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thesis/Masterthesis.out

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+\BOOKMARK [1][]{section.1}{Abstract}{}% 1
+\BOOKMARK [1][]{section.2}{Introduction}{}% 2
+\BOOKMARK [1][]{section.3}{Materials and Methods}{}% 3
+\BOOKMARK [2][]{subsection.3.1}{Notes:}{section.3}% 4
+\BOOKMARK [1][]{section.4}{Results}{}% 5
+\BOOKMARK [1][]{section.5}{Discussion}{}% 6

thesis/Masterthesis.tex

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+\documentclass[12pt,a4paper,pdftex]{article}
+\usepackage[left=25mm, right=25mm, top=20mm, bottom=25mm]{geometry}
+\usepackage{graphicx}
+\usepackage{amsmath}
+\usepackage{natbib}
+\usepackage[breaklinks=true,bookmarks=true,bookmarksopen=true,pdfpagemode=UseNone,pdfstartview=FitH,colorlinks=false,citecolor=blue]{hyperref}
+
+\usepackage[utf8x]{inputenc}
+\usepackage[english]{babel}
+%\usepackage{float}
+\usepackage{floatrow}
+
+\usepackage{listings} % für den code am Ende
+
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Ab hier beginnt der eigentliche Text:
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{document}
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Titelseite
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\begin{titlepage}
+		\begin{center}
+		{\Huge TITEL \par}
+		\vspace{0.75cm}
+		{\Large Masterthesis \par}
+		\vspace{0.25cm}
+		{der Mathematisch-Naturwissenschaftlichen Fakultät \par} {der Eberhard Karls Universität Tübingen \par}
+		\vspace{0.75cm}
+		{Erstkorrektor: \\
+		Zweitkorrektor: Prof.~Dr.~Jan Benda \par}
+		\vspace{0.25cm}
+		{Lehrbereich für Neuroethologie}
+		
+		\vfill
+		\large vorgelegt von \par
+		\large Alexander Mathias Ott \par
+		Abgabedatum: 30.11.2017
+	\end{center}
+\end{titlepage}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Erklärung
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section*{Eigenständigkeitserklärung}
+
+\vspace{0.5cm}
+
+Hiermit erkläre ich, dass ich die vorgelegte Arbeit selbstständig verfasst habe und keine anderen als die angegebenen Quellen und Hilfsmittel benutzt habe. 
+
+\vspace{2mm}
+\noindent
+Außerdem erkläre ich, dass die eingereichte Arbeit weder vollständig noch in wesentlichen Teilen Gegenstand eines anderen Prüfungsverfahrens gewesen ist.
+
+
+
+
+
+
+\vfill
+
+\begin{tabular}{ll}
+	$\overline{\text{Unterschrift}\hspace{6cm}}$ & $\overline{\text{Ort, Datum}\hspace{4cm}}$ \\
+\end{tabular}
+\newpage\newpage
+
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Inhalsverzeichnis
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+{
+ \hypersetup{linkcolor=black}
+ \tableofcontents
+}
+
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Zusammenfassung
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Abstract}
+%Einleitung + Ergebnisse der Diskussion in kurz
+
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Einleitung
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Introduction}
+
+\begin{enumerate}
+	\item electric fish
+	\begin{enumerate}
+		\item general: habitat, 
+		\item as model animal for ethology
+		\item electric organ + eod
+		\item sensory neurons p- and t(?)-type
+	\end{enumerate}
+	\item sensory perception
+	\begin{enumerate}
+		\item receptor -> heterogenic population
+		\item further analysis limited by what receptors code for
+		\item p-type neurons code AMs
+	\end{enumerate}
+	
+	\item goal be able to simulate heterogenic population to analyse full coding properties -> many cells at the same time needed -> only possible in vitro/ with model simulations
+	
+	\item Possible to draw representative values for model parameters to generate a population ?
+	
+
+\end{enumerate}
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Methoden
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+\section{Materials and Methods}
+
+\subsection{Notes:}
+
+\begin{enumerate}
+	
+	\item Construction of model
+	\begin{enumerate}
+		\item Explain general LIF
+		\item parameters explanation, dif. equations
+		\item Explain addition of adaption current
+		\item note addition of noise
+		\item check between alpha in fire-rate model adaption and a-delta in LIFAC
+		\item check for noise independence from step-size (?)
+	\end{enumerate}
+	
+	\item Data generation
+	\begin{enumerate}
+		\item How data was measured / which data used
+		\item How data was chosen -> at least 30s baseline, 7 contrasts with 7 trials
+		\item experimental protocells were allowed by XYZ (before 2012: All experimental protocols were approved and complied with national and regional laws (file no. 55.2-1-54-2531-135-09). between 2013-2016 ZP 1/13 Regierungspräsidium Tübingen and after 2016 ZP 1/16 Regierungspräsidium Tübingen)
+	\end{enumerate}
+	
+	\item behavior parameters:
+	\begin{enumerate}
+		\item which behaviors were looked at / calculated and why (bf, vs, sc, cv, fi-curve...)
+		\item how exactly were they calculated in the cell and model
+	\end{enumerate}		
+	
+	\item Fitting of model to data
+	\begin{enumerate}
+		\item which variables where determined beforehand (None, just for start parameters)
+		\item which variables where fit 
+		\item What method was used (Nelder-Mead) and why/(how it works?)
+		\item fit routine ? (currently just all at the same time)
+	\end{enumerate}
+\end{enumerate}
+
+
+\section{Results}
+
+\begin{enumerate}
+
+\item how well does the fitting work? 
+
+\item distribution of behavior parameters (cells and models)
+
+\item distributions of parameters
+
+\item correlations: between parameters between parameters and behavior
+
+\item correlation between final error and behavior parameters of the cell -> hard to fit cell types
+
+\item (response to SAM stimuli)
+\end{enumerate}
+
+
+\section{Discussion}
+
+
+
+\section{Possible Sources}
+
+\subsection{Henriette Walz - Thesis}
+\subsubsection{Nervous system - Signal encoding}
+\begin{enumerate}
+\item single neurons are the building blocks of the nervous system (Cajal 1899)
+\item encoding of information in spike frequency - rate code(first description(?) Adrian 1928) also find examples! (light flash intensity Barlow et al. 1971, )
+\item encoding info in inter spike intervals (Singer and Gary 1995)
+\item encoding time window (Theunissen and Miller 1995) "This time window is the time scale in which the encoding is assumed to take placewithin the nervous system
+\item encoding is noisy (Mainen and Sejnowski 1995, Tolhurst et al 1983, Tomko and Crapper 1974 -> review Faisal et al 2008) in part because of stimulus properties but also cell properties (Ion channel stochasticity (van Rossum et al.,2003))
+\item noise can be beneficial to encoding -> “stochastic
+resonance” (weak stimuli on thresholding devices like neurons, noice allows coding of sub threshold stimuli) (Benzi et al., 1981)
+\end{enumerate}
+
+
+\end{document}

thesis/Masterthesis.toc

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+\select@language {english}
+\contentsline {section}{\numberline {1}Abstract}{2}{section.1}
+\contentsline {section}{\numberline {2}Introduction}{2}{section.2}
+\contentsline {section}{\numberline {3}Materials and Methods}{2}{section.3}
+\contentsline {subsection}{\numberline {3.1}Notes:}{2}{subsection.3.1}
+\contentsline {section}{\numberline {4}Results}{3}{section.4}
+\contentsline {section}{\numberline {5}Discussion}{3}{section.5}