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<div id="content">
<h1 class="title">Neuron Simulation, notes</h1>
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#sec-1">Week 1 - Simulation Neuroscience: An Introduction</a>
<ul>
<li><a href="#sec-1-1">Understanding the brain</a></li>
<li><a href="#sec-1-2">Experimental data</a></li>
<li><a href="#sec-1-3">Caveats?</a></li>
<li><a href="#sec-1-4">Single neuron data.</a></li>
<li><a href="#sec-1-5">Extra Annotation.</a></li>
<li><a href="#sec-1-6">Synapses</a></li>
<li><a href="#sec-1-7">Graded Quiz 1: An introduction to Simulation Neuroscience</a></li>
<li><a href="#sec-1-8">Graded week quiz This content is graded</a></li>
</ul>
</li>
<li><a href="#sec-2">Week 2 - Neuroinformatics</a></li>
<li><a href="#sec-3">Week 3 - Modeling Neurons</a></li>
<li><a href="#sec-4">Week 4 - Modeling Synapses</a></li>
<li><a href="#sec-5">Week 5 - Constraining Neuron Models with Experimental Data</a></li>
</ul>
</div>
</div>
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 <a accesskey="h" href="index.html"> UP </a>
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<div id="outline-container-sec-1" class="outline-2">
<h2 id="sec-1">Week 1 - Simulation Neuroscience: An Introduction</h2>
<div class="outline-text-2" id="text-1">
<p>
<a href="img/ns-w1-learning-goals.png">Learning goals</a>
</p>
</div>
<div id="outline-container-sec-1-1" class="outline-3">
<h3 id="sec-1-1">Understanding the brain</h3>
<div class="outline-text-3" id="text-1-1">
<p>
Approaches, which, in turns, following out three branches of exploratory science:
</p>
<ul class="org-ul">
<li>Experimental, 
</li>
<li>Theoretical
<ol class="org-ol">
<li>Informatics neuroscience (looking at trend, correlations and patterns in data), 
</li>
<li>Theoretical neuroscience (explaining the data and predicting 
</li>
<li>Computational neuroscience (creating minimal model that fit specific experimental data), 
</li>
<li>Applied neuroscience (using neurosciences in medicine and engineering by notably building machine to see how the neurons work) 
</li>
</ol>
</li>
<li>&amp; Simulation (or <code>lqqd</code> that this course is about).
</li>
</ul>
<p>
Principles:
</p>
<ul class="org-ul">
<li>Dense reconstructions (it's about an <i>ordered</i> system so, opposite than it were about a <i>random system</i>) it's assumed to get done algorithmically (the smallest data set with &amp; the [algorithm|s] which [rule|s] over).
</li>
<li>Bottom-up reconstructions, 
</li>
<li>Iteratively reconstructions &amp; test.
</li>
</ul>
</div>
</div>
<div id="outline-container-sec-1-2" class="outline-3">
<h3 id="sec-1-2">Experimental data</h3>
<div class="outline-text-3" id="text-1-2">
<p>
I am going to track this exploration on the subject on a handful of idea tools as keystrokes, connections <code>|</code> flows &amp; systems <code>|</code> circuits. 
</p>
<ul class="org-ul">
<li>So, my first annotation here is the flow in which this approach about neuron as a whole is on, ion channels, synapses &amp; neuron circuits.
</li>
<li>Now lets track the info source in terms of simulation so we can control also the replication method (rationale &amp; the complexion itself got made)
<ul class="org-ul">
<li><code>ion channel</code> channel screening, biophysical screening so the explore the biophysics of these channels..  implying kinetics (open closed) of the channels, its distribution, combination, conductance, so modelling the ion channel, its morphology and | or its electrical behaviour,  
</li>
<li><code>neurons</code> paired recordings, staining the two..
</li>
<li><code>n. circuits</code> antibody staining, in situ hybridization, 
</li>
</ul>
</li>
</ul>
<p>
The question quiz here is indeed my point when defining the keystroke specially about (simulating) neuron.
</p>

<p>
&#x2014; What is, in your opinion, the main challenge in mining of existing knowledge on the brain.
I feel the keystroke about mining is the coding language we opted to interpret the data and build to simulations. As a programming language is necessary, the question easily gets deviation to the interface or media used itself, its virtues, shortcomings and so on. Especially if researchers are previously versed in any of them. I do not think this fact were intrinsic wrong, researchers should be able to explain their approaches within plenty of comfort zones. However this fact triggers at least two inconveniences: First, it narrows the replication, or, the result evaluation or, lets also call it, the discussion phase, into groups based on the language media used to expose the results or its eventual approaches. How many times me myself, as student or, just as, an intelligent plain man interested in the field have had to just observe what exposed and without ability to replying because of the programming language barrier. So that as soon as you decide to get levelled-enough literacy to, in turn, get into that specific discussion some more interactive, reply based on whatever different language tool there were out, shows up. So that, the easy route this question ends up is a kind of school of <i>exposition</i> problem.
</p>

<p>
A second inconvenience is the virtues of the media or language in question itself. A lot of discussions as I found got suck as function of packages used to expose approaches.
</p>

