Creating interactive, web-based and data-enriched maps with the Systems Biology Graphical Notation

Nature Protocols

Volumn 7, Issue 3, 2012, Pages 579-593

  Junker, Astrid ^a   Rohn, Hendrik ^a   Czauderna, Tobias ^a   Klukas, Christian ^a   Hartmann, Anja ^a   Schreiber, Falk ^a,b  

^a LEIBNIZ INSTITUTE OF PLANT GENETICS AND CROP PLANT RESEARCH IPK   (Germany)

^b MARTIN LUTHER UNIVERSITY HALLE WITTENBERG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUTOMATION; COMPUTER LANGUAGE; COMPUTER PROGRAM; DATA ANALYSIS; GENE CONTROL; GENE REGULATORY NETWORK; IMAGE ANALYSIS; INFORMATION SYSTEM; INTERNET; METABOLISM; PRIORITY JOURNAL; SYSTEMS BIOLOGY; SYSTEMS BIOLOGY GRAPHICAL NOTATION;

COMPUTER GRAPHICS; GENE REGULATORY NETWORKS; INFORMATION DISSEMINATION; INTERNET; METABOLIC NETWORKS AND PATHWAYS; SOFTWARE; SYSTEMS BIOLOGY;

EID: 84861726485     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2012.002     Document Type: Article

References (31)

1. Le Novere, N. et al. The systems biology graphical notation. Nat. Biotechnol. 27, 735-741 (2009).
2. Junker, A., Hartmann, A., Schreiber, F. & Baumlein, H. An engineer's view on regulation of seed development. Trends Plant Sci. 15, 303-307 (2010).
3. Caron, E. et al. A comprehensive map of the mTOR signaling network. Mol. Syst. Biol. 6, 453 (2010).
4. Kierzek, A.M., Zhou, L. & Wanner, B.L. Stochastic kinetic model of two component system signalling reveals all-or-none, graded and mixed mode stochastic switching responses. Mol. Biosyst. 6, 531-542 (2010).
5. Jansson, A. & Jirstrand, M. Biochemical modeling with systems biology graphical notation. Drug Discov. Today 15, 365-370 (2010).
6. Funahashi, A. et al. CellDesigner 3.5: a versatile modeling tool for biochemical networks. Proceedings of the IEEE 96, 1254-1265 (2008).
7. Zinovyev, A., Viara, E., Calzone, L. & Barillot, E. BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks. Bioinformatics 24, 876-877 (2008). (Pubitemid 351386933)
8. van Iersel, M.P. et al. Presenting and exploring biological pathways with PathVisio. BMC Bioinformatics 9, 399 (2008).
9. Czauderna, T., Klukas, C. & Schreiber, F. Editing, validating and translating of SBGN maps. Bioinformatics 26, 2340-2341 (2010).
10. Gehlenborg, N. et al. Visualization of omics data for systems biology. Nat. Methods 7, S56 S (2010).
11. Suderman, M. & Hallett, M. Tools for visually exploring biological networks. Bioinformatics 23, 2651-2659 (2007). (Pubitemid 350048327)
12. Sorokin, A. et al. The pathway editor: a tool for managing complex biological networks. IBM J. Res. Dev. 50, 561-573 (2006). (Pubitemid 44803989)
13. Kanehisa, M. & Goto, S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27-30 (2000). (Pubitemid 30047706)
14. Schreiber, F. et al. MetaCrop 2.0: managing and exploring information about crop plant metabolism. Nucleic Acid Res. published online, doi:10.1093/nar/GKR1004 (15 November, 2011).
15. Moodie, S., Le Novère, N., Emek, D., Huaiyu, M. & Villeger, A. Systems biology graphical notation: process description language level 1V3. Nature Precedings published online, doi:10.1038/npre.2011.3721.4 (17 February, 2011).
16. Grafahrend-Belau, E. et al. MetaCrop: a detailed database of crop plant metabolism. Nucleic Acids Res. 36, D954-D958 (2008). (Pubitemid 351149851)
17. Zimmermann, P., Hirsch-Hoffmann, M., Hennig, L. & Gruissem, W. GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol. 136, 2621-2632 (2004). (Pubitemid 41071302)
18. Junker, B.H. et al. Temporally regulated expression of a yeast invertase in potato tubers allows dissection of the complex metabolic phenotype obtained following its constitutive expression. Plant Mol. Biol. 56, 91-110 (2004). (Pubitemid 40134263)
19. Stone, S.L. et al. Arabidopsis LEAFY COTYLEDON2 induces maturation traits and auxin activity: implications for somatic embryogenesis. Proc. Natl. Acad. Sci. USA 105, 3151-3156 (2008). (Pubitemid 351723683)
20. To, A. et al. A network of local and redundant gene regulation governs Arabidopsis seed maturation. Plant Cell 18, 1642-1651 (2006). (Pubitemid 44025549)
21. Villeger, A.C., Pettifer, S.R. & Kell, D.B. Arcadia: a visualization tool for metabolic pathways. Bioinformatics 26, 1470-1471 (2010).
22. Chandran, D., Bergmann, F.T. & Sauro, H.M. Athena: modular CAM/CAD software for synthetic biology. arXiv.org published online, arXiv:0902.2598v1 (2009).
23. Chabrier-Rivier, N., Fages, F. & Soliman, S. in Computational Methods in Systems Biology. Lecture Notes in Computer Science Vol. 3082 (eds. Danos, V. & Schachter, V.) 172-191 (Springer-Verlag, 2005).
24. Olivier, B.G. & Snoep, J.L. Web-based kinetic modelling using JWS Online. Bioinformatics 20, 2143-2144 (2004). (Pubitemid 39236569)
25. Battke, F., Symons, S. & Nieselt, K. Mayday-integrative analytics for expression data. BMC Bioinformatics 11 (2010).
26. Wegner, K. et al. The NetBuilder' project: development of a tool for constructing, simulating, evolving, and analysing complex regulatory networks. BMC Syst. Biol. 1, P72 (2007).
27. Deckard, A., Bergmann, F.T. & Sauro, H.M. Supporting the SBML layout extension. Bioinformatics 22, 2966-2967 (2006). (Pubitemid 44811576)
28. Lammers, C.R. et al. Connecting parts with processes: SubtiWiki and SubtiPathways integrate gene and pathway annotation for Bacillus subtilis. Microbiology 156, 849-859 (2010).
29. Reyes Palomares, A. et al. Systems biology metabolic modeling assistant: an ontology-based tool for the integration of metabolic data in kinetic modeling. Bioinformatics 25, 834-835 (2009).
30. Dilek, A., Belviranli, M.E. & Dogrusoz, U. VISIBIOweb: visualization and layout services for BioPAX pathway models. Nucleic Acids Res. 38, W150-W154 (2010).
31. Elowitz, M. & Leibler, S. A synthetic oscillatory network of transcriptional regulators. Nature 403, 335-338 (2000). (Pubitemid 30062393)