Modeling and simulation using cellDesigner

Methods in Molecular Biology

Volumn 1164, Issue , 2014, Pages 121-145

  Matsuoka, Yukiko ^a   Funahashi, Akira ^a   Ghosh, Samik ^a   Kitano, Hiroaki ^a  

^a NONE

Author keywords

CellDesigner; Garuda platform; SBGN (systems biology graphical notation); SBML (systems biology markup language); Transcription regulatory network

Indexed keywords

ARTICLE; COMPUTER INTERFACE; COMPUTER MODEL; COMPUTER PROGRAM; COMPUTER SIMULATION; GENE REGULATORY NETWORK; MATHEMATICAL MODEL; MOLECULAR DYNAMICS; PRIORITY JOURNAL; WORKFLOW; ANIMAL; BIOLOGICAL MODEL; HUMAN; SYSTEMS BIOLOGY; TRANSCRIPTION INITIATION;

ANIMALS; COMPUTER SIMULATION; GENE REGULATORY NETWORKS; HUMANS; MODELS, BIOLOGICAL; MODELS, GENETIC; SOFTWARE; SYSTEMS BIOLOGY; TRANSCRIPTIONAL ACTIVATION;

EID: 84922481872     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-0805-9_11     Document Type: Article

References (37)

1. Ghosh S, Matsuoka Y, Asai Y, Hsin K-Y, Kitano H (2011) Software for systems biology: from tools to integrated platforms. Nat Rev Genet 12(12):821–832, http://www.nature.com/nrg/journal/v1.2/n1.2/suppinfo/nrg3096_S1.html
2. Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D’Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, Kandasamy K, Lopez-Fuentes AC, Mi H, Pichler E, Rodchenkov I, Splendiani A, Tkachev S, Zucker J, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, Blinov M, Brauner E, Corwin D, Donaldson S, Gibbons F, Goldberg R, Hornbeck P, Luna A, Murray-Rust P, Neumann E, Ruebenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl- Carrillo M, Cheung KH, Dahlquist K, Finney A, Gillespie M, Glass E, Gong L, Haw R, Honig M, Hubaut O, Kane D, Krupa S, Kutmon M, Leonard J, Marks D, Merberg D, Petri V, Pico A, Ravenscroft D, Ren L, Shah N, Sunshine M, Tang R, Whaley R, Letovksy S, Buetow KH, Rzhetsky A, Schachter V, Sobral BS, Dogrusoz U, McWeeney S, Aladjem M, Birney E, Collado-Vides J, Goto S, Hucka M, Le Novere N, Maltsev N, Pandey A, Thomas P, Wingender E, Karp PD, Sander C, Bader GD (2010) The BioPAX community standard for pathway data sharing. Nat Biotechnol 28(9):935–942. doi: 10.1038/nbt.1666.
3. 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 Novere 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, Forum S (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19(4):524–531. doi:10.1093/ bioinformatics/btg015.
4. Le Novère 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, Villéger A, Boyd SE, Calzone L, Courtot M, Doqurusoz 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. Nat Biotechnol 27(8):735–741. doi: 10.1038/nbt1558.
5. Funahashi A, Matsuoka Y, Jouraku A, Morohashi M, Kikuchi N, Kitano H (2008) Cell Designer 3.5: a versatile modeling tool for biochemical networks. Proc IEEE 96(8):1254–1265.
6. Funahashi A, Matsuoka Y, Jouraku A, Kikuchi N, Kitano H (2006) CellDesigner: a modeling tool for biochemical networks. In: Proceedings of the 2006 Winter Simulation Conference
7. Funahashi A, Morohashi M, Kitano H, Tanimura N (2003) Cell Designer: a process diagram editor for gene-regulatory and biochemical networks. Biosilico 1(5):159–162, http://dx.doi.org/10.1016/S1478-5382(03)02370-9.
8. Oda K, Matsuoka Y, Funahashi A, Kitano H (2005) A comprehensive pathway map of epidermal growth factor receptor signaling. Mol Syst Biol 1:2005.0010–2005.0010. doi: 10.1038/msb4100014.
9. Oda K, Kitano H (2006) A comprehensive map of the toll-like receptor signaling network. Mol Syst Biol 2:2006.0015–2006.0015. doi: 10.1038/msb4100057.
10. Kaizu K, Ghosh S, Matsuoka Y, Moriya H, Shimizu-Yoshida Y, Kitano H (2010) A comprehensive molecular interaction map of the budding yeast cell cycle. Mol Syst Biol 6:415–415. doi: 10.1038/msb.2010.73.
11. Caron E, Ghosh S, Matsuoka Y, Ashton- Beaucage D, Therrien M, Lemieux S, Perreault C, Roux PP, Kitano H (2010) A comprehensive map of the mTOR signaling network. Mol Syst Biol 6:453–453. doi:10.1038/msb.2010.108.
12. Calzone L, Gelay A, Zinovyev A, Radvanyi F, Barillot E (2008) A comprehensive modular map of molecular interactions in RB/E2F pathway. Mol Syst Biol 4:173–173. doi: 10.1038/msb.2008.7.
13. Goodman C (2008) Engineering ingenuity at iGEM. Nat Chem Biol 4(1):13. doi:10.1038/nchembio0108-13.
