on 900 publications Consists of 116 MATLAB files Incorporates over 1.900 experimentally observed parameters WHOLE-CELL MODEL KEY FIGURES Fig.: Karr et al. (2012), https://doi.org/10.1016/j.cell.2012.05.044 DAGMAR WALTEMATH | MODEL REUSE WITH JOY 67/4/2019
  • 7. Early simulation models Tyson‘s Cell Cycle Model (1991) (BIOM5 und BIOM6) history
  • 8. Publishing the model PAPER AVAILABLE INFORMATION 1) (textual) description of work and related efforts (referencing other papers) 2) (textual and visual) description of (biochemical) network 3) (printed) model parameters 4) (printed) mathematical equations 5) resulting plots DAGMAR WALTEMATH | MODEL REUSE WITH JOY 8 Fig.: http://doi.org/10.1073/pnas.88.16.7328 7/4/2019
  • 9. What can you do with this model? STUDY THE PAPER, BELIEVE RE-IMPLEMENT BASED ON THE PAPER DAGMAR WALTEMATH | MODEL REUSE WITH JOY 97/4/2019
  • 10. The year 2000 Novak‘s Cell Cycle model (1997) (BIOM7) history
  • 11. Publishing the model PAPER AVAILABLE INFORMATION 1) (textual) description of work and related efforts (referencing other papers) 2) (textual and visual) description of (biochemical) network 3) (printed) model parameters 4) (printed) mathematical equations 5) resulting plots DAGMAR WALTEMATH | MODEL REUSE WITH JOY 11 Fig.: http://doi.org/10.1073/pnas.94.17.9147 7/4/2019
  • 12. Publishing the model code SIMULATION MODEL AVAILABLE INFORMATION 1) Description of (biochemical) network in computer-readable format (SBML) 2) Mathematical equations in computer- readable format (MathML) 3) Model parameters inside model code DAGMAR WALTEMATH | MODEL REUSE WITH JOY 127/4/2019
  • 13. What can you do with this data? CHECK THE MODEL (REPRODUCIBILITY) RE-USE THE CODE IN ANOTHER SOFTWARE (INTEROPERABILITY) Fig. (left) JWS Online, http://jjj.mib.ac.uk/models. Fig. (right) courtesy M.Hucka (2016), https://www.slideshare.net/thehuck/recent-software-and-services-to-support-the-sbml-community DAGMAR WALTEMATH | MODEL REUSE WITH JOY 137/4/2019
  • 14. State-of-the-art (in theory) Calzone‘s Cell Cycle model (BIOM144) history
  • 15. Publishing the model & code PAPER SIMULATION MODEL DAGMAR WALTEMATH | MODEL REUSE WITH JOY 15 Fig.: https://doi.org/10.1038/msb4100171 7/4/2019
  • 16. Publishing the meta-data on repository – model – and entity level DAGMAR WALTEMATH | MODEL REUSE WITH JOY 16 Harmonised meta-data for simulation models in computational biology: Neal et al. (2018), Briefings in Bioinformatics (https://doi.org/10.1093/bib/bby087) 7/4/2019
  • 17. Publishing the simulation setups COMBINE ARCHIVE manifest.xml Omex Skeleton, automatically generated by WebCAT metadata.rdf Omex Skeleton, automatically generated by WebCAT README.md Markdown Human readable information for users stumbling upon the archive model/ BIOMD0000000144.xml SBML L2V1 origin: www.ebi.ac.uk/biomodels-main/download?mid=BIOMD0000000144 calzone_2007.svg SVG origin: models.cellml.org/workspace/calzone_thieffry_tyson_novak_2007 calzone_2007.ai Illustrator origin: models.cellml.org/workspace/calzone_thieffry_tyson_novak_2007 calzone_2007.png PNG origin: models.cellml.org/workspace/calzone_thieffry_tyson_novak_2007 calzone_thieffry_tyson_novak_2007.cellml CellML 1.0 origin: models.cellml.org/workspace/calzone_thieffry_tyson_novak_2007 sbgn/Calzone2007.gml GML SBGN compliant figure generated using SBGN-ED sbgn/Calzone2007.graphml GraphML SBGN compliant figure generated using SBGN-ED sbgn/Calzone2007.pdf PDF SBGN compliant figure generated using SBGN-ED sbgn/Calzone2007.png PNG SBGN compliant figure generated using SBGN-ED sbgn/Calzone2007.sbgn SBGN-ML SBGN-ML encoded figure generated using SBGN-ED experiment/ Calzone2007-default-simulation.xml SED-ML L1V1 Simulation description generated using SED-ML Web Tools Calzone2007-simulation-figure-1B.xml SED-ML L1V1 Simulation description generated using SED-ML Web Tools based on Calzone2007-default-simulation.xml documentation/ Calzone2007.pdf PDF Scientific publication “Dynamical modeling of syncytial mitotic cycles in Drosophila embryos”obtained from msb.embopress.org/content/3/1/131 Calzone2007-supplementary-material.pdf PDF Supplementary information for the publication obtained from msb.embopress.org/content/3/1/131 result/ Fig1B-bottom-COPASI.svg SVG Imagegenerated by executing Calzone2007-simulation-figure-1B.xml on BIOMD0000000144.xml in COPASI Fig1B-top-COPASI.svg SVG Imagegenerated by executing Calzone2007-simulation-figure-1B.xml on BIOMD0000000144.xml in COPASI Fig1B-bottom-webtools.png PNG Imagegenerated by executing Calzone2007-simulation-figure-1B.xml on BIOMD0000000144.xml in SED-ML Web Tools Fig1B-top-webtools.png PNG Imagegenerated by executing Calzone2007-simulation-figure-1B.xml on BIOMD0000000144.xml in SED-ML Web Tools AVAILABLE INFORMATION 1) Paper and additional information 2) Meta-data 3) Graphical representation of model (SBGN) 4) Alternative parametrisations (SED-ML) 5) Model versions 6) Simulation experiments (SED-ML) Example archive available from: https://github.com/SemsProject/CombineArchiveShowCase/ DAGMAR WALTEMATH | MODEL REUSE WITH JOY 177/4/2019
  • 18. What can you do with an archive? Explore data and meta-data Identify Data set of interest Run model Online/ offline Safe new versions and documentation in archive Modify, merge, extend, combine... Re-publish DAGMAR WALTEMATH | MODEL REUSE WITH JOY 18 Download Archive 7/4/2019
  • 19. What can you do with an archive? Example: Download archive from Github and run it in JWS Online DAGMAR WALTEMATH | MODEL REUSE WITH JOY 197/4/2019
  • 20. What does the (near) future bring? DAGMAR WALTEMATH | MODEL REUSE WITH JOY 207/4/2019
  • 21. Linking models and data simplifies verification of models, and experimental data sets. DAGMAR WALTEMATH | MODEL REUSE WITH JOY 21 Integrating Disease maps and Biomedical data (e.g., https://pdmap.uni.lu/minerva/) Linking models and experimental data sets (e.g., JWS Online) 7/4/2019
  • 22. Connecting pathways, ontologies and datasets leads to new means of data exploration. DAGMAR WALTEMATH | MODEL REUSE WITH JOY 22 Comprehensive knowledge of cancer signaling networks and linked data, working with interactive Pathway Maps, https://acsn.curie.fr/ACSN2/ACSN2.html 7/4/2019
  • 23. Easy access to patient-specific liver disease progression helps doctors choose a therapy. DAGMAR WALTEMATH | MODEL REUSE WITH JOY 23 Fig.: Koenig et al. (2016), ODLS, Halle (Saale), http://livermetabolism.com 7/4/2019
  • 24. The pillars of success WHAT‘S THE SECRET? DAGMAR WALTEMATH | MODEL REUSE WITH JOY 247/4/2019
  • 25. The research field develops and adheres to FAIR standards for modeling and simulation. Data formatsRecommendations Semantic / Ontologies DAGMAR WALTEMATH | MODEL REUSE WITH JOY 257/4/2019
  • 26. Data formats are interoperable and are being developed collaboratively. Editorial Boards Specifications Software tool support http://co.mbine.org/standards Standard development Meetings Annual special issue with list of latest specifications and errata DAGMAR WALTEMATH | MODEL REUSE WITH JOY 267/4/2019
  • 27. The community builds, feeds & uses open repositories for simulation studies. DAGMAR WALTEMATH | MODEL REUSE WITH JOY 277/4/2019
