Reading directions for reading material (kursbunten) 1=chapter of fundamental character/highest importance, 2=chapter of intermediate importance, 3=chapter with additional information. F0 Background for those who have not completed DD2401/HL1009/7E1201 Neuroscience. CellularNeuroBackground.pdf Skip the text about Cystic fibrosis. (can be found under lecture notes) NeuroscienceOverview.pdf (can be found under lecture notes) NumericsBackgroundDeSchutter1.pdf (can be found under lecture notes) http://www.biology-online.org/8/1_nervous_system.htm http://www.acm.uiuc.edu/sigbio/project/nervous/index.html See also: http://thalamus.wustl.edu/course/ http://normandy.sandhills.cc.nc.us/psy150/nervsys.html http://www.uta.edu/biology/restricted/3452nerv.htm http://www.educypedia.be/education/nervoussystem.htm F1 Introduction Bower & Bolouri, Computational modeling of genetic and biochemical networks, MIT Press Level 3 Chapter 10 The network within Bower & Beeman, The Book of Genesis, Internet edition If you have not completed DD2400/HL1008/7E1200 Cell and molecular biology or some other course in biochemistry, I reccomend that you read this on Level 2. F2 Physical biochemistry Westermark, del 1 1 Level 1 2 Level 1 (exept 2.2.1 Level 3) 3.1 Level 1 (exept 3.1.1 Level 2) 3.2 Level 1 4 Level 3 F3 Physical biochemistry Westermark, del 2 1 1.1 and 1.2 Level 1 but 1.2.2 Level 3 2 Level 3 F4 Chapter 2 Compartmental modeling Bower & Beeman, The Book of Genesis, Internet edition 2.1 Modeling neurons, Level 2 2.1.1 Detailed Compartemental Models, Level 1 2.1.2 Equivalent Cylinder Models, Level 1 2.1.3 Single and Few Compartment Models, Level 1 2.2 Equivalent circuit of a single compartment, Level 1 2.3 Axonal connections, synapses, and networks, Level 2 2.4 Simulation accuracy, Level 2 2.4.1 Choise of Numerical Integration Technique, Level 3 2.4.2 Integration Time Step, Level 3 Chapter 5.1-5.4 Cell membranes and ion movement Petersen, Basic Biophysics and cellular modeling, class notes Chapter 7.1 Cell membranes and ion movement Petersen, Basic Biophysics and cellular modeling, class notes Chapter 8.1-8.4 Cell membranes and ion movement Petersen, Basic Biophysics and cellular modeling, class notes Level for ch 5,7,8 is Level 1, to understand, know the prerequisites and be able to use: a) Nernst-Planck I eq b) Nernst eq c) Donnan rule d) GHK I eq e) GHK V eq F5 Chapter 4 The Hodgkin-Huxley model Bower & Beeman, The Book of Genesis, Internet edition 4.1, 4.2 Level 3 hela 4.3 Level 1 4.4 Level 2 F6 Chapter 5 Cable and compartmental models of dendritic trees Bower & Beeman, The Book of Genesis, Internet edition 5.1 Introduction, Level 2 5.2 Background, Level 2 5.2.1 Dendritic Trees: Anatomy, Physiology, and Synaptology, Level 3 5.3 The one-dimensional cable equation, Level 1 5.3.1 Basic Concepts and Assumptions, Level 2 5.3.2 The Cable Equation, Level 2 5.4 Solution of the cable equation for several cases, Level 2 5.4.1 Steady-state Voltage Attenuation with Distance, Level 2 5.4.2 Voltage Decay with Time, Level 2 5.4.3 Functional Significance of Lambda and Tau_m, Level 2 5.4.4 The Input Resistance Rin and "Trees Equivalent to a Cylinder", Level 1 5.5 Compartementalmodeling approach, Level 1 5.6 Compartementalmodeling experiments, Level 2 5.7 Main insights for passive dendrites with synapses, Level 1 5.8 Biophysics of excitable dendrites, Level 1 5.9 Computational function of dendrites, Level 1 F7 Chapter 6 Calcium dynamics in large neuronal models Koch & Segev, Methods in neuronal modeling 2ed, MIT press 6.2.1 Level 1 6.3.1 Level 1 6.3.2 Level 1 all 6.4 Level 1 all 6.6 Level 1 rest Level 3 You can also read the following on the web: chapter 3 in Gerstner and Kistler, Spiking Neuron Models. Single Neurons, Populations, Plasticity, Cambridge University Press, 2002 http://diwww.epfl.ch/~gerstner/SPNM/SPNM.html Models of development Sandberg (can be found under lecture notes) Level 3 F8 1 Modeling the activity of single genes Bower & Bolouri, Computational modeling of genetic and biochemical networks, MIT Press 1.1 1 1.2 3 1.3 2 1.4 1 1.5 1 Computational studies of gene regulatory networks Hasty & Co, Nature Level 3 Simulation of prokaryotic genetic circuits McAdams & Arkin, Annu Rev Biophys Biomol Struct Level 3 Understand lab3b, Level 1 F9 (only for D2435) Chapter 1 Kinetic models of synaptic transmission Koch & Segev, Methods in neuronal modeling 2ed, MIT press ch 1 1 ch 2 2 ch 3 2 ch 4 1 ch 5 1 Appendix 3 Synaptic plasticity Abbott & Nelson, Nature Level 3 Natural patterns of activity and long-term synaptic plasticity Paulsen & Sejnowski, Curr opinion neurobiol Level 3 You can also read the following on the web: chapter 10, 10.1 in Gerstner and Kistler, Spiking Neuron Models. Single Neurons, Populations, Plasticity, Cambridge University Press, 2002 http://diwww.epfl.ch/~gerstner/SPNM/SPNM.html F10 (only for D2435) Chapter 8 Central pattern generators Bower & Beeman, The Book of Genesis, Internet edition 8.1 1 8.2 1 8.2.1 1 8.2.2 3 8.2.3 2 8.2.4 2 8.2.5 3 8.3 3 Computational models of association cortex Gisiger & Co, Curr opinion neurobiol Introduction, första paragrafen 1 Introduction, resten 2 From cortical organization to perception 2 The gensiss of cortical maps 2 Re-entrance and the binding problem 3 Binoculatity and perception 3 Cognitive learnign 2 Reward-motivated learning, sid 253 2 Reward-motivated learning, sid 254 3 Auto-evalluation and hierarcical ... 3 The problem of consciousness 3 Dynamic core model 3 Global workspace model 3 Conclusions 1 You can also read the following on the web: chapter 6, 6.1 in Gerstner and Kistler, Spiking Neuron Models. Single Neurons, Populations, Plasticity, Cambridge University Press, 2002 http://diwww.epfl.ch/~gerstner/SPNM/SPNM.html