RCytoscape: Tools for exploratory network analysis

BMC Bioinformatics

Volumn 14, Issue 1, 2013, Pages

  Shannon, Paul T ^a,b   Grimes, Mark ^c   Kutlu, Burak ^b   Bot, Jan J ^d   Galas, David J ^e  

^a Fred Hutchinson Cancer Research Center   (United States)

^b INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^c UNIVERSITY OF MONTANA   (United States)

^d DELFT UNIVERSITY OF TECHNOLOGY   (Netherlands)

^e PACIFIC NORTHWEST RESEARCH INSTITUTE   (United States)

Author keywords

Bioinformatics; Biological networks; Exploratory data analysis; Statistical programming; Visualization

Indexed keywords

BIOLOGICAL NETWORKS; COMPLEX BIOLOGICAL SYSTEMS; COMPUTATIONAL BIOLOGY; EXPLORATORY DATA ANALYSIS; GLIOBLASTOMA MULTIFORME; NETWORK VISUALIZATION; PREDICTION AND CONTROL; PROGRAMMING ENVIRONMENT;

BIOINFORMATICS; DATA HANDLING; DATA VISUALIZATION; FLOW VISUALIZATION; GRAPHICAL USER INTERFACES; VISUALIZATION;

COMPLEX NETWORKS;

BIOLOGICAL MODEL; BIOLOGY; CHROMOSOME MAP; COMPUTER PROGRAM; GENETICS; GLIOBLASTOMA; HUMAN; HUMAN GENOME; ARTICLE;

CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; GENOME, HUMAN; GLIOBLASTOMA; HUMANS; MODELS, GENETIC; SOFTWARE;

EID: 84880001502     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-217     Document Type: Article

References (26)

1. Vidal M, Cusick ME, Albert-Laszlo B. Interactome networks and human disease. Cell 2011, 144(6):986-998. 10.1016/j.cell.2011.02.016, 3102045, 21414488.
2. Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell 2011, 144(5):646-674. 10.1016/j.cell.2011.02.013, 21376230.
3. Nadeau JH. Modifier genes in mice and humans. Nat Rev Genet 2001, 2.3:165-174.
4. Liu Y-Y, Jean-Jacques S, Albert-László B. Controllability of complex networks. Nature 2011, 473.7346f:167-173.
5. Bodenmiller B, et al. Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast. Sci Signal 2010, 3.153:rs4.
6. Gehlenborg N, O'Donoghue SI, Baliga NS, Goesmann A, Hibbs MA, et al. Visualization of omics data for systems biology. Nat Methods 2010, 7:S56-68. 10.1038/nmeth.1436, 20195258.
7. Working Definition of Bioinformatics and Computational Biology [http://www.bisti.nih.gov/docs/CompuBioDef.pdf].
8. Tukey JW. Exploratory Data Analysis 2007, Indianapolis: Addison-Wesley.
9. Tufte ER. The Visual Display of Quantitative Information 2001, Connecticut: Graphics Press.
10. John Tukey Quotations [http://en.wikipedia.org/wiki/John_Tukey#Quotes].
11. Edward Tufte Qutotations [http://52weeksofux.com/post/963764429/information-overload-is-not-the-problem.
12. Shannon P, Markiel 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, 3(11):2498-504.
13. Kohl M, Wiese S, Warscheid B. Cytoscape: software for visualization and analysis of biological networks. Methods Mol Biol 2011, 696:291-303. 10.1007/978-1-60761-987-1_18, 21063955.
14. Scientific Computing Tools For Python - Numpy [http://www.numpy.org/], 3533878, 22647087.
15. Bot JJ, Marcel J, Reinders T. CytoscapeRPC: a plugin to create, modify and query Cytoscape networks from scripting languages. Bioinformatics 2011, 27.17:2451-2452.
16. XML-RPC [http://en.wikipedia.org/wiki/XML-RPC].
17. The R Project for Statistical Computing [http://www.r-project.org/].
18. Bioconductor Mailing List Archive [https://stat.ethz.ch/pipermail/bioconductor/] vs. The Biopython Archives [http://lists.open-bio.org/pipermail/biopython/].
19. The Popularity of Data Analysis Software [http://r4stats.com/articles/popularity/].
20. RCytoscape [http://www.bioconductor.org/packages/release/bioc/html/RCytoscape.html].
21. Gentleman R, Temple Lang D. "Statistical Analyses and Reproducible Research" (May 2004). Bioconductor Project Working Papers Working Paper 2 http://biostats.bepress.com/bioconductor/paper2.
22. Knuth, Donald E. Literate programming. Comput J 1984, 27.2:97-111.
23. Skipper, Magdalena, Ritu D, Philip C. Presenting ENCODE. Nature 2012, 489.7414:45-45.
24. Gentleman RC, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004, 5.10:R80.
25. Rest [http://en.wikipedia.org/wiki/Representational_state_transfer].
26. Grimes, Mark L, et al. Wrangling phosphoproteomic data to elucidate cancer signaling pathways. PLoS One 2013, 8.1:e52884.