initial commit

.gitignore

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+_site
+.DS_Store
+*.sublime-project
+*.sublime-workspace
+codekit-config.json
+node_modules
+Gemfile.lock
+.sass-cache

404.md

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+---
+layout: page
+title: "Page Not Found"
+description: "Page not found. Your pixels are in another canvas."
+comments: false
+share: false
+permalink: /404.html
+---  
+
+Sorry, but the page you were trying to view does not exist --- perhaps you can try searching for it below.
+
+<script type="text/javascript">
+  var GOOG_FIXURL_LANG = 'en';
+  var GOOG_FIXURL_SITE = '{{ site.url }}'
+</script>
+<script type="text/javascript"
+  src="//linkhelp.clients.google.com/tbproxy/lh/wm/fixurl.js">
+</script>

Gemfile

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+source 'https://rubygems.org'
+
+gem 'github-pages'
+gem 'octopress', '~> 3.0.0.rc.12'

Gruntfile.js

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+'use strict';
+module.exports = function(grunt) {
+
+  grunt.initConfig({
+    jshint: {
+      options: {
+        jshintrc: '.jshintrc'
+      },
+      all: [
+        'Gruntfile.js',
+        'assets/js/*.js',
+        '!assets/js/plugins/*.js',
+        '!assets/js/vendor/*.js',
+        '!assets/js/scripts.min.js'
+      ]
+    },
+    uglify: {
+      dist: {
+        files: {
+          'assets/js/scripts.min.js': [
+            'assets/js/plugins/*.js',
+            'assets/js/_*.js'
+          ]
+        }
+      }
+    },
+    imagemin: {
+      dist: {
+        options: {
+          optimizationLevel: 7,
+          progressive: true
+        },
+        files: [{
+          expand: true,
+          cwd: 'images/',
+          src: '{,*/}*.{png,jpg,jpeg}',
+          dest: 'images/'
+        }]
+      }
+    },
+    svgmin: {
+      dist: {
+        files: [{
+          expand: true,
+          cwd: 'images/',
+          src: '{,*/}*.svg',
+          dest: 'images/'
+        }]
+      }
+    },
+    watch: {
+      js: {
+        files: [
+          '<%= jshint.all %>'
+        ],
+        tasks: ['jshint','uglify']
+      }
+    },
+    clean: {
+      dist: [
+        'assets/js/scripts.min.js'
+      ]
+    },
+
+    githooks: {
+      all: {
+        'pre-commit': 'clean jshint uglify imagemin svgmin'
+      }
+    }
+
+  });
+
+  // Load tasks
+  grunt.loadNpmTasks('grunt-contrib-clean');
+  grunt.loadNpmTasks('grunt-contrib-jshint');
+  grunt.loadNpmTasks('grunt-contrib-uglify');
+  grunt.loadNpmTasks('grunt-contrib-watch');
+  grunt.loadNpmTasks('grunt-contrib-imagemin');
+  grunt.loadNpmTasks('grunt-svgmin');
+  grunt.loadNpmTasks('grunt-githooks');
+
+  // Register tasks
+  grunt.registerTask('default', [
+    'clean',
+    'uglify',
+    'imagemin',
+    'svgmin'
+  ]);
+  grunt.registerTask('dev', [
+    'watch'
+  ]);
+
+};

LICENSE

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+The MIT License (MIT)
+
+Copyright (c) 2015 Aron Bordin
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