14. Smolke CD (2009) Building outside of the box: iGEM and the BioBricks Foundation. Nat Biotechnol 27(12):1099–1102. doi:10.1038/nbt1209-1099.
15. Machné R, Finney A, Müller 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. doi: 10.1093/bioinformatics/btl086.
16. 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. doi: 10.1093/bioinformatics/btl485.
17. Keller R, Dorr A, Tabira A, Funahashi A, Ziller MJ, Adams R, Rodriguez N, Novere NL, Hiroi N, Planatscher H, Zell A, Drager A (2013) The systems biology simulation core algorithm. BMC Syst Biol 7:55. doi: 10.1186/1752-0509-7-55.
18. Sauro HM, Hucka M, Finney A, Wellock C, Bolouri H, Doyle J, Kitano H (2003) Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration. OMICS 7(4):355–372. doi: 10.1089/153623103322637670.
19. 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:D689–691. doi: 10.1093/nar/gkj092.
20. Olivier BG, Snoep JL (2004) Web-based kinetic modelling using JWS Online. Bioinformatics 20(13):2143–2144. doi: 10.1093/bioinformatics/bth200.
21. Mi H, Lazareva-Ulitsky B, Loo R, Kejariwal A, Vandergriff J, Rabkin S, Guo N, Muruganujan A, Doremieux O, Campbell MJ, Kitano H, Thomas PD (2005) The PANTHER database of protein families, subfamilies, functions and pathways. Nucleic Acids Res 33(suppl 1):D284–D288. doi: 10.1093/nar/gki078.
22. Mi H, Guo N, Kejariwal A, Thomas PD (2007) PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways. Nucleic Acids Res 35:D247–252. doi: 10.1093/nar/gkl869.
23. Funahashi A, Jouraku A, Matsuoka Y, Kitano H (2007) Integration of Cell Designer and SABIO-RK. In Silico Biol 7(2):S81–90.
24. Fujibuchi W, Goto S, Migimatsu H, Uchiyama I, Ogiwara A, Akiyama Y, Kanehisa M (1998) DBGET/LinkDB: an integrated database retrieval system. Pac Symp Biocomput 96:683–694.
25. Cherry JM, Adler C, Ball C, Chervitz SA, Dwight SS, Hester ET, Jia Y, Juvik G, Roe T, Schroeder M, Weng S, Botstein D (1998) SGD: saccharomyces genome database. Nucleic Acids Res 26(1):73–79.
26. Fernandez JM, Hoffmann R, Valencia A (2007) iHOP web services. Nucleic Acids Res 35(Web Server issue):W21–W26. doi: 10.1093/nar/gkm298.
27. Maglott D, Ostell J, Pruitt KD, Tatusova T (2005) Entrez gene: gene-centered information at NCBI. Nucleic Acids Res 33:D54–58. doi: 10.1093/nar/gki031.
28. Huss JW 3rd, Lindenbaum P, Martone M, Roberts D, Pizarro A, Valafar F, Hogenesch JB, Su AI (2010) The Gene Wiki: community intelligence applied to human gene annotation. Nucleic Acids Res 38:D633–639. doi: 10.1093/nar/gkp760.
29. Caspi R, Altman T, Dreher K, Fulcher CA, Subhraveti P, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Pujar A, Shearer AG, Travers M, Weerasinghe D, Zhang P, Karp PD (2012) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 40:D742–753. doi: 10.1093/nar/gkr1014.
30. Mi H, Muruganujan A, Demir E, Matsuoka Y, Funahashi A, Kitano H, Thomas PD (2011) BioPAX support in Cell Designer. Bioinformatics 27(24):3437–3438. doi: 10.1093/bioinformatics/btr586.
31. Kitano H (2003) A graphical notation for biochemical networks. Biosilico 1(5):169–176, http://dx.doi.org/1.0.1.01.6/S1478-5382(03)02380-1.
32. Kitano H, Funahashi A, Matsuoka Y, Oda K (2005) Using process diagrams for the graphical representation of biological networks. Nat Biotechnol 23(8):961–966. doi:10.1038/ nbt1111.
33. van Iersel MP, Villeger AC, Czauderna T, Boyd SE, Bergmann FT, Luna A, Demir E, Sorokin A, Dogrusoz U, Matsuoka Y, Funahashi A, Aladjem MI, Mi H, Moodie SL, Kitano H, Le Novere N, Schreiber F (2012) Software support for SBGN maps: SBGN-ML and LibSBGN. Bioinformatics 28(15):2016–2021. doi: 10.1093/bioinformatics/bts270.
34. Elowitz MB, Leibler S (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403(6767):335–338.
35. Le Novère 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(12):1509–1515. doi: 10.1038/nbt1156.
36. Hucka M, Finney A, Sauro HM, Bolouri H, Doyle J, Kitano H (2002) The ERATO systems biology workbench: enabling interaction and exchange between software tools for computational biology. Pac Symp Biocomput 450–461.
37. Cohen D, Kuperstein I, Barillot E, Zinovyev A, Calzone L (2013) From a biological hypothesis to the construction of a mathematical model. In: Schneider MV (ed) In silico systems biology, vol 1021, Methods in molecular biology. Humana, Totowa, NJ, pp 107–125, doi:10.1007/978-1-62703-450-0_6