ALC: Automated reduction of rule-based models

BMC Systems Biology

Volumn 2, Issue , 2008, Pages

  Koschorreck, Markus ^a   Gilles, Ernst Dieter ^a  

^a MAX PLANCK INSTITUTE FOR DYNAMICS OF COMPLEX TECHNICAL SYSTEMS   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTOMATION; BINDING SITE; BIOLOGICAL MODEL; COMPUTER INTERFACE; COMPUTER PROGRAM; COMPUTER SIMULATION; INTERNET; KINETICS; PHOSPHORYLATION; STATISTICS;

AUTOMATION; BINDING SITES; COMPUTER SIMULATION; INTERNET; KINETICS; MODELS, BIOLOGICAL; PHOSPHORYLATION; SOFTWARE; STOCHASTIC PROCESSES; USER-COMPUTER INTERFACE;

EID: 61349127270     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-2-91     Document Type: Article

References (45)

1. Hlavacek WS Faeder JR Blinov ML Perelson AS Goldstein B The complexity of complexes in signal transduction Biotechnol Bioeng 2003, 84(7):783-94. 14708119
2. Hlavacek WS Faeder JR Blinov ML Posner RG Hucka M Fontana W Rules for modeling signal-transduction systems Sci STKE 2006, 2006(344):rE6. 16849649
3. Koschorreck M Conzelmann H Ebert S Ederer M Gilles ED Reduced modeling of signal transduction - a modular approach BMC Bioinformatics 2007, 8:336. 2216040 17854494
4. Borisov NM Markevich NI Hoek JB Kholodenko BN Signaling through receptors and scaffolds: Independent interactions reduce combinatorial complexity Biophys J 2005, 89(2):951-966. 1366644 15923229
5. Conzelmann H Saez-Rodriguez J Sauter T Kholodenko B Gilles E A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks BMC Bioinformatics 2006, 7:34. 1413560 16430778
6. Heinrich R Schuster S The Regulation of Cellular Systems Chapman & Hall 1996.
7. Atkins P Paula Jd Physical Chemistry Oxford University Press 2006.
8. Asthagiri A Lauffenburger D A computational study of feedback effects on signal dynamics in a mitogen-activated protein kinase (MAPK) pathway model Biotechnol Prog 2001, 17:227-239. 11312698
9. Sedaghat AR Sherman A Quon MJ A mathematical model of metabolic insulin signaling pathways Am J Physiol Endocrinol Metab 2002, 283(5):E1084-101. 12376338
10. Hatakeyama M Kimura S Naka T Kawasaki T Yumoto N Ichikawa M Kim JH Saito K Saeki M Shirouzu M Yokoyama S Konagaya A A computational model on the modulation of mitogen-activated protein kinase (MAPK) and Akt pathways in heregulin-induced ErbB signalling Biochem J 2003, 373(Pt 2):451-463. 1223496 12691603
11. Haugh J Schooler K Well A Wiley H Lauffenburger D Effect of epidermal growth factor receptor internalization on regulation of the phosphoslipase C-gamma1 signaling pathway J Biol Chem 1999, 274:8958-8965. 10085141
12. Haugh J Well A Lauffenburger D Mathematical modeling of epidermal growth factor receptor signaling through the phospholipase C pathway: mechanistic insights and predictions for molecular interventions Biotechnol Bioeng 2000, 70:225-238. 10972934
13. Kholodenko BN Demin OV Moehren G Hoek JB Quantification of Short Term Signaling by the Epidermal Growth Factor Receptor J Biol Chem 1999, 274(42):30169-30181. 10514507
14. Moehren G Markevich N Demin O Kiyatkin A Goryanin I Hoek JB Kholodenko BN Temperature dependence of the epidermal growth factor receptor signaling network can be accounted for by a kinetic model Biochemistry 2002, 41:306-20. 11772030
15. Schoeberl B Eichler-Jonsson C Gilles ED Müller G Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors Nat Biotechnol 2002, 20(4):370-375. 11923843
16. Liu G Swihart MT Neelamegham S Sensitivity, principal component and flux analysis applied to signal transduction: The case of epidermal growth factor mediated signaling Bioinformatics 2005, 21(7):1194-202. 15531606
17. Koschorreck M Gilles ED Mathematical modeling and analysis of insulin clearance in vivo BMC Systems Biology 2008, 2:43. 2430945 18477391
18. Faeder J Blinov M Goldstein B Hlavacek W Combinatorial complexity and dynamical restriction of network flows in signal transduction Syst Biol (Stevenage) 2005, 2(5):15. 17091578
