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@BOOK{bioconductor,
  title = {{Bioinformatics and computational biology solutions using R and bioconductor}},
  publisher = {Springer},
  year = {2005},
  author = {Gentleman, R. and Carey, V. and Huber, W. and Irizarry, R. and Dudoit,
	S.}
}

@MISC{GTK,
  author = {GTK+},
  title = {The {G}imp {T}ool {K}it},
  year = {2007},
  owner = {larman},
  timestamp = {2006.08.21},
  url = {http://www.gtk.org/}
}

@MISC{explorase-website,
  author = {Lawrence, Michael},
  title = {ExploRase website},
  year = {2007},
  owner = {larman},
  timestamp = {2007.01.30},
  url = {http://www.metnetdb.org/MetNet\_exploRase.htm}
}

@MISC{RGtk2-website,
  author = {Michael Lawrence},
  title = {R{G}tk2},
  year = {2007},
  owner = {larman},
  timestamp = {2006.10.07},
  url = {http://www.ggobi.org/rgtk2}
}

@MANUAL{R,
  title = {R: A Language and Environment for Statistical Computing},
  author = {{R Development Core Team}},
  organization = {R Foundation for Statistical Computing},
  address = {Vienna, Austria},
  year = {2005},
  note = {{ISBN} 3-900051-07-0},
  url = {http://www.R-project.org}
}

@ARTICLE{cytoscape,
  author = {Shannon, Paul and Markiel, Andrew and Ozier, Owen and Baliga, Nitin
	S. and Wang, Jonathan T. and Ramage, Daniel and Amin, Nada and Schwikowski,
	Benno and Ideker, Trey},
  title = {{Cytoscape: A Software Environment for Integrated Models of Biomolecular
	Interaction Networks}},
  journal = {Genome Res.},
  year = {2003},
  volume = {13},
  pages = {2498-2504},
  number = {11},
  abstract = {Cytoscape is an open source software project for integrating biomolecular
	interaction networks with high-throughput expression data and other
	molecular states into a unified conceptual framework. Although applicable
	to any system of molecular components and interactions, Cytoscape
	is most powerful when used in conjunction with large databases of
	protein-protein, protein-DNA, and genetic interactions that are increasingly
	available for humans and model organisms. Cytoscape's software Core
	provides basic functionality to layout and query the network; to
	visually integrate the network with expression profiles, phenotypes,
	and other molecular states; and to link the network to databases
	of functional annotations. The Core is extensible through a straightforward
	plug-in architecture, allowing rapid development of additional computational
	analyses and features. Several case studies of Cytoscape plug-ins
	are surveyed, including a search for interaction pathways correlating
	with changes in gene expression, a study of protein complexes involved
	in cellular recovery to DNA damage, inference of a combined physical/functional
	interaction network for Halobacterium, and an interface to detailed
	stochastic/kinetic gene regulatory models.},
  doi = {10.1101/gr.1239303},
  eprint = {http://www.genome.org/cgi/reprint/13/11/2498.pdf},
  url = {http://www.genome.org/cgi/content/abstract/13/11/2498}
}

@INCOLLECTION{Limma,
  author = {Smyth, G. K.},
  title = {Limma: linear models for microarray data},
  booktitle = {Bioinformatics and Computational Biology Solutions using R and Bioconductor},
  publisher = {Springer},
  year = {2005},
  editor = {R. Gentleman and V. Carey and S. Dudoit and R. Irizarry and W. Huber},
  pages = {397-420},
  journal = {Bioinformatics and Computational Biology Solutions using R and Bioconductor},
  owner = {larman},
  timestamp = {2006.04.21}
}

@ARTICLE{ggobi,
  author = {Deborah F. Swayne and Duncan {Temple Lang} and Andreas
	
	 Buja and Dianne Cook},
  title = {{GG}obi: evolving from {XG}obi into an extensible framework
	
	 for interactive data visualization},
  journal = {Computational Statistics \& Data Analysis},
  year = {2003},
  volume = {43},
  pages = {423--444}
}

@MISC{rggobi-website,
  author = {Hadley Wickham and Michael Lawrence},
  title = {rggobi},
  year = {2006},
  owner = {larman},
  timestamp = {2006.10.07},
  url = {http://www.ggobi.org/rggobi}
}

@MISC{rattle,
  author = {Graham Williams},
  title = {Rattle: gnome {R} data mining},
  year = {2006},
  owner = {larman},
  timestamp = {2006.10.05},
  url = {http://rattle.togaware.com/}
}

@ARTICLE{metnet,
  author = {E.S. Wurtele and J. Li and L. Diao and H. Zhang and C.M. Foster and
	B. Fatland and J. Dickerson and A. Brown and Z. Cox and D. Cook and
	E.K. Lee and H. Hofmann},
  title = {MetNet: Software to build and model the biogenetic lattice of Arabidopsis},
  journal = {Comp. Funct. Genom.},
  year = {2003},
  volume = {4},
  pages = {239-245},
  owner = {larman},
  timestamp = {2006.05.03}
}

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