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KordingLab · Feb 2, 2016 · 537192c · 537192c
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diff --git a/.gitignore b/.gitignore
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+
+# Created by https://www.gitignore.io/api/jekyll,pycharm,osx
+
+### Jekyll ###
+_site/
+.sass-cache/
+.jekyll-metadata
+
+
+### PyCharm ###
+# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio and Webstorm
+
+*.iml
+
+## Directory-based project format:
+.idea/
+# if you remove the above rule, at least ignore the following:
+
+# User-specific stuff:
+# .idea/workspace.xml
+# .idea/tasks.xml
+# .idea/dictionaries
+# .idea/shelf
+
+# Sensitive or high-churn files:
+# .idea/dataSources.ids
+# .idea/dataSources.xml
+# .idea/sqlDataSources.xml
+# .idea/dynamic.xml
+# .idea/uiDesigner.xml
+
+# Gradle:
+# .idea/gradle.xml
+# .idea/libraries
+
+# Mongo Explorer plugin:
+# .idea/mongoSettings.xml
+
+## File-based project format:
+*.ipr
+*.iws
+
+## Plugin-specific files:
+
+# IntelliJ
+/out/
+
+# mpeltonen/sbt-idea plugin
+.idea_modules/
+
+# JIRA plugin
+atlassian-ide-plugin.xml
+
+# Crashlytics plugin (for Android Studio and IntelliJ)
+com_crashlytics_export_strings.xml
+crashlytics.properties
+crashlytics-build.properties
+fabric.properties
+
+
+### OSX ###
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
diff --git a/404.md b/404.md
@@ -0,0 +1,6 @@
+---
+title: 404 Not Found
+permalink: /404.html
+---
+
+Sorry, but the page you were trying to view does not exist.
diff --git a/README.md b/README.md
@@ -0,0 +1,3 @@
+# kording lab's blog
+
+Follow instruction [here](https://jekyllrb.com/) to run Jekyll. To run jekyll server locally, use `jekyll serve`.
diff --git a/_config.yml b/_config.yml
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+# # # # # # # #
+#   K i k o   #
+# # # # # # # #
+
+# Basic
+name:               "kording lab's blog"
+title:              "blog for kording lab"
+description:        "this is an awesome blog for kording lab"
+
+
+# URL
+url:                http://kordinglab.github.io
+baseurl:
+#baseurl:            "" #For Root Domain
+permalink:          /:year/:month/:day/:title.html
+
+# Markdown
+markdown:           kramdown
+
+# Navigation
+nav:
+  - name:           "home"
+    href:           "//kordinglab.github.io/"
+  - name:           "about"
+    href:           "//kordinglab.github.io/about"
+  - name:           "blog"
+    href:           "//kordinglab.github.io/blog"
+  - name:           "reference"
+    href:           "//kordinglab.github.io/reference"
+
+# Sass
+sass:
+  style:            :compressed
+
+# Scopes
+defaults:
+  -
+    scope:
+      path:         ""
+      type:         "pages"
+    values:
+      layout:       "page"
+  -
+    scope:
+      path:         ""
+      type:         "posts"
+    values:
+      layout:       "post"
diff --git a/_layouts/default.html b/_layouts/default.html
@@ -0,0 +1,36 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+  <meta charset="utf-8">
+  <meta name="viewport" content="width=device-width, initial-scale=1">
+  <title>{% if page.title %}{{ page.title }}{% else %}{{ site.name }}{% endif %}</title>
+  <link rel="stylesheet" href="//fonts.googleapis.com/css?family=Source+Sans+Pro:300,300i,600">
+  <link rel="stylesheet" type="text/css" href="//fonts.googleapis.com/css?family=Ubuntu+Mono" />
+  <link rel="stylesheet" type="text/css" href="//fonts.googleapis.com/css?family=Roboto" />
+  <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/font-awesome/4.5.0/css/font-awesome.min.css">
+  <link rel="stylesheet" href="{{ site.baseurl }}/style.css">
+
+  <!-- favicon -->
+  <link rel="shortcut icon" href="{{ site.url }}/favicon.ico">
+  <link rel="shortcut icon" href="{{ site.url }}/favicon.png">
+  <link rel="apple-touch-icon-precomposed" href="{{ site.url }}/images/logo/apple-touch-icon-precomposed.png">
+  <link rel="apple-touch-icon-precomposed" sizes="72x72" href="{{ site.url }}/images/logo/apple-touch-icon-72x72-precomposed.png">
+  <link rel="apple-touch-icon-precomposed" sizes="114x114" href="{{ site.url }}/images/logo/apple-touch-icon-114x114-precomposed.png">
+  <link rel="apple-touch-icon-precomposed" sizes="144x144" href="{{ site.url }}/images/logo/apple-touch-icon-144x144-precomposed.png">
+
+  <!-- open graph -->
+  <meta property="og:locale" content="en_US">
+  <meta property="og:type" content="article">
+  <meta property="og:url" content="{{ site.url }}">
+  <meta property="og:title" content="{{ site.title }}">
