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Retrospective about SBML on the occasion of the 10th Anniversary of SBML
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Retrospective about SBML on the occasion of the 10th Anniversary of SBML

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Slides from presentation given at the SBML 10th Anniversary symposium in Edingburgh, UK, October 9, 2010.

Slides from presentation given at the SBML 10th Anniversary symposium in Edingburgh, UK, October 9, 2010.

Published in: Technology, Education

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  • 1. In the beginning...Saturday, July 7, 12 1
  • 2. Saturday, July 7, 12 2
  • 3. Saturday, July 7, 12 3
  • 4. DR. KITANO DR. DOYLE BIOLOGYSaturday, July 7, 12 4
  • 5. Saturday, July 7, 12 5
  • 6. Saturday, July 7, 12 6
  • 7. Bolouri. Hamid Bolouri.Saturday, July 7, 12 6
  • 8. Mike Herbert AndrewSaturday, July 7, 12 7
  • 9. 0 00 2 The ERATO Systems Biology Workbench C SB I Hamid Bolouri ERATO Kitano Systems Biology Project California Institute of Technology & University of Hertfordshire, UK Project PIs: Hiroaki Kitano and John Doyle Software development team: Andrew Finney, Michael Hucka, Herbert Sauro Collaborators: Adam Arkin (BioSpice), Dennis Bray (StochSim), Igor Goryanin (DBsolve), Les Loew (VirtualCell), Pedro Mendes (Gepasi), Masaru Tomita (Ecell) Acknowledgements: Mark Borisuk, Eric Mjolsness, Tau-Mu YiSaturday, July 7, 12 8
  • 10. 0 00 2 The ERATO Systems Biology Workbench C SB I Hamid Bolouri ERATO Kitano Systems Biology Project California Institute of Technology & University of Hertfordshire, UK Project PIs: Hiroaki Kitano and John Doyle Software development team: Shortly after, also Andrew Finney, Michael Hucka, Herbert Sauro CellML & ProMoT/DIVA Collaborators: Adam Arkin (BioSpice), Dennis Bray (StochSim), Igor Goryanin (DBsolve), Les Loew (VirtualCell), Pedro Mendes (Gepasi), Masaru Tomita (Ecell) Acknowledgements: Mark Borisuk, Eric Mjolsness, Tau-Mu YiSaturday, July 7, 12 8
  • 11. ERATO Systems Biology Workbench: driving principles • Integrate, don’t reinvent! – integrate existing simulators – use standard application integration methods • object oriented, XML, Java and related technologies • Accommodate future tools – minimize need for ad hoc solutions • object oriented, XML, Java and related technologies – XML & API standards for future contributors • Make sure contributors benefit – symmetric plug-in infrastructure – open source code infrastructure software – widen user-base, but protect IPR of contributorsSaturday, July 7, 12 9
  • 12. Saturday, July 7, 12 10
  • 13. The ensuing years...Saturday, July 7, 12 11
  • 14. Jarnac SBedit (CellDesigner) JDesigner GepasiSaturday, July 7, 12 12
  • 15. LibSBML ๏ Reads, writes, validates SBML Original version 1.0.0 released Mar. 2003 ๏ Unit checking & conversion ๏ Written in portable C++ • Linux, Mac, Windows, FreeBSD Latest stable version: 4.2.0 ๏ C, C++, C#, Java, Octave, Perl, released Oct. 2010 Python, Ruby, MATLAB ๏ Can use Expat, libxml2, or Xerces Latest dev. version: 5.0.0-a1 released Oct. 2010 ๏ Open-source (LGPL) ๏ http://sbml.org/Software/libSBMLSaturday, July 7, 12 13
  • 16. SBMLSaturday, July 7, 12 14
  • 17. Akira Funahashi Ben Bornstein Sarah Keating Bruce Shapiro Akija JourakuSaturday, July 7, 12 15
  • 18. Nicolas Le NovèreSaturday, July 7, 12 16
  • 19. SBML Editors, past and present Andrew Finney Herbert Sauro Hamid Bolouri Nicolas Le Novère Sarah Keating Stefan Hoops Frank Bergmann Sven Sahle Jim Schaff Lucian Smith Darren Wilkinson Mike Hucka (chair)Saturday, July 7, 12 17
  • 20. Where are we today?Saturday, July 7, 12 18
  • 21. Where are we today? (or, what have you done?)Saturday, July 7, 12 18
