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

AT2 – Neuromodeling Tutorial

Anatoly Buchin & Fleur ZeldenrustFebruary 11th, 2013

anatolii.buchin@ens.fr fleur.zeldenrust@ens.fr

• 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