Whiteglass theme

Gemfile

@@ -12,7 +12,7 @@ ruby RUBY_VERSION
 gem "jekyll", "3.4.3"
 
 # This is the default theme for new Jekyll sites. You may change this to anything you like.
-gem "minima", "~> 2.0"
+gem "jekyll-whiteglass"
 
 # If you want to use GitHub Pages, remove the "gem "jekyll"" above and
 # uncomment the line below. To upgrade, run `bundle update github-pages`.

Gemfile.lock

@@ -17,20 +17,28 @@ GEM
       pathutil (~> 0.9)
       rouge (~> 1.7)
       safe_yaml (~> 1.0)
+    jekyll-archives (2.1.1)
+      jekyll (>= 2.4)
     jekyll-feed (0.9.2)
       jekyll (~> 3.3)
+    jekyll-paginate (1.1.0)
     jekyll-sass-converter (1.5.0)
       sass (~> 3.4)
+    jekyll-sitemap (1.1.1)
+      jekyll (~> 3.3)
     jekyll-watch (1.5.0)
       listen (~> 3.0, < 3.1)
+    jekyll-whiteglass (1.3.0)
+      jekyll (~> 3.3)
+      jekyll-archives (~> 2.1)
+      jekyll-paginate (~> 1.1)
+      jekyll-sitemap (~> 1.0)
     kramdown (1.13.2)
     liquid (3.0.6)
     listen (3.0.8)
       rb-fsevent (~> 0.9, >= 0.9.4)
       rb-inotify (~> 0.9, >= 0.9.7)
     mercenary (0.3.6)
-    minima (2.1.1)
-      jekyll (~> 3.3)
     pathutil (0.14.0)
       forwardable-extended (~> 2.6)
     public_suffix (2.0.5)
@@ -52,7 +60,7 @@ PLATFORMS
 DEPENDENCIES
   jekyll (= 3.4.3)
   jekyll-feed (~> 0.6)
-  minima (~> 2.0)
+  jekyll-whiteglass
   tzinfo-data
 
 RUBY VERSION

_config.yml

@@ -26,9 +26,21 @@ github_username:  mdyzma
 
 # Build settings
 markdown: kramdown
-theme: minima
+theme: jekyll-whiteglass
 gems:
-  - jekyll-feed
+  - jekyll-archives
+  - jekyll-paginate
+  - jekyll-sitemap
 exclude:
   - Gemfile
   - Gemfile.lock
+permalink: /:year/:month/:day/:title/
+paginate_path: /posts/:num/
+paginate: 5
+
+jekyll-archives:
+  enabled:
+    - categories
+  layout: category_archives
+  permalinks:
+    category: /categories/:name/

_data/navigation.yml

@@ -0,0 +1,9 @@
+# If you want to link only specific pages in your header, add the path to the
+# pages in order as they should show up.
+main:
+  - title: "About"
+    url: /about/
+  - title: "Archives"
+    url: /archives/
+  - title: "GitHub"
+    url: https://github.com/yous/whiteglass

_posts/2017-04-13-welcome-to-jekyll.markdown → _posts/2017-04-15-welcome-to-jekyll.markdown

@@ -1,19 +1,19 @@
 ---
 layout: post
-title:  "Welcome to my Blog!"
-date:   2017-04-13 21:23:35 +0200
-categories: jekyll update
+title:  "Python, R and Julia in one notebook!"
+date:   2017-04-14 14:51:25 +0200
+categories: python R julia jupyter
 ---
 You’ll find this post in your `_posts` directory. Go ahead and edit it and re-build the site to see your changes. You can rebuild the site in many different ways, but the most common way is to run `jekyll serve`, which launches a web server and auto-regenerates your site when a file is updated.
 
 To add new posts, simply add a file in the `_posts` directory that follows the convention `YYYY-MM-DD-name-of-post.ext` and includes the necessary front matter. Take a look at the source for this post to get an idea about how it works.
 
