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Design and Analysis of Biomolecular Circuits pp 281–293Cite as

Data Model Standardization for Synthetic Biomolecular Circuits and Systems

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Abstract

While biological engineers strive to capture the biophysical theory essential in predicting how a newly designed synthetic organism will behave, the current state of this knowledge is far from ideal. To facilitate the research towards this goal, specifically through the application of computational tools, the data required to engineer biological systems should be electronically accessible and interpretable. The challenge to represent such information computationally is complicated by the enormous diversity and size of biological data. There is a plethora of biological components, interacting physically and chemically, with implications for behavior at multiple time and spatial scales. The many scientists working to move the synthetic biology field forward have to communicate their research findings and should understand each other despite their diverse academic backgrounds. The challenge and demand for data standardization arises from the need to collaborate in order to engineer ever more complex biomolecular circuits and to understand and control biological systems. The bioinformatics field provides us with a history of experience in its attempts to facilitate collaboration in the biomedical research community. We draw on the lessons from the application of information technology solutions to inform and inspire the new efforts in synthetic biology. Furthermore, we acknowledge fundamental differences in the nature of the two fields and discuss the need to standardize data models for the purpose of engineering and design of novel biomolecular circuits and systems.

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References

  1. Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M (2004) UniProt: the universal protein knowledgebase. Nucleic Acids Res 32(suppl 1):D115

    Article  Google Scholar 

  2. Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, et al (2002) Standards for microarray data. Science 298:539

    Google Scholar 

  3. Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Marshall Ka, Phillippy KH, Sherman PM, Muertter RN, Edgar R (2009) NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res 37:D885–D890

    Article  Google Scholar 

  4. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL (2006) GenBank. Nucleic Acids Res 34:D16–D20

    Article  Google Scholar 

  5. Berman HM (2008) The Protein Data Bank: a historical perspective. Acta crystallogr A 64: 88–95

    Article  Google Scholar 

  6. Bornstein BJ, Keating SM, Jouraku A, Hucka M (2008) LibSBML: an API library for SBML. Bioinformatics 24:880–881

    Article  Google Scholar 

  7. Brazma A (2001) On the importance of standardisation in life sciences. Bioinformatics 17: 113–114

    Article  Google Scholar 

  8. Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 29:365–371

    Article  Google Scholar 

  9. Cai Y, Hartnett B, Gustafsson C, Peccoud J (2007) A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts. Bioinformatics 23(20):2760–2767

    Article  Google Scholar 

  10. Cai Y, Lux MW, Adam L, Peccoud J (2009) Modeling structure-function relationships in synthetic DNA sequences using attribute grammars. PLoS Comput Biol 5(10):e1000529

    Article  MathSciNet  Google Scholar 

  11. Cai Y, Wilson ML, Peccoud J (2010) GenoCAD for iGEM: a grammatical approach to the design of standard-compliant constructs. Nucleic Acids Res 38(8):2637–2644

    Article  Google Scholar 

  12. Canton B, Labno A, Endy D (2008) Refinement and standardization of synthetic biological parts and devices. Nat Biotechnol 26:787–793

    Article  Google Scholar 

  13. Chandran D, Bergmann FT, Sauro HM (2009) TinkerCell: modular CAD tool for synthetic biology. J Biol Eng 3(19)

    Google Scholar 

  14. Clancy K, Voigt CA (2010) Programming cells: towards an automated ‘Genetic Compiler’. Curr Opin Biotechnol 21(4):572–581

    Article  Google Scholar 

  15. Czar MJ, Cai Y, Peccoud J (2009) Writing DNA with GenoCAD. Nucleic Acids Res 37(suppl 2):W40–W47

    Article  Google Scholar 

  16. de Jong H (2002) Modeling and simulation of genetic regulatory systems: a literature review. J Comput Biol 9:67–103

    Article  Google Scholar 

  17. Densmore D, Van Devender A, Johnson M, Sritanyaratana N (2009) A platform-based design environment for synthetic biological systems. In: The fifth Richard Tapia celebration of diversity in computing conference: intellect, initiatives, insight, and innovations. ACM, pp 24–29