Rakefile.rb

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+require "rubygems"
+require "bundler/setup"
+require "stringex"
+
+## -- Config -- ##
+
+public_dir      = "public"    # compiled site directory
+posts_dir       = "_posts"    # directory for blog files
+new_post_ext    = "md"  # default new post file extension when using the new_post task
+new_page_ext    = "md"  # default new page file extension when using the new_page task
+
+
+#############################
+# Create a new Post or Page #
+#############################
+
+# usage rake new_post
+desc "Create a new post in #{posts_dir}"
+task :new_post, :title do |t, args|
+  if args.title
+    title = args.title
+  else
+    title = get_stdin("Enter a title for your post: ")
+  end
+  filename = "#{posts_dir}/#{Time.now.strftime('%Y-%m-%d')}-#{title.to_url}.#{new_post_ext}"
+  if File.exist?(filename)
+    abort("rake aborted!") if ask("#{filename} already exists. Do you want to overwrite?", ['y', 'n']) == 'n'
+  end
+  tags = get_stdin("Enter tags to classify your post (comma separated): ")
+  puts "Creating new post: #{filename}"
+  open(filename, 'w') do |post|
+    post.puts "---"
+    post.puts "layout: post"
+    post.puts "title: \"#{title.gsub(/&/,'&')}\""
+    post.puts "modified: #{Time.now.strftime('%Y-%m-%d %H:%M:%S %z')}"
+    post.puts "tags: [#{tags}]"
+    post.puts "image:"
+    post.puts "  feature: "
+    post.puts "  credit: "
+    post.puts "  creditlink: "
+    post.puts "comments: "
+    post.puts "share: "
+    post.puts "---"
+  end
+end
+
+# usage rake new_page
+desc "Create a new page"
+task :new_page, :title do |t, args|
+  if args.title
+    title = args.title
+  else
+    title = get_stdin("Enter a title for your page: ")
+  end
+  filename = "#{title.to_url}.#{new_page_ext}"
+  if File.exist?(filename)
+    abort("rake aborted!") if ask("#{filename} already exists. Do you want to overwrite?", ['y', 'n']) == 'n'
+  end
+  tags = get_stdin("Enter tags to classify your page (comma separated): ")
+  puts "Creating new page: #{filename}"
+  open(filename, 'w') do |page|
+    page.puts "---"
+    page.puts "layout: page"
+    page.puts "permalink: /#{title.to_url}/"
+    page.puts "title: \"#{title}\""
+    page.puts "modified: #{Time.now.strftime('%Y-%m-%d %H:%M')}"
+    page.puts "tags: [#{tags}]"
+    page.puts "image:"
+    page.puts "  feature: "
+    page.puts "  credit: "
+    page.puts "  creditlink: "
+    page.puts "share: "
+    page.puts "---"
+  end
+end
+
+def get_stdin(message)
+  print message
+  STDIN.gets.chomp
+end
+
+def ask(message, valid_options)
+  if valid_options
+    answer = get_stdin("#{message} #{valid_options.to_s.gsub(/"/, '').gsub(/, /,'/')} ") while !valid_options.include?(answer)
+  else
+    answer = get_stdin(message)
+  end
+  answer
+end