  • 22. Where are we today? (or, what have you done?) (or, my God, what have you done?!)Saturday, July 7, 12 18
  • 23. Workshops to date: 27 Apr. 2000 First general workshop Pasadena, California, US Nov. 2000 Second general workshop Tokyo, Japan Jun. 2001 Third general workshop Pasadena, California, US Dec. 2001 Fourth general workshop Pasadena, California, US Jul. 2002 Fifth general workshop U. Hertfordshire, UK Dec. 2002 Sixth SBML Forum meeting Stockholm, Sweden May 2003 Seventh SBML Forum meeting Ft. Lauderdale, Florida, US Jul. 2003 First SBML Hackathon Blacksburg, Virginia, US Nov. 2003 Eight SBML Forum meeting St. Louis, Missouri, US Apr. 2004 Second SBML Hackathon Cambridge, UK Oct. 2004 Ninth SBML Forum meeting Heidelberg, Germany May 2005 Third SBML Hackathon Tokyo, Japan Oct. 2005 Tenth SBML Forum meeting Boston, Massachusetts, US Apr. 2006 Fourth SBML Hackathon Nové Hrady, Czech Republic Oct. 2006 Eleventh SBML Forum meeting Tokyo, Japan Jun. 2007 Fifth SBML Hackathon Newcastle, UK Sep. 2007 SBML Composition Workshop U. Connecticut, Connecticut, US Oct. 2007 Twelfth SBML Forum meeting Long Beach, California, US Dec. 2007 SBML Multi* Workshop Cambridge, UK Apr. 2008 Sixth SBML Hackathon Stellenbosch, South Africa Aug. 2008 SBML Alt. Modeling Frameworks Cambridge, UK Aug. 2008 Thirteenth SBML Forum meeting Göteborg, Sweden Mar. 2009 Seventh SBML Hackathon Cambridge, UK May 2010 SBML-NeuroML Interfacing Cambridge, UK May 2010 SBML Annotations Pkg Workshop Cambridge, UK May 2010 BioModels.net-SBML Hackathon U. Washington, Washington, US Oct. 2011 COMBINE 2010 Edinburgh, UKSaturday, July 7, 12 19
  • 24. Workshops to date: 27 Apr. 2000 First general workshop Pasadena, California, US Nov. 2000 Second general workshop Tokyo, Japan Jun. 2001 Third general workshop Pasadena, California, US Dec. 2001 Fourth general workshop Pasadena, California, US Jul. 2002 Fifth general workshop U. Hertfordshire, UK Dec. 2002 Sixth SBML Forum meeting Stockholm, Sweden May 2003 Seventh SBML Forum meeting Ft. Lauderdale, Florida, US Jul. 2003 First SBML Hackathon Blacksburg, Virginia, US Nov. 2003 Eight SBML Forum meeting St. Louis, Missouri, US Apr. 2004 Second SBML Hackathon Cambridge, UK Oct. 2004 Ninth SBML Forum meeting Heidelberg, Germany May 2005 Third SBML Hackathon Tokyo, Japan Oct. 2005 Tenth SBML Forum meeting Boston, Massachusetts, US Apr. 2006 Fourth SBML Hackathon Nové Hrady, Czech Republic Oct. 2006 Eleventh SBML Forum meeting Tokyo, Japan Jun. 2007 Fifth SBML Hackathon Newcastle, UK Sep. 2007 SBML Composition Workshop U. Connecticut, Connecticut, US Oct. 2007 Twelfth SBML Forum meeting Long Beach, California, US Dec. 2007 SBML Multi* Workshop Cambridge, UK Apr. 2008 Sixth SBML Hackathon Stellenbosch, South Africa Aug. 2008 SBML Alt. Modeling Frameworks Cambridge, UK Aug. 2008 Thirteenth SBML Forum meeting Göteborg, Sweden Mar. 2009 Seventh SBML Hackathon Cambridge, UK May 2010 SBML-NeuroML Interfacing Cambridge, UK May 2010 SBML Annotations Pkg Workshop Cambridge, UK May 2010 BioModels.net-SBML Hackathon U. Washington, Washington, US Oct. 2011 COMBINE 2010 Edinburgh, UKSaturday, July 7, 12 19
  • 25. Known software today: over 200 200 150 100 50 0 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 Count as of October 8: 201Saturday, July 7, 12 20
  • 26. Paper citations to date: 570 Citations to the original 2003 paper about SBML: ISI Web of Science: 570 Google Scholar: 1390Saturday, July 7, 12 21
