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SOFTWARE:

MARIMBA relies on the power of the BANJO (Bayesian Network Inference with Java Objects) system developed by Alex J. Hartemink at Duke University for Bayesian analysis. BANJO is implemented in MARIMBA in accord with the BANJO Non-Commercial Use License Agreement (2005).

"Banjo is licensed from Duke University. Copyright © 2005 by Alexander J. Hartemink. All rights reserved."

MARIMBA implements Pycluster, a freely available implementation of the C Cluster library for the Python programming language. "Copyright © 2002-2005 Michiel Jan Laurens de Hoon."

JPEG images for network topology are generated using GraphViz software from AT&T. MARIMBA implements GraphViz in accord with the GraphViz Common Public License Version 1.0.

Finally, MARIMBA implements the following technologies: PHP, MySQL, R, Perl, Python, Dojo and Java.:

REFERENCES:

  1. Hodges AP et al. (2010) Bayesian network expansion identifies novel ROS and biofilm regulators. PLoS One 5(3):e9513.
  2. Hodges AP, Woolf P, He Y. (2010). BN+1 Bayesian Network Expansion for Identifying Molecular Pathway Elements. Communicative and Integrative Biology. In press.
  3. Sladeczek J, Hartemink AJ, and Robinson J. Bayesian Network Inference with Java Objects: User Guide. Duke University, 2005. http://www.cs.duke.edu/~amink/software/banjo/documentation/banjo.user.pdf
  4. Sladeczek J, Hartemink AJ, and Robinson J. Bayesian Network Inference with Java Objects: Developer Guide. Duke University, 2005. http://www.cs.duke.edu/~amink/software/banjo/documentation/banjo.developer.pdf
  5. Gansner E, Koutsofios E, and North S. Drawing graphs with dot . 4 Feb. 2005. http://www.graphviz.org/Documentation/dotguide.pdf
  6. Hartemink, A. (2005) “Reverse Engineering Gene Regulatory Networks.” Nature Biotechnology, 23, May 2005. pp. 554–555.
  7. Barrett T, Suzek TO, Troup DB, Wilhite SE, Ngau WC, Ledoux P, Rudnev D, Lash AE, Fujibuchi W, Edgar R. NCBI GEO: mining millions of expression profiles—database and tools Nucleic Acids Res. 2005 Jan 1;33 Database Issue:D562-6
  8. Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository Nucleic Acids Res. 2002 Jan 1;30(1):207-10
  9. De Hoon M, Imoto S, and Miyano S. The C Clustering Library for cDNA microarray data. Institute of medical science, human genome center. University of Tokyo. 26 Feb. 2006. "Copyright © 2002-2005 Michiel Jan Laurens de Hoon." http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/cluster.pdf
  10. Eppig JT et al. (2005). The Mouse Genome Database (MGD) : from genomes to mice--a community resource for mouse biology. Nucleic Acids Res 33:D471-475.
  11. Kanehisa, M. and Goto, S. (2000). KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30.