+  <meta property="og:site_name" content="{{ site.title }}">
+  <meta property="og:image" content="{{ site.url }}/images/logo/logo_square.jpg">
+  <meta property="og:description" content="{{ site.description }}" />
+
+</head>
+<body>
+  <div class="container">
+    {{ content }}
+  </div>
+</body>
+</html>
diff --git a/_layouts/page.html b/_layouts/page.html
@@ -0,0 +1,14 @@
+---
+layout: default
+---
+<header class="masthead">
+  <nav class="masthead-nav">
+    {% for nav in site.nav %}
+    <a href="{{ nav.href }}">{{ nav.name }}&nbsp&nbsp&nbsp/</a>
+    {% endfor %}
+  </nav>
+</header>
+<div class="content page">
+  <!-- <h1 class="page-title">{{ page.title }}</h1> -->
+  {{ content }}
+</div>
diff --git a/_layouts/post.html b/_layouts/post.html
@@ -0,0 +1,14 @@
+---
+layout: default
+---
+<header class="masthead">
+  <nav class="masthead-nav">
+    {% for nav in site.nav %}
+    <a href="{{ nav.href }}">{{ nav.name }}&nbsp&nbsp&nbsp/</a>
+    {% endfor %}
+  </nav>
+</header>
+<div class="content post">
+  <strong><p>{{ page.title }}</strong>, {{ page.date | date_to_string }}</p>
+  {{ content }}
+</div>
diff --git a/_posts/2016-01-01-test.md b/_posts/2016-01-01-test.md
@@ -0,0 +1,6 @@
+---
+title: welcome to kording lab blog
+---
+
+some how we have a lot of good material on the page and it will be nice to
+share it on the nice blog!
diff --git a/_references/2016-01-01-firstreference.md b/_references/2016-01-01-firstreference.md
@@ -0,0 +1,5 @@
+---
+title: Paper Writing 101
+---
+
+This document is meant to give a simple check list for paper writing (journal articles) in cognitive science and neuroscience, originally put together for the Kording lab. It includes a range of insights I adapted from the (highly recommendable) and more general list by [Dan Simons](http://www.dansimons.com/resources/writing_tips.html). Also added some ideas from Tony Zador. Comments are welcome. Keep in mind that these rules (under rare circumstances) may be broken.
diff --git a/about.md b/about.md
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+---
+title: About
+permalink: /about/
+---
+
+### about us
+
+Our research fluctuates a bit based on what interests us and the strengths of our lab members. We invite you to contact us with collaboration ideas. We tend to focus on Bayesian and data analysis methods and we want to help in the production of data.
+
+
+### research
+
+We are data scientists with an interest in understanding the brain. Making sense of data is possibly the biggest problem in Neuroscience. We build algorithms to analyze data. We also use theory as well as computational and [neural modeling](https://en.wikipedia.org/wiki/Computational_neuroscience) to understand how information is processed in the nervous system, explaining data obtained in collaboration with [electrophysiologists](https://en.wikipedia.org/wiki/Electrophysiology) and in [psychophysical](https://en.wikipedia.org/wiki/Psychophysics) experiments. Lastly, we constrain and develop new technologies aimed at obtaining data about brains.
+
+
+Our conceptual work in the Bayesian Behavior Lab addresses information processing in the nervous system from two angles: (1) By analyzing and explaining electrophysiological data, we study what neurons do. (2) By analyzing and explaining human behavior, we study what all these neurons do together. Much of our work looks at these questions from a normative viewpoint, asking what problems the nervous system should be solving. This often means taking a Bayesian approach. Bayesian decision theory is the systematic way of calculating how the nervous system may make good decisions in the presence of uncertainty.
+
+We've pursued projects that involve handshake greetings, human movement, [cell-phone related parkinson's research](http://journal.frontiersin.org/article/10.3389/fneur.2012.00158/abstract), competitions at [Kaggle](https://www.kaggle.com/), [meta-science analysis](http://www.nature.com/nature/journal/v489/n7415/full/489201a.html), data sharing initiatives, and [recording from all neurons in a mouse](http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002291).
+
+
+### lab members
+
+Our research group is remarkably interdisciplinary. Our interests span statistics, physics, biology, applied mathematics, molecular biology, metascience, cognitive science, and many other disciplines. Visit our [people page](http://klab.smpp.northwestern.edu/wiki/index.php5/People) to see more information on each person who works in the lab (publications, contact information, photos).
