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AT2 – Neuromodeling Tutorial Anatoly Buchin & Fleur Zeldenrust February 11 th, 2013

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Essentially, all models are wrong, but some are useful George Edward Pelham Box

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How modeling works Real object Model Research progress, t Modeling Formalization Interpretation

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How modeling works Real object Model Research progress, t Modeling Formalization Interpretation Results Experiment

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Introduction Course outline What you will get: An overview of computational neuroscience: - describe neural systems with quantitative methods - simulate neural systems - learn about some specific topics Some numerical simulation basics - learn basic programming schemes - data management Scientific writing basics - writing reports - plotting nice figures etc

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Introduction Course outline But also: You should learn from each other: Learn to collaborate on projects especially across disciplins (Mathematicians vs. Biologists, etc…) We should learn form you! Feedback: tell us what do you think, which topics you would like to hear about Some help for your personal modeling projects

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Introduction Topics examples Reinforcement learning in biological systems Spike train statistics Single neuron dynamics Biophysics of neurons, integrate-and-fire, current-based models Much more (tell us what do you want)

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Introduction Course validation Marking: 50% homework, 50% final project Course work: Hand in work reports every 2/3 weeks or so (every project). Reports should be well redacted (i.e. not only consist of plots etc…) Home work: Background reading

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Introduction Course material Website: What youll find there: - lecture slides - problem sets, solutions - reading material Background reading: - P Dayan, LF Abbott Theoretical Neuroscience - MATLAB tutorials - SciLab tutorials - Numpy, Scipy tutorials

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Introduction Programming environments Scilab and Matlab is the preferred solution But Python as well, you could use any programming language Who knows about those? Who has used one of them? You need your laptop for every course Who doesnt have a laptop? Matlab

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Report Commented code

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Report Commented code Interpretation

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Report Commented code Interpretation Conclusions

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Report Commented code Interpretation Answers/Conclusions GOOD FIGURES!

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What is on this Figure?

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Axis

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Axis+Labels

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Axis+Labels+Title

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Axis+Labels+Title+Units

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Axis+Labels+Title+Units+Explanation

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Axis+Labels+Title+Units+Explanation+Legend Dotted line – linear interpolation Points – data with standard error Dotted line – linear interpolation Points – data with standard error

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Introduction TO DO now If you have: a) Installed all of the packages already b) some knowledge of programming, arrays, functions, etc… c) signed the attendance sheet Then you can either go through the first project, or you are free to go now. For the others: 1) install the packages etc… 2) learn about some key concepts in programming 3) start working on the tutorial project

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Introduction Key concepts in programming Basic operators, command line, scripts Variables Arrays Functions Loops Conditional statements

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