    Google Scholar 

  18. Edgar R, Domrachev M, Lash AE (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30:207–210

    Article  Google Scholar 

  19. Endy D (2005) Foundations for engineering biology. Nature 438:449–453

    Article  Google Scholar 

  20. Field D, Sansone S-A, Collis A, Booth T, Dukes P, Gregurick SK, Kennedy K, Kolar P, Kolker E, Maxon M, Millard S, Mugabushaka A-M, Perrin N, Remacle JE, Remington K, Rocca-Serra P, Taylor CF, Thorley M, Tiwari B, Wilbanks J (2009) OMICS: 2009, 2010, and beyond. OMICS 326:234–236

    Google Scholar 

  21. Galdzicki M, Chandran D, Nielsen A, Morrison J, Cowell M, Grunberg R, Sleight S, Sauro H (2009) BBF RFC 31: Provisional BioBrick Language (PoBoL). doi:1721.1/45537

    Google Scholar 

  22. Galdzicki M, Rodriguez C, Chandran D, Sauro HM, Gennari JH (2011) Standard biological parts knowledgebase. PLoS ONE 6(2):e17005

    Google Scholar 

  23. Grunberg R (2009) BBF RFC 30: Draft of an RDF-based framework for the exchange and integration of synthetic biology data. doi: 1721.1/45143

    Google Scholar 

  24. Hill AD, Tomshine JR, Weeding EMB, Sotiropoulos V, Kaznessis YN (2008) SynBioSS: the synthetic biology modeling suite. Bioinformatics 24(21):2551–2553

    Article  Google Scholar 

  25. Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, et al (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19:524

    Article  Google Scholar 

  26. Ikeo K, Ishi-i J, Tamura T, Gojobori T, Tateno Y (2003) CIBEX: center for information biology gene expression database. C R Biol 326:1079–82

    Article  Google Scholar 

  27. Kahn HJ (1995) EDIF version 350/400 and information modelling. In: Design automation conference, 1995. Proceedings of the ASP-DAC ’95/CHDL ’95/VLSI ’95, IFIP international conference on hardware description languages; IFIP international conference on very large scale integration, Asian and South Pacific

    Google Scholar 

  28. Kelly JR, Rubin AJ, Davis JH, Ajo-Franklin CM, Cumbers J, Czar MJ, de Mora K, Glieberman AL, Monie DD, Endy D (2009) Measuring the activity of BioBrick promoters using an in vivo reference standard. J Biol Eng 3:1–13

    Article  Google Scholar 

  29. Knight TF (2003) Idempotent vector design for standard assembly of BioBricks. Technical report, Massachusetts Institute of Technology Artificial Intelligence Lab, Cambridge, Massachusetts

    Google Scholar 

  30. Le Novere N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, et al (2009) The systems biology graphical notation. Nat Biotechnol 27(8):735–741

    Article  Google Scholar 

  31. Le Novere N, Bornstein B, Broicher A, Courtot M, Donizelli M, Dharuri H, Li L, Sauro H, Schilstra M, Shapiro B, Snoep JL, Hucka M (2006) BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res 34:D689–D691

    Article  Google Scholar 

  32. Le Novere N, Finney A, Hucka M, Bhalla US, Campagne F, Collado-Vides J, Crampin EJ, Halstead M, Klipp E, Mendes P, Nielsen P, Sauro H, Shapiro B, Snoep JL, Spence HD, Wanner BL (2005) Minimum information requested in the annotation of biochemical models (MIRIAM). Nat Biotechnol 23:1509–1515

    Article  Google Scholar 

  33. Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novere N, Laibe C (2010) Biomodels database: an enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol 4:92

    Article  Google Scholar 

  34. Lloyd CM, Halstead MDB, Nielsen PF (2004) CellML: its future, present and past. Prog Biophys Mol Biol 85:433–450

    Article  Google Scholar 

  35. Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M, Abeygunawardena N, Berube H, Dylag M, Emam I, Farne A, Holloway E, Lukk M, Malone J, Mani R, Pilicheva E, Rayner TF, Rezwan F, Sharma A, Williams E, Bradley XZ, Adamusiak T, Brandizi M, Burdett T, Coulson R, Krestyaninova M, Kurnosov P, Maguire E, Neogi SG, Rocca-Serra P, Sansone S-A, Sklyar N, Zhao M, Sarkans U, Brazma A (2009) ArrayExpress update–from an archive of functional genomics experiments to the atlas of gene expression. Nucleic Acids Res 37: D868–D872

