Systems Biology: Computational and Mathematical Methods

by E. Mjolsness, P. Baldi, and B. Shapiro

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wiki:chapter_3:emergent_properties_of_small_networks [2013/03/24 17:04] – created emjwiki:chapter_3:emergent_properties_of_small_networks [2013/04/03 15:45] (current) – emj
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-====== Chapter 3: Emergent Properties ======+====== Chapter 3: Emergent Properties of Small Networks ======
  
  
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-    * Mass action kinetics +    * {{:wiki:chapter_3:goldbeter-koshland-1981-v3.nb|Goldbeter-Koshland ultrasensitivity}} 
-    *  +    * {{:wiki:chapter_3:hillfeedbackanalysis.nb|Hill feedback analysis}} 
-    * Analytic solution of trivalent reaction A+B <–> C+    * {{: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
  
  
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-    * Hill functions +    * Emergent dynamics 
-    * Master equation +    * MAPK exercises
-    * Trivalent mass action+
  
  
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-    * Hill functions, n=1 and n=2 +    * MAPK cascade and transfer function 
-    * S-E-P stochastic simulation+    * 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 2 ====+==== Bibliography - electronic access - chapter 3 ====
  
  
-    * [[:wiki:chapter_2:chapter_2_electronic_bibliography|Here]]+    * [[:wiki:chapter_3:chapter_3_electronic_bibliography|Here]]
  
  
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-    * 2.1 Example: Growth factor response +    * 3.1 Network behavior 
-    *  +    * 3.2 Elementary network analysis 
-    * 2.5 Summary+    * 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 ===== ===== Missing Topics =====
  

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