  • 27. Real uses of SBML PERSPECTIVE Consensus yeast metabolic network model A consensus yeast metabolic network reconstruction © 2008 Nature Publishing Group http://www.nature.com/naturebiotechnology obtained from a community approach to systems biology Markus J Herrgård1,19,20, Neil Swainston2,3,20, Paul Dobson3,4, Warwick B Dunn3,4, K Yalçin Arga5, Mikko Arvas6, Nils Blüthgen3,7, Simon Borger8, Roeland Costenoble9, Matthias Heinemann9, Michael Hucka10, Nicolas Le Novère11, Peter Li2,3, Wolfram Liebermeister8, Monica L Mo1, Ana Paula Oliveira12, Dina Petranovic12,19, Stephen Pettifer2,3, Evangelos Simeonidis3,7, Kieran Smallbone3,13, Irena Spasić2,3, Dieter Weichart3,4, 2342 reactions Roger Brent14, David S Broomhead3,13, Hans V Westerhoff 3,7,15, Betül Kırdar5, Merja Penttilä6, Edda Klipp8, Bernhard Ø Palsson1, Uwe Sauer9, Stephen G Oliver3,16, Pedro Mendes2,3,17, Jens Nielsen12,18 & Douglas B Kell*3,4 Genomic data allow the large-scale manual or semi-automated of their parameters. Armed with such information, it is then possible to assembly of metabolic network reconstructions, which provide provide a stochastic or ordinary differential equation model of the entire 2657 chemical species highly curated organism-specific knowledge bases. Although metabolic network of interest. An attractive feature of metabolism, for the several genome-scale network reconstructions describe purposes of modeling, is that, in contrast to signaling pathways, metabo- Saccharomyces cerevisiae metabolism, they differ in scope lism is subject to direct thermodynamic and (in particular) stoichiometric and content, and use different terminologies to describe the constraints3. Our focus here is on the first two stages of the reconstruction same chemical entities. This makes comparisons between them process, especially as it pertains to the mapping of experimental metabo- difficult and underscores the desirability of a consolidated lomics data onto metabolic network reconstructions. metabolic network that collects and formalizes the ‘community Besides being an industrial workhorse for a variety of biotechnological knowledge’ of yeast metabolism. We describe how we have products, S. cerevisiae is a highly developed model organism for biochemi- produced a consensus metabolic network reconstruction cal, genetic, pharmacological and post-genomic studies5. It is especially for S. cerevisiae. In drafting it, we placed special emphasis attractive because of the availability of its genome sequence6, a whole series on referencing molecules to persistent databases or using of bar-coded deletion7,8 and other9 strains, extensive experimental ’omics database-independent forms, such as SMILES or InChI strings, data10–14 and the ability to grow it for extended periods under highly con- as this permits their chemical structure to be represented trolled conditions15. The very active scientific community that works on unambiguously and in a manner that permits automated S. cerevisiae has a history of collaborative research projects that have led to reasoning. The reconstruction is readily available via a publicly substantial advances in our understanding of eukaryotic biology6,8,13,16,17. accessible database and in the Systems Biology Markup Furthermore, yeast metabolic physiology has been the subject of inten- Language (http://www.comp-sys-bio.org/yeastnet). It can be sive study and most of the components of the yeast metabolic network maintained as a resource that serves as a common denominator are relatively well characterized. Taken together, these factors make yeast for studying the systems biology of yeast. Similar strategies metabolism an attractive topic to test a community approach to build should benefit communities studying genome-scale metabolic models for systems biology. networks of other organisms. Several groups18–21 have reconstructed the metabolic network of yeast from genomic and literature data and made the reconstructions freely Accurate representation