DMSP - Database for modeling signaling pathways: Combining biological and mathematical modeling knowledge for pathways

Methods of Information in Medicine

Volumn 47, Issue 2, 2008, Pages 140-148

  Visvanathan, Mahesh ^a   Breit, M ^a   Pfeifer, B ^a   Baumgartner, C ^a   Modre Osprian, R ^b   Tilg, B ^a  

^a UNIVERSITY FOR HEALTH SCIENCES   (Austria)

^b ARC SEIBERSDORF RESEARCH GMBH   (Austria)

Author keywords

Database; Modeling; Signaling and pathways

Indexed keywords

PROTEIN; TUMOR NECROSIS FACTOR ALPHA;

ARTICLE; BIOMEDICAL ENGINEERING; COMPUTER MODEL; DATA BASE; DATABASE FOR MODELING SIGNALING PATHWAYS; INFORMATION PROCESSING; INFORMATION SYSTEM; MATHEMATICAL MODEL; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION;

COMPUTER SIMULATION; DATABASES, PROTEIN; HUMANS; MODELS, BIOLOGICAL; SIGNAL TRANSDUCTION; USER-COMPUTER INTERFACE;

EID: 41149097539     PISSN: 00261270     EISSN: None     Source Type: Journal    
DOI: 10.3414/ME0461     Document Type: Article

References (28)

1. Arkin A, Ross J. Computational functions in biochemical reaction networks. J Biophys 1994; 67: 560-578.
2. Asthagiri AR. Bioengineering models of cell signaling. Annual Revison of Biomed Eng 2000; 2: 31-53.
3. Bhalla US, Iyengar R. Emergent properties of networks of biological signaling pathways. Sciences 1999; 283: 381-387.
4. Deville Y, Gilbert D, Helden J, Wodak S. An Overview of Data Models for the Analysis of Biochemical Pathways. Brief Bioinformatics 2003; 4 (3): 246-259.
5. Xenarios I, Salwinski L, Duan J, Higney P, Kim S, Eisenberg D. DIP: The Database of interacting proteins. A search tool for studying cellular networks of protein interactions. Nucleic Acid Res 2002; 30: 303-305.
6. Bader GD, Hogue CW. BIND - a data specification for storing and describing bimolecular interactions, molecular complexes and pathways. Bioinformatics 2000; 16: 465-477.
7. Dongsoo H, Kim HS, Seo J, Jang W. A Domain Combination Based Probabilistic Framework for Protein-Protein Interaction Prediction. Genome Informatics 2003; 14: 250-259.
8. Hoebeke M, Chiapello H, Noirot P, Bessières P. SPiD: a subtilis protein interaction database. Bioinformatics 2001; 17: 1209-1212.
9. Sivakumaran S, Hariharaputran S, Mishra J, Bhalla US. DOQCS - The database of quantitative cellular signaling: management and analysis of chemical kinetic models of signalling networks. Bioinformatics 2002; 19: 408-415.
10. Reshetnikov V, Karpov A, Pot D, Tereshchenko F. Vector PathBlazer: A New Pathway Analysis and Visualization Tool (cited 2007, April 12). Available from: http://www.iscb.orgismb2003/posters/feodorATinformaxinc.com_468.html
11. Bhalla US. A network within signaling pathways. In: Bower JM, Beeman D (eds). The Book of Genesis. Exploring realistic neural models within the general neural simulation system, 1998.
12. Kuroda S, Schweighofer N, Kawato M. Exploration of signal transduction in cerebellar long-term depression by kinetic simulation. J Neuroscience 2001; 21: 5693-5702.
13. Achard F, Vaysseix G, Barillot E. XML-bioinformatics and data integration. Bioinformatics 2001; 17: 115-125
14. Cho KH, Shin SY, Kolch W, Wolkenhauer O. Experimental Design in Systems Biology Based on Parameter Analysis with Monte Carlo Simulation: A Case Study for TNFα Mediated NF-κB Signal Transduction Pathway. Simulation 2003; 79: 726-739.
15. Cho KH, Wolkenhauer O. Analysis and modeling of signal transduction pathways in systems biology. J Biochemical Society Transactions 2003; 31: 1503-1509.
16. Schacherer F, Choi C, Götze U, Krull M, Pistor S, Wingender E. The TRANSPATH signal transduction database: a knowledge base on signal transduction networks. Bioinformatics 2001; 17: 1053-1057.
17. Kolpakov FA, Ananko EA, Kolesov GB, Kolchanov NA. GeneNet: a gene network database and its automated visualization. Bioinformatics 1998; 14: 529-537.
18. Gilman A. A letter to the signaling community. AfCS (cited 2007, April 12). Available from: http://www.afcs.org/
19. SigPath (Database) (cited 2007, April 12). Available from: http://www.sigpath.org/
20. Le Novère N, Benjamin B, Alexander B, Mélanie C, Marco D, Harish D, Lu L, Herbert S, Maria S, Bruce S, Jacky L, Michael H. BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res 2006; 34: D689-D691.
21. Kolpakov FA. BIOUML - Framework for visual modeling and simulation of biological systems. Proc Int Conf Bioinformatics of Genome Regulations and Structures; 2002.
22. Shannon P, Markie A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res 2003; 13: 2498-2504.
23. Joshi G, Gillespie M, Vastrik I, D'Eustachio P, Schmidt E, de Bono B, Jassal B, Gopinath G, Wu R, Matthews L, Lewis S, Birney, E, Stein L. Reactome: a knowledgebase of biological pathways. Nucleic Acids Res 2005; 33: D428-432.
24. Finney A. Developing SBML Beyond Level 2: Proposal for Development. Lee Notes in Computer Science 2005 (Jan); 3082.
25. Funahashi A, Tanimura N, Morohashi M, Kitano H. CellDesigner: a process diagram editor for gene-regulatory and biochemical networks. BioSilico 2003; 5: 159-162.
26. BioPAX (cited 2007, April 12). Available from: http://www.biopax.org/
27. Visvanathan M, Breit M, Pfeifer B, Modre-Osprian R, Baumgartner C, Tilg B. Systematic analysis of signaling pathways using an integrative environment. Methods Inf Med 2007; 46: 386-391.
28. Cannataro M, Cuda G, Veltri P. Modeling and Designing a Proteomics Application on PROTEUS. Methods Inf Med 2005; 44: 221-226.