Database of Dynamic Signatures Generated by Regulatory Networks (DSGRN)

被引:11
作者
Cummins, Bree [1 ]
Gedeon, Tomas [1 ]
Harker, Shaun [2 ]
Mischaikow, Konstantin [2 ]
机构
[1] Montana State Univ, Dept Math Sci, Bozeman, MT 59715 USA
[2] Rutgers State Univ, Dept Math, New Brunswick, NJ USA
来源
COMPUTATIONAL METHODS IN SYSTEMS BIOLOGY (CMSB 2017) | 2017年 / 10545卷
关键词
D O I
10.1007/978-3-319-67471-1_19
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
We present a computational tool DSGRN for exploring network dynamics across the global parameter space for switching model representations of regulatory networks. This tool provides a finite partition of parameter space such that for each region in this partition a global description of the dynamical behavior of a network is given via a directed acyclic graph called a Morse graph. Using this method, parameter regimes or entire networks may be rejected as viable models for representing the underlying regulatory mechanisms.
引用
收藏
页码:300 / 308
页数:9
相关论文
共 22 条
  • [1] [Anonymous], 1978, AM MATH SOC CBMS
  • [2] Temporal logic analysis of gene networks under parameter uncertainty
    Batt, Gregory
    Belta, Calin
    Weiss, Ron
    [J]. IEEE TRANSACTIONS ON AUTOMATIC CONTROL, 2008, 53 : 215 - 229
  • [3] Bogomolov Sergiy, 2015, Hardware and Software: Verification and Testing. 11th International Haifa Verification Conference, HVC 2015. Proceedings: LNCS 9434, P19, DOI 10.1007/978-3-319-26287-1_2
  • [4] Bornholt S, 2008, J R SOC INTERFACE, V5, P134, DOI DOI 10.1098/RSIF.2008.0132.F0CUS
  • [5] Chaouiya C, 2004, POSITIVE SYSTEMS, V294, DOI [10.1007/978-3-540-44928-7_17, DOI 10.1007/978-3-540-44928-7_17]
  • [6] Integrative analysis of cell cycle control in budding yeast
    Chen, KC
    Calzone, L
    Csikasz-Nagy, A
    Cross, FR
    Novak, B
    Tyson, JJ
    [J]. MOLECULAR BIOLOGY OF THE CELL, 2004, 15 (08) : 3841 - 3862
  • [7] Combinatorial Representation of Parameter Space for Switching Networks
    Cummins, Bree
    Gedeon, Tomas
    Harker, Shaun
    Mischaikow, Konstantin
    Mok, Kafung
    [J]. SIAM JOURNAL ON APPLIED DYNAMICAL SYSTEMS, 2016, 15 (04): : 2176 - 2212
  • [8] Global dynamics for steep nonlinearities in two dimensions
    Gedeon, Tomas
    Harker, Shaun
    Kokubu, Hiroshi
    Mischaikow, Konstantin
    Oka, Hiroe
    [J]. PHYSICA D-NONLINEAR PHENOMENA, 2017, 339 : 18 - 38
  • [9] LOGICAL ANALYSIS OF CONTINUOUS, NONLINEAR BIOCHEMICAL CONTROL NETWORKS
    GLASS, L
    KAUFFMAN, SA
    [J]. JOURNAL OF THEORETICAL BIOLOGY, 1973, 39 (01) : 103 - 129
  • [10] COOPERATIVE COMPONENTS, SPATIAL LOCALIZATION AND OSCILLATORY CELLULAR DYNAMICS
    GLASS, L
    KAUFFMAN, SA
    [J]. JOURNAL OF THEORETICAL BIOLOGY, 1972, 34 (02) : 219 - &