19. Faeder JR Blinov ML Goldstein B Hlavacek WS Rule-based modeling of biochemical networks Complexity 2005, 10:22-41.
20. Blinov ML Faeder JR Goldstein B Hlavacek WS BioNetGen: Software for rule-based modeling of signal transduction based on the interactions of molecular domains Bioinformatics 2004, 20(17):3289-91. 15217809
21. Faeder JR Blinov ML Hlavacek WS Graphical rule-based representation of signal transduction networks Proc ACM Symp Appl Computing 2005, 133-140.
22. Blinov ML Yang J Faeder JR Hlavacek WS Graph theory for rule-based modeling of biochemical networks Lect Notes Comput Sci 2006, 4230:89-106.
23. Novère NL Shimizu T STOCHSIM: Modelling of stochastic biomolecular processes Bioinformatics 2001, 17(6):575-6. 11395441
24. Lok L Brent R Automatic generation of cellular reaction networks with Moleculizer 1.0 Nat Biotechnol 2005, 23:131-6. 15637632
25. Calzone L Fages F Soliman S BIOCHAM: An environment for modeling biological systems and formalizing experimental knowledge Bioinformatics 2006, 22(14):1805-7. 16672256
26. Sedwards S Mazza T Cyto-Sim: A formal language model and stochastic simulator of membrane-enclosed biochemical processes Bioinformatics 2007, 23(20):2800-2. 17855418
27. Gillespie DT A rigorous derivation of the chemical master equation Physica A 1992, 188:404-425.
28. Blinov ML Faeder JR Yang J Goldstein B Hlavacek WS 'On-the-fly' or 'generate-first' modeling? Nat Biotechnol 2005, 23(11):1344-5. 16273053
29. Pawson T Nash P Assembly of cell regulatory systems through protein interaction domains Science 2003, 300(5618):445-452. 12702867
30. Conzelmann H Gilles ED Functional Proteomics: Methods and Protocols Humana Press 2008 chap. Dynamic pathway modeling of signal transduction networks - A domain-oriented approach 557-576.
31. Conzelmann H Fey D Gilles E Exact model reduction of combinatorial reaction networks BMC Syst Biol 2008, 2:78. 2570670 18755034
32. Hartwell L Hopfield J Leibler S Murray A From molecular to modular cell biology Nature 1999, 402(6761 Suppl):C47-52. 10591225
33. Saez-Rodriguez J Kremling A Conzelmann H Bettenbrock K Gilles ED Modular Analysis of Signal Transduction Networks. IEEE Contr Syst Mag 2004, 24(4):35-52.
34. Saez-Rodriguez J Kremling A Gilles ED Dissecting the puzzle of life: Modularization of signal transduction networks Comput Chem Eng 2005, 29(3):619-629.
35. Ederer M Sauter T Bullinger E Gilles ED Allgöwer F An Approach for Dividing Models of Biological Reaction Networks into Functional Units Simulation 2003, 79(12):703-716.
36. Isidori A Nonlinear control systems Springer 1995 chap. Global decomposition of control systems 77-105.
37. ALC website http://layer.mpi-magdeburg.mpg.de
38. Hucka M Finney A Sauro H Bolouri H Doyle J Kitano H Arkin A Bornstein B Bray D Cornish-Bowden A Cuellar A Dronov S Gilles E Ginkel M Gor V Goryanin I Hedley W Hodgman T Hofmeyr JH Hunter P Juty N Kasberger J Kremling A Kummer U Novère NL Loew L Lucio D Mendes P Minch E Mjolsness E Nakayama Y Nelson M Nielsen P Sakurada T Schaff J Shapiro B Shimizu T Spence H Stelling J Takahashi K Tomita M Wagner J Wang J Forum S The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models Bioinformatics 2003, 19(4):524-31. 12611808
39. Lamport L LaTeX: A Document Preparation System: User's Guide and Reference Manual Addison-Wesley Longman, Amsterdam 1994.
40. Comprehensive TeX Archive Network http://www.ctan.org
41. Wall L Christiansen T Orwant J Programming Perl. There's More Than One Way To Do It O'Reilly Media 2000.
42. Comprehensive Perl Archive Network http://www.cpan.org
43. Apache HTTP Server Project http://httpd.apache.org
44. ALC on SourceForge.net http://sourceforge.net/projects/alc/
45. Shapiro BE Hucka M Finney A Doyle J MathSBML: A package for manipulating SBML-based biological models Bioinformatics 2004, 20(16):2829-31. 1409765 15087311