    Article  Google Scholar 

  36. Peccoud J, Anderson JC, Chandran D, Densmore D, Galdzicki M, Lux MW, Rodriguez CA, Stan GB, Sauro HM (2011) Essential information for synthetic DNA sequences. Nat Biotechnol 29(1):22

    Article  Google Scholar 

  37. Peccoud J, Blauvelt MF, Cai Y, Cooper KL, Crasta O, DeLalla EC, Evans C, Folkerts O, Lyons BM, Mane SP, Shelton R, Sweede MA, Waldon SA (2008) Targeted development of registries of biological parts. PLoS ONE 3:7

    Article  Google Scholar 

  38. Sauro HM (2006) Standards, platforms, and applications. In: Kriete A, Eils R (ed) Computational systems biology. Elsevier Academic Press, Burlington, Massachusetts, p 103

    Chapter  Google Scholar 

  39. Searls DB (2010) The roots of bioinformatics. PLoS Comput Biol 6:e1000809

    Article  Google Scholar 

  40. Shetty RP, Endy D, Knight TF (2008) Engineering BioBrick vectors from BioBrick parts. J Biol Eng 2:5

    Article  Google Scholar 

  41. Swainston N, Mendes P (2009) libAnnotationSBML: a library for exploiting SBML annotations. Bioinformatics 25:2292–2293

    Article  Google Scholar 

  42. Tamames J, Valencia A (2006) The success (or not) of HUGO nomenclature. Genome Biol 7:402

    Article  Google Scholar 

  43. Weeding E, Houle J, Kaznessis YN (2010) Synbioss designer: a web-based tool for the automated generation of kinetic models for synthetic biological constructs. Brief Bioinform 11(4):394–402

    Article  Google Scholar 

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Acknowledgements

The data model standardization work was carried out in collaboration with members of the Synthetic Biology Data Exchange Group. We would like to especially thank Cesar A. Rodriguez, Laura Adam, J. Christopher Anderson, Douglas Densmore, Drew Endy, Raik Gruenberg, Timothy Ham, Matthew Lux, Akshay Maheshwari, Barry Moore, Chris J. Myers, Jean Peccoud, Cesar A. Rodriguez, Nicholas Roehner, Guy-Bart Stan, and Mandy Wilson for their ideas and support. This work was partially supported by grants from the National Library of Medicine (R41 LM010745, T15 LM007442), and the National Institute of Biomedical Imaging and Bioengineering (BE08407).

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Authors and Affiliations

  1. Department of Bioengineering, University of Washington, Seattle, Washington, USA

    Herbert M. Sauro

Authors
  1. Michal Galdzicki
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  2. Deepak Chandran
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  3. John H. Gennari
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  4. Herbert M. Sauro
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Corresponding author

Correspondence to Herbert M. Sauro .

Editor information

Editors and Affiliations

  1. , Automatic Control Laboratory, ETH Zurich, Physikstrasse 3, Zurich, 8092, Switzerland

    Heinz Koeppl

  2. ARCES, Università di Bologna, Via Toffano 2/2, Bologna, 40125, Italy

    Gianluca Setti

  3. Università di Napoli Federico II, Via Claudio 21, Napoli, 80125, Italy

    Mario di Bernardo

  4. , Department of Electrical and Computer En, Boston University, Saint Mary's St. 8, Boston, 02446, Massachusetts, USA

    Douglas Densmore

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Galdzicki, M., Chandran, D., Gennari, J.H., Sauro, H.M. (2011). Data Model Standardization for Synthetic Biomolecular Circuits and Systems. In: Koeppl, H., Setti, G., di Bernardo, M., Densmore, D. (eds) Design and Analysis of Biomolecular Circuits. Springer, New York, NY. https://doi.org/10.1007/978-1-4419-6766-4_13

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  • DOI: https://doi.org/10.1007/978-1-4419-6766-4_13

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