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====== Chapter 3: Emergent Properties of Small Networks ======


===== Supplementary Material =====


==== Electronic Notebooks ====


    * {{:wiki:chapter_3:goldbeter-koshland-1981-v3.nb|Goldbeter-Koshland ultrasensitivity}}
    * {{:wiki:chapter_3:hillfeedbackanalysis.nb|Hill feedback analysis}}
    * {{:wiki:chapter_2:huang_ferrell_1996_mapkv2.nb|Huang and Ferrell 1996 MAPK}}
    * {{:ch_4:nadji_2006_asp_thr_biosynthesis.nb|Najdi 2006 Asp Thr biosynthesis}}
    * MAPK cascade in solution with feedback, according to models of {{:wiki:chapter_3:bardwell_mapk_4.nb|Bardwell}} and {{:wiki:chapter_3:mapk-kholodenko.nb|Kholodenko}}
    * MAPK cascade stochastic
    * MAPK cascade on scaffold (old Cellerator {{:wiki:chapter_3:mapk-on-scaffold.nb|model}})
    * more


==== Exercises ====


    * Emergent dynamics
    * MAPK exercises


==== Figures - electronic sources ====


    * MAPK cascade and transfer function
    * Asp Thr biosynthesis
    * elementary behaviors
    * Brusselator (Figure 3.13c) {{:wiki:chapter_3:brusselator.nb|model file}} and {{:wiki:chapter_3:brusselator-phase-limit-cycle.pdf|pdf}}.
    * feedback loop nullclines
    * repressilator oscillations
    * MAPK with feedback transfer functions
    * stochastic MAPK
    * scaffolded MAPK


==== Bibliography - electronic access - chapter 3 ====


    * [[:wiki:chapter_3:chapter_3_electronic_bibliography|Here]]


===== Text Outline =====


    * 3.1 Network behavior
    * 3.2 Elementary network analysis
    * 3.3 Small network examples: S-E-P, MAPK, and threonine metabolism
    * 3.4 Dynamical consequences of feedback
    * 3.5 Building larger networks: MAPK in depth
    * 3.6 Summary


===== Missing Topics =====