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AT2 – Neuromodeling Tutorial
Anatoly Buchin & Fleur ZeldenrustFebruary 11th, 2013
• Essentially, all models are wrong, but some are usefulGeorge Edward Pelham Box
How modeling works
Real object
Model
Research progress, t
Modeling
Formalization Interpretation
How modeling works
Real object
Model
Research progress, t
Modeling
Formalization Interpretation
Results Experiment
IntroductionCourse 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
IntroductionCourse 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
IntroductionTopics 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)
IntroductionCourse 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
IntroductionCourse material
Website: http://www.gnt.ens.fr/~fzeldenrust/AT2_2013.html
What you’ll find there:- lecture slides- problem sets, solutions- reading material
Background reading:- P Dayan, LF Abbott Theoretical Neuroscience- MATLAB tutorials- SciLab tutorials- Numpy, Scipy tutorials
IntroductionProgramming 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 courseWho doesn’t have a laptop?
Matlab
Report
• Commented code
Report
• Commented code
• Interpretation
Report
• Commented code
• Interpretation
• Conclusions
Report
• Commented code
• Interpretation
• Answers/Conclusions
• GOOD FIGURES!
What is on this Figure?
Axis
Axis+Labels
Axis+Labels+Title
Axis+Labels+Title+Units
Axis+Labels+Title+Units+Explanation
Axis+Labels+Title+Units+Explanation+Legend
Dotted line – linear interpolationPoints – data with standard error
IntroductionTO DO now
If you have:a) Installed all of the packages alreadyb) 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 programming3) start working on the tutorial project
IntroductionKey concepts in programming
Basic operators, command line, scripts
Variables
Arrays
Functions
Loops
Conditional statements