of biochemical, metabolic and signaling net- available. However, due to different approaches used to create them, as works by mathematical models is a central goal of integrative systems well as different interpretations of the literature, the existing reconstruc- biology. This undertaking can be divided into four stages1. The first is tions have many differences. Additionally, the naming of metabolites and a qualitative stage in which are listed all the reactions that are known enzymes in the existing reconstructions was, at best, inconsistent, and to occur in the system or organism of interest; in the modern era, and there were no systematic annotations of the chemical species in the form especially for metabolic networks, these reaction lists are often derived of links to external databases that store chemical compound informa- in part from genomic annotations2,3 with curation based on literature tion. This lack of model annotation complicated the use of the models (‘bibliomic’) data4. A second stage, again qualitative, adds known effectors, for data analysis and integration. Members of the yeast systems biology whereas the third and fourth stages—essentially amounting to molecular community therefore recognized that a single ‘consensus’ reconstruction enzymology—include the known kinetic rate equations and the values and annotation of the metabolic network was highly desirable as a starting point for further investigations. *A list of affiliations appears at the end of the paper. A crucial factor that enabled the building of a consensus network recon- Published online 9 October 2008; doi:10.1038/nbt1492 struction is the ability to describe and exchange biochemical network Herrgård et al., Nature Biotech, 26:10, 2008 NATURE BIOTECHNOLOGY VOLUME 26 NUMBER 10 OCTOBER 2008 1155Saturday, July 7, 12 22
  • 28. Real uses of SBML RefRec: comprehensive yeast molecular interaction network reconstruction 30,965 reactions! 36,263 species! Aho et al., PLoS One. 2010 May 14;5(5):e10662.Saturday, July 7, 12 23
  • 29. Real uses of SBML Comparing and clustering models in semanticSBML (Slide from Wolfram Liebermeister)Saturday, July 7, 12 24
  • 30. SBRMLSaturday, July 7, 12 25
  • 31. SBRMLSaturday, July 7, 12 25
  • 32. SBRMLSaturday, July 7, 12 25
  • 33. SBRMLSaturday, July 7, 12 25
  • 34. SBRMLSaturday, July 7, 12 25
  • 35. SBRMLSaturday, July 7, 12 25
  • 36. SBRMLSaturday, July 7, 12 25
  • 37. SBRMLSaturday, July 7, 12 25
  • 38. SBRMLSaturday, July 7, 12 25
  • 39. SBRMLSaturday, July 7, 12 25
  • 40. Lessons learned, lessons lostSaturday, July 7, 12 26
  • 41. What worked and is portable to other efforts? ๏ Actual stakeholders with real needs • And make sure there’s more than one... ๏ Transparent and inclusive process • Critical to legitimacy ๏ Continue to engage people • Not getting responses? Find a new approach! ๏ Have independent organizers/shepherds/leaders • Avoid even the appearance of bias or agenda ๏ Give credit freely • “What goes around, comes around”Saturday, July 7, 12 27
  • 42. Lessons lost ๏ Over-dependence on one or small number of people • Bottleneck to progress • Fragile—whole effort at risk if they become unavailable, or difficult ๏ Inadequate balance between open process & making progress • Democratic, open processes move slowly • “Design by committee” is rarely good • But you have to do it ... ๏ Inadequate testing before releasing/freezing ๏ Not sorting out intellectual property issues early onSaturday, July 7, 12 28
  • 43. Where do we go from here?Saturday, July 7, 12 29
  • 44. Remember why we’re doing thisSaturday, July 7, 12 30
  • 45. We need to COMBINE our effortsSaturday, July 7, 12 31
  • 46. ... and that is up to you.Saturday, July 7, 12 32