  • 28. The community actively develops open, standard-compliant libraries & tools. MODELING AND SIMULATION SOFTWARE REPOSITORIES & MANAGEMENT TOOLS … Full list available at: http://sbml.org/SBML_Software_Guide/ DAGMAR WALTEMATH | MODEL REUSE WITH JOY 287/4/2019
  • 29. The (data) Science DEVELOPMENT OF MODEL MANAGEMENT STRATEGIES BY SEMS & FRIENDS (2011-2019) DAGMAR WALTEMATH | MODEL REUSE WITH JOY 29
  • 30. Characteristics of the data Heterogeneous Big Distributed Complex Highly connected But Good standards available to represent the data Agreed-upon semantic annotation schemes & ontologies to enrich the data Open data movement Community spirit DAGMAR WALTEMATH | MODEL REUSE WITH JOY 307/4/2019
  • 31. Issues that SEMS investigated 2012-17 Handling the steadily increasing size & numbers of models and studies (database performance) Increasing the quality of published models (semantic annotations, reproducibility of results) Keeping track of model changes and relations (comprehensibility) Identifying and handling similarities in model representations (reuse) DAGMAR WALTEMATH | MODEL REUSE WITH JOY 31 ~ 300.000 models in BioModels Database, on average 5 versions per model. XML, RDF, OWL 7/4/2019
  • 32. A graph-based approach keeps storage and retrieval efficient. DAGMAR WALTEMATH | MODEL REUSE WITH JOY 32 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 Document Tyson1991 Cell Cycle 6 var C2 pM CellReaction3 CP Uniprot:P04551 Uniprot:P04551 GO:0005623 Interpro: IPR006670isVersionOf isVersion hasPart is asProduct asReactant isContainedIn Pubmed: 1831270 Kegg Pathway sce04111 isDescribedBy is EC-Code: 3.1.3.16 isVersionOf Example: Tyson 1991 (BIOM5), Source: Waltemath & Henkel, Neo4j Life & Health Sciences Day - Berlin, 21st June, 2017, adapted from Henkel et al. (2015) DATABASE (https://doi.org/10.1093/database/bau130) SBO: Ontology SBO:0000 SBO:544 SBO:236SBO:231 isA SBO:064 SBO:545SBO:004 SBO:003 Models Simulation Annotation 7/4/2019
  • 33. The linking of data sets on graph-level allows for complex queries. DAGMAR WALTEMATH | MODEL REUSE WITH JOY 33 2 experiments, 3 model versions, changes, meta-data Fig.: Martin Peters, SEMS Fig (right): Henkel et al. (2015) DATABASE, https://doi.org/10.1093/database/bau130 7/4/2019
  • 34. Lucene-based indices incorporate all relevant information for later search & comparison. DAGMAR WALTEMATH | MODEL REUSE WITH JOY 34 Model Publication Annotation Person Simulation 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 • Id • Name • Title • Journal • Abstract • Authors • … • Id • Name • Component • Variable • Species • Reaction • Compartment • First name • Last name • Organization • Email • URI • Description Fig.: Henkel et al. (2015) DATABASE 7/4/2019
  • 35. A weighted ranked-retrieval methods returns only most relevant models. DAGMAR WALTEMATH | MODEL REUSE WITH JOY 35 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 Annotation Person Show me models by Tyson describing the cell cycle and having cdc2 1. (0.859) Tyson1991 - Cell Cycle 6 var 2. (0.854) Tyson2001_Cell_Cycle_Regulation 3. (0.477) Chen2004 - Cell Cycle Regulation Which are the most frequently used GO annotations in my model set? Which models contain reactions with 'ATP' as reactant and 'ADP' as product? Find good candidates for features describing my model set. Which models are annotated with ‘Ubiquitin'’? Give me all the files I need to run this simulation study. Fig.: Henkel et al. (2015) DATABASE 7/4/2019
  • 36. A method to detect and track differences in model versions ensures transparency. How did my model change between version x and X+1? DAGMAR WALTEMATH | MODEL REUSE WITH JOY 36 „Sophisticated“ XYDIFF & change ontology How often did this model change, when and wy?Give me all versions of this model.Figs.: Waltemath et al. (2015) Oxford Bioinformatics (https://doi.org/10.1093/bioinformatics/btt018); Implementation: M. Scharm, https://github.com/SemsProject/BiVeS 7/4/2019