<p>
I think we have to agree in a kind of standard, a kind of <i>pseudo code</i> as a default language so that any researcher were able to replicate results.
</p>

<ul class="org-ul">
<li>Hey, &#x2014;mmm&#x2026; &#x2014;when, a kind of, <i>positive</i> difference, should not be considered an advantage, is that like, as I should get it rendered this, kind of, dissonance? Look at <a href="img/advantage-as-or-disavantage.png">this question</a> [ref: week1, practice quiz :reconstruction strategies] or is it just another issue for my <code>WTF</code> series collection?
</li>
</ul>
</div>
</div>

<div id="outline-container-sec-1-3" class="outline-3">
<h3 id="sec-1-3">Caveats?</h3>
<div class="outline-text-3" id="text-1-3">
<p>
Let's list some of them.
</p>
<ul class="org-ul">
<li>critical data may be missing
</li>
<li>biological data has a lot of mistakes (actually there are much more mistakes than accurate data)
</li>
<li>there are a lot of disciplines involved (which is not a caveat, really, though it get things complicated, critically complicated, actually).


<div class="figure">
<p><img src="img/week1-summary.png" alt="week1-summary.png" />
</p>
</div>
</li>
</ul>
</div>
</div>

<div id="outline-container-sec-1-4" class="outline-3">
<h3 id="sec-1-4">Single neuron data.</h3>
<div class="outline-text-3" id="text-1-4">
<p>
Basically in search of: IR-DC microscope, 
</p>
<ul class="org-ul">
<li>its electrical profile
</li>
<li>morphological profile,
</li>
<li>molecular profile.
</li>
</ul>
</div>
</div>


<div id="outline-container-sec-1-5" class="outline-3">
<h3 id="sec-1-5">Extra Annotation.</h3>
<div class="outline-text-3" id="text-1-5">
<p>
Hey, following a crash course on <code>#mozillaNetwork</code> projects I run out with this by itself gorgeous tools: The <a href="http://brainbox.pasteur.fr/">brain box</a> and <a href="http://js.cytoscape.org/#introduction">Cytoscape</a> a graph JS library useful as we are here trying to perform visual simulation, so let's check for it later in this course.
</p>
</div>
</div>
<div id="outline-container-sec-1-6" class="outline-3">
<h3 id="sec-1-6">Synapses</h3>
</div>
<div id="outline-container-sec-1-7" class="outline-3">
<h3 id="sec-1-7">Graded Quiz 1: An introduction to Simulation Neuroscience</h3>
</div>
<div id="outline-container-sec-1-8" class="outline-3">
<h3 id="sec-1-8">Graded week quiz This content is graded</h3>
</div>
</div>

<div id="outline-container-sec-2" class="outline-2">
<h2 id="sec-2">Week 2 - Neuroinformatics</h2>
<div class="outline-text-2" id="text-2">
<p>
Learning goals
Setup
Introduction to neuroinformatics
Knowledge graphs and ontologies
Neuroinformatics data
Acquisition of neuron electrophysiology and morphology
Morphological feature extraction
Graded Quiz 2: Neuroinformatics
Graded week quiz This content is graded
Graded assignment 1
Weekly graded assignment This content is graded
</p>
</div>
</div>

<div id="outline-container-sec-3" class="outline-2">
<h2 id="sec-3">Week 3 - Modeling Neurons</h2>
<div class="outline-text-2" id="text-3">
<p>
Learning goals
Introduction to the single neuron
The neuron
Electrical neuron model
Tutorials creating single cell electrical models
Graded Assignment 2
Weekly graded assignment This content is graded
Graded quiz 3
Graded week quiz This content is graded
</p>
</div>
</div>

<div id="outline-container-sec-4" class="outline-2">
<h2 id="sec-4">Week 4 - Modeling Synapses</h2>
<div class="outline-text-2" id="text-4">
<p>
Introduction and modeling synaptic potential
Modeling synaptic transmissions between neurons
Set up your Collab week 4
Tutorial: Modeling dynamic synapses
Graded Assignment 3
Weekly graded assignment This content is graded
Graded quiz 4
Graded week quiz This content is graded
</p>
</div>
</div>

<div id="outline-container-sec-5" class="outline-2">
<h2 id="sec-5">Week 5 - Constraining Neuron Models with Experimental Data</h2>
<div class="outline-text-2" id="text-5">
<p>
Constraining neuron models with experimental data
Set up you Collab week 5
Tutorials for optimisation
Graded Assignment 4
Weekly graded assignment This content is graded
Graded quiz 5
Graded week quiz This content is graded
</p>
</div>
</div>
</div>
<div id="postamble" class="status">
<p class="date">Date: 06 Dec. 2017</p>
<p class="author">Author: txarly</p>
<p class="date">Created: 2018-02-03 Sat 19:21</p>
<p class="creator"><a href="http://www.gnu.org/software/emacs/">Emacs</a> 25.3.1 (<a href="http://orgmode.org">Org</a> mode 8.2.10)</p>
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