186 lines
5.3 KiB
TeX
186 lines
5.3 KiB
TeX
\documentclass[12pt]{book}
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\input{header}
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\newcommand{\includechapter}[1]{%
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\graphicspath{{#1/lecture/}{#1/lecture/figures/}{#1/images/}}%
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\setcodepath{#1/code}%
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\include{#1/lecture/#1}%
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}
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%\includeonly{regression/lecture/regression}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\begin{document}
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\selectlanguage{english}
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\hypersetup{pageanchor=false}
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\maketitle
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\hypersetup{pageanchor=true}
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\frontmatter
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\clearpage
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\tableofcontents
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\clearpage
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\listoffigures
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\clearpage
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\lstlistoflistings
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\clearpage
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\listofexercisefs
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\clearpage
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\listofiboxfs
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\mainmatter
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% add introduction:
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% - data analysis skills way beyond basic statistical test are at the
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% core of modern neuroscience
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% - *understanding* of basic concepts of data analysis concepts is important
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% - math is the universal language of natural sciences, including neuroscience.
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% it is the most precise way to express relation.
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% We therefore expose you to some mathematical equations
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% that do not go beyond what you learned at school.
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% - most concepts are also quite relevant for the brain itself!
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% The brain also needs to analyse the data coming in from the senses.
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% - modern approaches:
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% * open source science (open data, open code, open algorithmns in contrast
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% to closed source license models), FAIR
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% * knowledge is freedom ...
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% * do not consume what companies offer you but know what you want and implement it
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% * no screenshots on how to use a stupid GUI program
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% * python as a modern and popular programming language in modern science
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% (i.e. machine learning, others?) with a strong community support.
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\part{Programming basics}
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\includechapter{programming}
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\includechapter{debugging}
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\includechapter{plotting}
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\includechapter{codestyle}
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\includechapter{designpattern}
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\part{Data analysis}
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%\subpart{Basic statistics}
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% With an intro saying statistical tests are overrated!
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% add chapter on stochastic simulations (draw random numbers, draw random functions)
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%\includechapter{simulations}
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\includechapter{statistics}
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% add chapter on statistical tests
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\includechapter{bootstrap}
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\includechapter{regression}
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% add chapter on nonlinear fitting (methods, initial values, local minima, power law fits on log-log data)
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\includechapter{likelihood}
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% add chapter on multivariate analysis/generalized linear models (in addition to ANOVA)
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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%\subpart{Time series}
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% add chapter on simulations of dynamical systems/time series (euler
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% forward, odeint, iterated maps, dynamical system, bifurcations?)
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% !!! this would be a nice and simple starter !!!
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% introduces derivatives which are also needed for fitting
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% add chapter on time series (amplitude distribution, autocorrelation, crosscorrelation)
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%\includechapter{spectral}
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% add chapter on filtering (1. order, butter and kernel convolution) and envelopes
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% add chapter on event detection (local maxima, threshold crossings,
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% peak detection), signal detection, ROC
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\includechapter{pointprocesses}
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% add a chapter on simulating point-processes/spike trains
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% (Poisson spike trains, LMP models, integrate-and-fire models, full HH like models)
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% add chapter on information theory, mutual information, stimulus reconstruction, coherence
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% move STA here!
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% add a chapter on Bayesian inference (the Neuroscience of it and a
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% bit of application for statistical problems).
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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%\subpart{Machine learning}
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% add chapters on linear algebra, PCA, clustering, see linearalgebra/
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% add chapter on logistic regression, see logistic/
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% add chapter on simple machine learning, perceptron
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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%\part{Tools}
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% add chapter on Markup and LaTeX -> see latex/
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% - if you know LaTeX you also know how to better use word/libreoffice
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% - with an introduction on mark-up in general, an outlook to markdown, html, xml, jason, yaml
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% - make notes, data, and texts understandable by computers!
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% - easily generate markup from python scripts via mako .
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% bash basics:
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% - calling a (python) script/program with arguments
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% - files: ls, cp, mkdir, find, etc.
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% - text file manipulations: grep, diff, sed, awk
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% - pipes, for loop, if, test
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% Makefile
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% distributed computing (ssh and grid engines)
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% see replicability/ :
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% - version control (git and github) only put source files into repository!
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% - data handling (structure, storage (rsync), backup, data bases)
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% - data annotation, meta data, FAIR
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\appendix
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\addtocontents{toc}{\setcounter{tocdepth}{0}}
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%\chapter{Cheat-Sheet}
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%%%% solutions: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\printallsolutions
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%%%% indices: %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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\backmatter
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\printindex[enterm]
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\selectlanguage{ngerman}
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\printindex[determ]
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\selectlanguage{english}
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%\setindexprenote{Some explanations.}
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%\printindex[pcode]
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\printindex[mcode]
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\end{document}
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