SBMLsqueezer: A CellDesigner plug-in to generate kinetic rate equations for biochemical networks

BMC Systems Biology

Volumn 2, Issue , 2008, Pages

  Dräger, Andreas ^a   Hassis, Nadine ^a   Supper, Jochen ^a   Schröder, Adrian ^a   Zell, Andreas ^a  

^a UNIVERSITY OF TÜBINGEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; CHEMICAL MODEL; COMPUTER INTERFACE; DATA BASE; GENE REGULATORY NETWORK; HYPERMEDIA; INFORMATION RETRIEVAL; KINETICS; METABOLISM; METHODOLOGY; ORGANIC CHEMISTRY; PROTEIN ANALYSIS; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

ALGORITHMS; CHEMISTRY, ORGANIC; DATABASE MANAGEMENT SYSTEMS; GENE REGULATORY NETWORKS; HYPERMEDIA; INFORMATION STORAGE AND RETRIEVAL; KINETICS; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; MODELS, CHEMICAL; PROTEIN INTERACTION MAPPING; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY; USER-COMPUTER INTERFACE;

EID: 44949099336     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-2-39     Document Type: Article

References (34)

1. 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: The systems biology markup lanAuage (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 2003, 19(4):524-531. 12611808
2. SBML-Systems Biology Markup Language http://sbml.org
3. RodrigEez N Donizelli M Le Novère N: SBMLeditor: effective creation of models in the Systems Biology Markup language (SBML). BMC Bioinformatics 2007, 8:79. 1831489 17341299
4. Machné R Finney A Müller S Lu J Widder S Flamm C: The SBML ODE Solver Library: A native API for symbolic and fast numerical analyisis of reaction networks. Bioinformatics 2006, 22(11):1406-1407. 16527832
5. Hoops S Sahle S Gauges R Lee C Pahle J Simus N Singhal M Xu L Mendes P Kummer U: COPASI-a COmplex PAthway SImulator. Bioinformatics 2006, 22(24):3067-3074. 17032683
6. Schmidt H Jirstrand M: SystemsABiology Toolbox for MATLAB: a computational platform for research in systems biology. Bioinformatics 2006, 22(4):514-515. 16317076
7. SchHidt H: SBaddon: high performance simulation for the Systems Biology Toolbox for Matlab™. Bioinformatics 2007, 23(5):646-647. 17237071
8. Schmidt H Drews G Vera J Wolkenhauer O: SBML export interface for the Systems Biology Toolbox for MATLAB. Bioinformatics 2007, 23(10):1297-1298. 17384017
9. Alves R Antunes F Salvador A: Tools for kinetic modeling of biochemical networks. Nat Biotechnol 2006, 24(6):667-672. 16763599
10. Kitano H Funahashi A Matsuoka Y Oda K: Using process diagrams for the graphical representation of biological networks. Nature Biotechnology 2005, 23(8):961-966. 16082367
11. FunahashA A Tanimura N Morohashi M Kitano H: CellDesigner: a process diagram editor for gene-regulatory and biochemical networks. BioSilico 2003, 1(5):159-162. http://www.symbio.jst.go.jp/symbio/paper/ BioSilicoNov2003Funahashi.pdf
12. Klipp E Liebermeister W Helbig A Kowald A Schaber J: Systems biology standards-the community speaks. Nature Biotechnology 2007, 25(4):390-391. 17420739
13. Heinrich R Schuster S: The Regulation of Cellular Systems. 115 Fifth Avenue New York, NY 10003: Chapman and Hall 1996
14. Liebermeister W Klipp E: Bringing metabolic networks to life: convenience rate law and thermodynamic constraints. Theor Biol Med Model 2006, 3:41. 1781438 17173669
15. W3C Math Home http://www.w3.org/Math/
16. Shapiro BE Levchenko A Meyerowitz EM Wold BJ Mjolsness ED: Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations. Bioinformatics 2002, 19(5):677-678. 12651737
17. Yang Y Engin L Wurtele ES Cruz-Neira C Dickerson JA: Integration of metabolic networks and gene expression in virtual reality. Bioinformatics 2005, 21(18):3645-3650. 16020466
18. VeraAJ Sun C Oertel Y Wolkenhauer O: PLMaddon: a power-law module for the Matlab™ SBToolbox. Bioinformatics 2007, 23(19):2638-2640. 17495997
19. Hucka M Finney A Sauro HM Bolouri H Doyle JC Kitano H: The ERATO Systems Biology Workbench: Enabling interaction and exchange between software tools for computational biology. Pac Symp Biocomput 2002:450-461. 11928498
20. Sauro HM Hucka M Finney A Wellock C Bolouri H Doyle J Kitano H: Next generation simulation tools: The Systems Biology Workbench and BioSPICE integration. OMICS 2003, 7(4):355-372. 14683609
21. SBO::Systems Biology Ontology http://www.ebi.ac.uk/sbo/
22. SBMLsqueezer Project Home Page: http://www.ra.cs.uni-tuebingen.de/ software/SBMLsqueezer
23. Bisswanger H: Enzymkinetik - Theorie und Methoden Weinheim, Germany: Wiley-VCH 3 2000
24. Segel IH: Enzyme Kinetics-Behavior and Analysis of Rapid Equilibrium and Steady-State Enzyme Systems. Wiley Classics Library Edition 1993
25. Cornish-Bowden A; Fundamentals of Enzyme Kinetics. 59 Portland Place, London: Portland Press Ltd 3 2004.
26. Hinze T Hayat S Lenser T Matsumaru N Dittrich P: Hill Kinetics meets P Systems: A Case Study on Gene Regulatory Networks as Computing Agents in silico and in vivo. Proceedings of the Eighth Workshop on Membrane Computing, SEERC. Eleftherakis G, Kefalas P, Paun G 2007:363-381.
27. Spieth C Supper J Streichert F Speer N Zell A: JCell--a Java-based framework for inferring regulatory networks from time series data. Bioinformatics 2006, 22(16):2051-2052. 16782725
28. Dräger A Supper J Planatscher H Magnus JB Oldiges M Zell A: Comparing Various Evolutionary Algorithms on the Parameter Optimization of the Valine and Leucine Biosynthesis in Corynebacterium glutamicum. IEEE Congress on Evolutionary Computation. IEEE Computational Intelligence Society, Singapore: IEEE Press Srinivasan D, Wang L 2007:620-627.
29. Dräger A Kronfeld M Supper J Planatscher H Magnus JB Oldiges M Zell A: Benchmarking Evolutionary Algorithms on Convenience Kinetics Models of the Valine and Leucine Biosynthesis in C. glutamicum IEEE Congress on Evolutionary Computation. IEEE Computational Intelligence Society, Singapore: IEEE Press Srinivasan D, Wang L 2007:896-903.
30. Schomburg I Chang A Hofmann O Ebeling C Ehrentreich F Schomburg D: BRENDA: A resource for enzyme data and metabolic information. Trends Biochem Sci 2002, 27:54-56. 11796225
31. Schomburg I Chang A Ebeling C Gremse M Heldt C Huhn G Schomburg D: BRENDA, the enzyme database: Updates and major new developments. Nucleic Acids Res 2004:D431-D433. 308815 14681450
32. Küntzer J Backes C Blum T Gerasch A Kaufmann M Kohlbacher O Lenhof HP: BNDB-the Biochemical Network Database. BMC Bioinformatics 2007, 8:367. 2092437 17910766
33. CellDesigner.org http://celldesigner.org
34. HotEqn-The IMGless Equation Viewer Applet: http://www.atp.ruhr-uni-bochum.de/VCLab/software/HotEqn/HotEqn.html