 Jekyll also offers powerful support for code snippets:
 
-{% highlight ruby %}
+{% highlight python %}
 def print_hi(name)
-  puts "Hi, #{name}"
-end
+  print("Hi, {0}".format(name))
+
 print_hi('Tom')
 #=> prints 'Hi, Tom' to STDOUT.
 {% endhighlight %}

about.md

@@ -1,15 +1,44 @@
 ---
-layout: page
-title: About
-permalink: /about/
+layout: default
+title:  About
+type: about
+resume: I'm Michal Dyzma, a data scientist from Poland. I enjoy building beautiful projects for science. Biology is my love, Data Science is my choice, Software Development is my way to combine them together.
 ---
 
-This is the base Jekyll theme. You can find out more info about customizing your Jekyll theme, as well as basic Jekyll usage documentation at [jekyllrb.com](https://jekyllrb.com/)
+Story and experience
+====================
 
-You can find the source code for the Jekyll new theme at:
-{% include icon-github.html username="jekyll" %} /
-[minima](https://github.com/jekyll/minima)
+Science is my passion. I graduated University of Lodz holding two M.Sc in my hand one in **Genetics** and one in **Neurobiology**. I was facinated how brain and basic blocks of our structure can influence each other. 
 
-You can find the source code for Jekyll at
-{% include icon-github.html username="jekyll" %} /
-[jekyll](https://github.com/jekyll/jekyll)
+Experimental research
+---------------------
+After graduation I began very humbly as a Lab technitian in Occupational Medicine Institute. Conducting behavioral and lab experiments for large EU project **Devnertox**. In 2006 I was granted Marie Curie Felowship and left Poland to do experimental work in very prestigious and very inteeresting topic - Effects of sleep restriction on human health. Project was realised in Andre Vesale Hospital near Brussels. In Vesale I was amazed by posibilities of the software clasifying human brain waives. It was my first, but not last contact with Matlab.
+
+Theoretical research
+--------------------
+After spending some time working on experimental side of the field (Devnertox, Sleep) I decided to go theoretical. As a result I defended PhD thesis in 2016, which expanded currently used mathematical models of the calcium dynamics in the eukaryotic cells. Adding microdomains to the equation and tracing calcium concentration in different cell compartments I was able to recreate initial steps of apoptosis, which is a process leading to the cells death. Numerical analysis of the model was done in Matlab. [**PhD Thesis (in Polish)**][phd-thesis]. 
+
+After my advanture with mathematical modelling I started to develop software using it. I have done some  protein-RNA docking during my post-doc training in one of the best labs in Europe [**IIMCB Laboratory of Bioinformatics and Protein Engineering**][bujnicki-lab] in Warsaw. Over there I got familiar with python and theoretical research on nucleic acids and proteins. 
+
+Corporate expeience
+-------------------
+
+That same year, [**GMV Aerospace**][gmv] hired me and I had the chance to work in very exciting and promising field - space projects. I maintained and developed software for ESA data processing centers.
+
+I'm currently living in Warsaw, Poland and working in [**GMV Aerospace**][gmv], developing softwre responsible for data processing from several satelites launched as a part of Living Planet Programm, a Euoropean Space Agency initiative dedicated to observe Earth from space and provide research data about Earth's atmosphere, magnetic field and photosythesis on the surface of the planet. Please visit [**Living Planet**][living-planet] for details.
+
+Here I am. Scientific background, author of many peer reviewed papers on biology, mathematical mmodels and bioinformatics with corporate, large software house, experience in one. 
+
+From time to time I write stuff on [Twitter][tw] and throw some code on [GitHub][gh].
+
+**Enjoy!**
+
+
+
+[tw]: https://twitter.com/MichalDyzma
+[gh]: https://github.com/mdyzma
+[phd-thesis]: https://github.com/mdyzma/phd_thesis/
+[living-planet]: http://www.esa.int/Our_Activities/Observing_the_Earth/The_Living_Planet_Programme
+
+[bujnicki-lab]: http://genesilico.pl
+[gmv]: http://www.gmv.com/en/

archives.md

@@ -0,0 +1,5 @@
+---
+layout: archive
+title: "Blog Archive"
+permalink: /archives/
+---

feed.xml

@@ -0,0 +1,3 @@
+---
+layout: feed
+---

index.md → index.html

@@ -1,6 +1,6 @@
 ---
 # You don't need to edit this file, it's empty on purpose.
-# Edit theme's home layout instead if you wanna make some changes
+# Edit whiteglass' home layout instead if you want to make some changes.
 # See: https://jekyllrb.com/docs/themes/#overriding-theme-defaults
 layout: home
 ---