Tools and Databases

  • YAGNS (Yet Another Gene Network Simulator)
    – Simulation tool of biochemical networks with web interface
    – Parameter estimation algorithm based on DIDC for kinetic models
    If you have any question, please contact us
  • Mathematical model
    • c-Fos model (T. Nakakuki, et al., “Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics”, Cell, 141, 884-896, 2010)
      Matlab (The MathWorks, Inc.) codes (here).
    • MCF-7 model (M. R. Birtwistle, et al., “Ligand-Dependent Responses of the ErbB Signaling Network: Experimental and Modeling Analysis”, Molecular Systems Biology 3:144 doi:10.1038/msb4100188, 2007)
      Matlab (The MathWorks, Inc.) codes with readme document (here).
    • CHO model (T. Nakakuki, et al., “Topological Analysis of MAPK Cascade for Kinetic ErbB Signaling”, PLoS ONE, Mar 12;3(3):e1782, 2008)
      Matlab (The MathWorks, Inc.) codes with readme document (here).
    • Cross-talk model between ERK and Akt pathways (M. Hatakeyama, et al., “A computational model on the modulation of MAPK and Akt pathways in heregulin induced ErbB signaling”, Biochem J., 373, 451-462, 2003)
      Mathematica (Wolfram Research, Inc.) codes (here).
  • Estimation tool for cluster-based gene network (Y. Shiraishi, et al., “Inferring cluster-based networks from differently stimulated multiple time-course gene expression data”, Bioinformatics 2010)
    Matlab (The MathWorks, Inc.) codes with readme document (here).