  • 37. Identification of frequent pattern in network graphs helps determine structural similarity. DAGMAR WALTEMATH | MODEL REUSE WITH JOY 37 Fig.: Size and number of reactions and participating species (left), and identified frequent patterns (right). Implementation: Fabienne Lambusch. Figure: Lambusch et al. (2018) DATABASE (https://doi.org/10.1093/database/bay051) 7/4/2019
  • 38. Identification of frequent pattern in network graphs helps determine structural similarity. DAGMAR WALTEMATH | MODEL REUSE WITH JOY 38 Fig.: Tyson BIOM5 (left), and identified patterns based on the (right). Implementation: Fabienne Lambusch. Figure: Lambusch et al. (2018) DATABASE (https://doi.org/10.1093/database/bay051) How similar are these two models with respect to structure? Give me all models with this particular sub-structure. 7/4/2019
  • 39. Example applications MODEL RETRIEVAL | MODEL VERSION CONTROL & PROVENANCE | DAGMAR WALTEMATH | MODEL REUSE WITH JOY 39
  • 40. Implementing model version control in the FAIRDOMHub Internal use of BIVES difference detection for SBML models DAGMAR WALTEMATH | MODEL REUSE WITH JOY 407/4/2019
  • 41. Change statistics for model versions Internal use of BIVES difference detection for SBML and CellML models, Change ontology COMODI, SBGN Visualisation tool DiViL; https://most.bio.informatik.uni-rostock.de, Scharm et al (2018), BMC SysBio (https://doi.org/10.1186/s12918-018-0553-2) DAGMAR WALTEMATH | MODEL REUSE WITH JOY 41 BIOM7 7/4/2019
  • 42. Change statistics for model versions Internal use of BIVES difference detection for SBML and CellML models, Change ontology COMODI, SBGN Visualisation tool DiViL; https://most.bio.informatik.uni-rostock.de, Scharm et al (2018), BMC SysBio (https://doi.org/10.1186/s12918-018-0553-2) DAGMAR WALTEMATH | MODEL REUSE WITH JOY 42 BIOM7 7/4/2019
  • 43. Change statistics for model versions Internal use of BIVES difference detection for SBML and CellML models, Change ontology COMODI, SBGN Visualisation tool DiViL; https://most.bio.informatik.uni-rostock.de, Scharm et al (2018), BMC SysBio (https://doi.org/10.1186/s12918-018-0553-2) DAGMAR WALTEMATH | MODEL REUSE WITH JOY 43 BIOM7 7/4/2019
  • 44. Ranked retrieval of reproducible simulation studies Internal use of the COMBINEArchive-library, MORRE, MASYMOS, http://cellml.org/models Internal use of the COMBINEArchive library, SEDMLlibrary, https://jjj.biochem.sun.ac.za/ DAGMAR WALTEMATH | MODEL REUSE WITH JOY 447/4/2019
  • 45. …we can help you manage it, so it can be retrieved and reused by others. If your work is standardised, documented, and open DAGMAR WALTEMATH | MODEL REUSE WITH JOY 45
  • 46. Summary DAGMAR WALTEMATH | MODEL REUSE WITH JOY 46
  • 47. Standardisation and integration of data improved model accessibility and reusability. COPPIC FOREST (DECORTICATED) Matlab logo: By Jarekt (Own work) [Public domain], via Wikimedia Commons; Python logo: By www.python.org [GPL, via Wikimedia Commons]; Java logo: By Cguevara94 (Own work) [CC BY-SA 4.0], via Wikimedia Commons, modified. DAGMAR WALTEMATH | MODEL REUSE WITH JOY 47 PATH (ACCESSIBLE) 7/4/2019
  • 48. Biological data is well-integrated with simulation models, but biomedical/clinical data lacks behind. DAGMAR WALTEMATH | MODEL REUSE WITH JOY 48
  • 49. Thank you for your attention Dagmar Waltemath University Medicine Greifswald @dagmarwaltemath 0000-0002-5886-5563 Contact me to adopt a SEMS – work in Greifswald or clone a github repository!