_config.yml

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+title:            Systems Biology Lab
+description:      Systems Biology Lab webpage @ Institute of Molecular Biology and Genetics of NASU
+# put your disqus here
+disqus_shortname: 
+reading_time:     true # if true, shows the estimated reading time for a post
+words_per_minute: 200
+logo:             images/logo.svg # logo visible in the topbar
+# Your site's domain goes here (eg: //mmistakes.github.io, http://mademistakes.com, etc)
+# When testing locally leave blank or use http://localhost:4000
+
+url:
+
+# draw your top menu here
+# each item must have a title and a url.
+#   To list post categories. use type: 'categories'
+#   To create sub categories. add a submenu item
+# See the example
+menu:
+  - title: 'Home'
+    url: '/'
+  - title: 'Research'
+    url: '/research'
+    submenu:
+      - title: 'Projects'
+        url: '/research/projects'
+      - title: 'Publications'
+        url: '/research/publications'
+      - title: 'Tools'
+        url: '/research/tools'
+      #- title: 'Protocols'
+      #  url: '/research/protocols'
+      #- title: 'Data'
+      #  url: '/research/data'
+  - title: 'Team'
+    url: '/team'
+  #- title: 'Tags'
+  #  url: '/tags'
+  - title: 'Contacts'
+    url: '/contacts'
+
+# Owner/author information
+owner:
+  name:           Alina Frolova
+  site:           https://github.com/alnf
+  avatar:         images/avatar.jpg
+  bio:            "Juniout Scientific Researcher at the Institute of Molecular Biology and Genetics of NASU"
+  email:          [email protected]
+  # GitHub nick for use in follow button in author block.
+  github: alnf
+
+# Twitter account associated with the site if different from owner/author twitter account.
+# Used in Twitter cards.
+twitter: 
+
+# Social networking links used in author block underneath posts. Update and remove as you like.
+social:
+  - title: "github"
+    url: "https://github.com/alnf"
+# Background image to be tiled on all pages
+background:
+
+# Analytics and webmaster tools stuff goes here
+google_analytics:
+google_verify:
+# https://ssl.bing.com/webmaster/configure/verify/ownership Option 2 content= goes here
+bing_verify:
+
+# http://en.wikipedia.org/wiki/List_of_tz_database_time_zones
+timezone:    Europe/Kiev
+locale:      en_US
+future:      true
+highlighter: rouge
+markdown:    kramdown
+gems:
+  - jekyll-sitemap
+sass:
+  sass_dir: _sass
+  style: compressed
+
+# https://github.com/mojombo/jekyll/wiki/Permalinks
+permalink:   /:categories/:title/
+
+# Amount of post to show on home page
+paginate: 5
+
+# if true, shows the floatting share buttons
+float_share: true
+
+kramdown:
+  auto_ids: true
+  footnote_nr: 1
+  entity_output: as_char
+  toc_levels: 1..6
+  syntax_highlighter: coderay
+
+  syntax_highlighter_opts:
+    line_numbers: nil
+    line_numbers_start: 1
+    tab_width: 4
+    bold_every: 10
+    css: class
+
+# Octopress
+# Default extensions
+post_ext: md
+page_ext: md
+# Found in _templates/
+post_layout: post
+page_layout: page
+# Format titles with titlecase?
+titlecase: true
+
+include: [".htaccess"]
+exclude: ["lib", "config.rb", "Capfile", "config", "Gemfile", "Gemfile.lock", "README.md", "LICENSE", "log", "Rakefile", "Rakefile.rb", "tmp", "less", "*.sublime-project", "*.sublime-workspace", "test", "spec", "Gruntfile.js", "package.json", "node_modules"]
+gems: [jekyll-paginate]

_includes/author.html

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+<div class="read-more">
+  <div class="read-more-header">
+    <a href="{{ site.owner.site }}" class="read-more-btn">About the Author</a>
+  </div><!-- /.read-more-header -->
+  <div class="read-more-content author-info">
+    <h3>{{site.owner.name}}</h3>
+    <div class="author-container">
+      <img class="author-img" src="{{site.url}}/{{site.owner.avatar}}" alt="{{site.owner.name}}" />
+      <div class="author-bio">{{site.owner.bio}}</div>
+    </div>
+    <div class="author-share">
+      <ul class="list-inline social-buttons">
+        {% for network in site.social %}
+          <li><a href="{{ network.url }}" target="_blank"><i class="fa fa-{{ network.title }} fa-fw"></i></a></li>
+        {% endfor %}
+      </ul>
+      {% if site.owner.github %}
+        <a aria-label="Follow @{{site.owner.github}} on GitHub" data-style="mega" href="https://github.com/{{site.owner.github}}" class="github-button">Follow @{{site.owner.github}}</a>
+      {% endif %}
+      <br>
+      {% if site.owner.twitter %}
+        <a href="https://twitter.com/{{site.owner.twitter}}" class="twitter-follow-button" data-show-count="false" data-size="large">Follow @{{site.owner.twitter}}</a>
+      {% endif %}
+    </div>
+  </div>
+</div>

_includes/browser-upgrade.html

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+<!--[if lt IE 9]><div class="upgrade"><strong><a href="http://whatbrowser.org/">Your browser is quite old!</strong> Why not upgrade to a different browser to better enjoy this site?</a></div><![endif]-->