Encoding neuronal models in SBML

Computational Systems Neurobiology

Volumn , Issue , 2012, Pages 459-488

  Keating, Sarah M ^a   Le Novère, Nicolas ^a  

^a EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER AIDED SOFTWARE ENGINEERING; ENCODING (SYMBOLS); MARKUP LANGUAGES; NEURONS;

COMPUTATIONAL MODEL; DE FACTO STANDARD; NEURONAL MODEL; STANDARD FORMAT; SYSTEMS BIOLOGY; SYSTEMS BIOLOGY MARKUP LANGUAGES;

SIGNAL ENCODING;

EID: 84902395300     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-94-007-3858-4_15     Document Type: Chapter

References (28)

1. Ausbrooks R, Buswell S, Carlisle D, Dalmas S, Devitt S, Diaz A, Froumentin M, Hunter R, Ion P, Kohlhase M, Miner R, Poppelier N, Smith B, Soiffer N, Sutor R, Watt S (2003) Mathematical Markup language (MathML) version 2.0, 2nd edn. Available via the World Wide Web at http://www. w3. org/TR/MathML2/
2. Bhalla US, Iyengar R (1999) Emergent properties of networks of biological signaling pathways. Science 283(5400):381-387
3. Bray T, Paoli J, Sperberg-McQueen CM, Maler E (2000) Extensible Markup Language (XML) 1.0, W3C recommendation 6-October-2000, 2nd edn. Available via the World Wide Web at http://www. w3. org/TR/1998/REC- xml-19980210
4. Cohen P (1992) Signal integration at the level of protein kinases, protein phosphatases and their substrates. Trends Biochem Sci 17(10):408-413
5. Curto R, Voit EO, Sorribas A, Cascante M (1998) Mathematical models of purine metabolism in man. Math Biosci 151(1): 1—49
6. Elowitz MB, Leibler S (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403(6767):335-338
7. Fernandez E, Schippa R, Girault J, Le Novere N (2006) DARPP-32 is a robust integrator of dopamine and glutamate signals. PLoS Comput Biol 2(12):e176
8. FitzHugh R (1961) Impulses and physiological states in theoretical models of nerve membrane. Biophys J 1:445-466
9. Gleeson P, Crook S, Cannon RC, Hines ML, Billings GO, Farinella M, Morse TM, Davison AR, Ray S, Bhalla UP, Barnes SR, Dimitrova YD, Silver RA (2010) NeuroML: A language for describing data driven models of neurons and networks with a high degree of biological detail. PLoS Comput Biol 6:e1000815 (in press)
10. Goldbeter A (1991) A minimal cascase model for the mitotic oscillator involving cyclin and cdc2 kinase. Proc Natl Acad Sci USA 88(20):9107-9111
11. Hedley W, Nelson MR, Bullivant DP, Nielsen PF (2001) A short introduction to CellML. Philos Trans R Soc Lond A 359(5):1073-1079
12. Hodgkin AL, Huxley AF (1952) A quantitative description of membrane current and its application to conduction and excitation in nerve. J Physiol 117(5):500-544
13. Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, Singhal M, Xu L, Mendes P, Kummer U (2006) COPASI-a COmplex PAthway Simulator. Bioinformatics 22(24):3067-3074
14. Hucka M, Finney A, Sauro HM, Bolouri H (2001) Systems Biology Markup Language (SBML) Level 1: structures and facilities for basic model definitions. Available via the World Wide Web at http://www.sbml.org/Documents/Specifications
15. Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novère N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J (2003) The Systems Biology Markup Language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19(4):524-531
16. Hucka M, Hoops S, Keating SM, Le Novere N, Sahle S, Wilkinson DJ (2008) Systems Biology Markup Language (SBML) Level 2: structures and facilities for model definitions. Available via the World Wide Web at http://www.sbml.org/Documents/Specifications
17. Hucka M, Bergmann F, Hoops S, Keating SM, Sahle S, Wilkinson DJ (2009) The Systems Biology Markup Language (SBML) Language specification for Level 3 Version 1 Core. Available via the World Wide Web at http://www.sbml.org/Documents/Specifications
18. Izhikevich EM (2004a) Simple model of spiking neurons. IEEE Trans Neural Netw 14(6): 1569— 1573
19. Izhikevich EM (2004b) Which model to use for cortical spiking neurons? IEEE Trans Neural Netw 15(5):1063-1070
20. Kell D, Mendes P (2008) The markup is the model: Reasoning about systems biology models in the semantic web era. J Theor Biol 252:538-543
21. Kohn D, Le Novere N (2008) SED-ML - an XML format for the implementation of the MIASE guidelines. In: Heiner M, Uhrmacher A (eds) Proceedings of the 6th conference on Computational Methods in Systems Biology, Rostock. Lecture Notes in Bioinformatics, vol 5307. Springer, Berlin/New York, pp 176-190
22. 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
23. Le Novere N, Courtot M, Laibe C (2007) Adding semantics in kinetics models of biochemical pathways. In: Proceedings of the 2nd international symposium on experimental standard conditions of enzyme characterizations, Rudesheim. Logos Verlag, Berlin, pp 137-153
24. Le Novere N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, Bergman FT, Gauges R, Ghazal P, Kawaji H, Li L, Matsuoka Y, Villeger A, Boyd SE, Calzone L, Courtot M, Dogrusoz U, Freeman TC, Funahashi A, Ghosh S, Jouraku A, Kim S, Kolpakov F, Luna A, Sahle S, Schmidt E, Watterson S, Wu G, Goryanin I, Kell DB, Sander C, Sauro H, Snoep JL, Kohn K, Kitano H (2009) The Systems Biology Graphical Notation. Nature biotechnol 27(8):735-741
25. Machne R, Finney A, Muller S, Lu J, Widder S, Flamm C (2006) The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks. Bioinformatics 22(11):1406-1407
26. Manola F, Miller E (2004) RDF primer. Tech. rep., W3C, URL http://www.w3.org/TR/2004/REC-rdf-primer-20040210/
27. Shapiro BE, Hucka M, Finney A, Doyle J (2004) MathSBML: a package for manipulating SBML-based biological models. Bioinformatics 20(16):2829-2831
28. Stromback L, Lambrix P (2005) Representations of molecular pathways: an evaluation of SBML, PSI ML and BioPAX. Bioinformatics 21(24):4401-4407s