+
+
+### publications
+
+For PDFs of our work, visit our [publications page](http://klab.smpp.northwestern.edu/wiki/index.php5/Publications).
diff --git a/blog.md b/blog.md
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+---
+title: Blog
+permalink: /blog/
+---
+
+**all the blog post from the lab**
+
+<div class="content list">
+
+  {% for post in site.posts %}
+    <div class="list-item">
+      <p class="list-post-title">
+        <a href="{{ site.baseurl }}{{ post.url }}">- {{ post.title }}</a>
+      </p>
+    </div>
+  {% endfor %}
+
+</div>
diff --git a/favicon.ico b/favicon.ico
diff --git a/favicon.png b/favicon.png
diff --git a/feed.xml b/feed.xml
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+---
+layout: null
+---
+<?xml version="1.0" encoding="UTF-8"?>
+<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom" xmlns:dc="http://purl.org/dc/elements/1.1/">
+	<channel>
+		<title>{{ site.name | xml_escape }}</title>
+		<link>{{ site.url }}</link>
+		<atom:link href="{{ site.url }}/feed.xml" rel="self" type="application/rss+xml" />
+		{% for post in site.posts %}
+			<item>
+				<title>{{ post.title | xml_escape }}</title>
+        <description>{{ post.content | xml_escape }}</description>
+				<pubDate>{{ post.date | date_to_rfc822 }}</pubDate>
+				<link>{{ site.url }}{{ post.url }}</link>
+				<guid isPermaLink="true">{{ site.url }}{{ post.url }}</guid>
+			</item>
+		{% endfor %}
+	</channel>
+</rss>
diff --git a/images/blog/botanic/1.jpg b/images/blog/botanic/1.jpg
diff --git a/images/blog/botanic/2.jpg b/images/blog/botanic/2.jpg
diff --git a/images/blog/botanic/3.jpg b/images/blog/botanic/3.jpg
diff --git a/images/blog/botanic/4.jpg b/images/blog/botanic/4.jpg
diff --git a/images/blog/nyc/1.jpg b/images/blog/nyc/1.jpg
diff --git a/images/blog/nyc/2.jpg b/images/blog/nyc/2.jpg
diff --git a/images/blog/nyc/3.jpg b/images/blog/nyc/3.jpg
diff --git a/images/blog/nyc/4.jpg b/images/blog/nyc/4.jpg
diff --git a/images/blog/nyc/5.jpg b/images/blog/nyc/5.jpg
diff --git a/images/logo/apple-icon-114x114.png b/images/logo/apple-icon-114x114.png
diff --git a/images/logo/apple-icon-144x144.png b/images/logo/apple-icon-144x144.png
diff --git a/images/logo/apple-icon-72x72.png b/images/logo/apple-icon-72x72.png
diff --git a/images/logo/apple-icon-precomposed.png b/images/logo/apple-icon-precomposed.png
diff --git a/images/logo/logo_share.jpg b/images/logo/logo_share.jpg
diff --git a/images/logo/logo_share.png b/images/logo/logo_share.png
diff --git a/images/logo/logo_square.jpg b/images/logo/logo_square.jpg
diff --git a/images/pdf/Titipat_CV.pdf b/images/pdf/Titipat_CV.pdf
diff --git a/images/titipata.jpg b/images/titipata.jpg
diff --git a/index.html b/index.html
@@ -0,0 +1,25 @@
+---
+layout: default
+---
+<header class="masthead">
+  <nav class="masthead-nav">
+    {% for nav in site.nav %}
+    <a href="{{ nav.href }}">{{ nav.name }}&nbsp&nbsp&nbsp/</a>
+    {% endfor %}
+  </nav>
+  <h1 class="masthead-title">
+    {{ site.name }}
+  </h1>
+
+  <p><em>Brain, behavior and cognition, science and scientists,
+    and the dream that our ideas and not our data limit the questions we can ask.</em></p>
+
+  <p>Rehabilitation Institute of Chicago, Northwestern University<br>
+    345 E Superior St, Rm 1479, Chicago, IL
+    <br>
+    <br>
+  <a href="http://klab.smpp.northwestern.edu/wiki/index.php5/Main_Page"><i class="fa fa-share-alt"></i> website</a><br>
+  <a href="https://github.com/KordingLab"><i class="fa fa-github"></i> Github</a><br>
+  <a href="https://twitter.com/KordingLab"><i class="fa fa-twitter"></i> Twitter</a>
+  </p>
+</header>
diff --git a/references.md b/references.md
@@ -0,0 +1,18 @@
+---
+title: Reference
+permalink: /reference/
+---
+
+**all the useful stuff from Kording lab page**
+
+<div class="content list">
+
+  {% for ref in site.references %}
+    <div class="list-item">
+      <p class="list-post-title">
+        <a href="{{ site.baseurl }}{{ ref.url }}">- {{ ref.title }}</a>
+      </p>
+    </div>
+  {% endfor %}
+
+</div>