architecture overview and development guidelines added, categories and tags updated

49 files changed, 154 insertions, 113 deletions

diff --git a/_includes/themes/tom/default.html b/_includes/themes/tom/default.html
index 615389c..ddf4dfe 100644
--- a/_includes/themes/tom/default.html
+++ b/_includes/themes/tom/default.html
@@ -23,7 +23,7 @@
       <a href="{{ HOME_PATH }}">{{ site.title }}</a>
 
       <a class="extra" href="{{ BASE_PATH }}{{ site.JB.archive_path }}">Archive</a>
-      <a class="extra" href="{{ BASE_PATH }}{{ site.JB.pages_path }}">Pages</a>
+      <a class="extra" href="{{ BASE_PATH }}{{ site.JB.pages_path }}">Test</a>
       <a class="extra" href="{{ BASE_PATH }}{{ site.JB.categories_path }}">Categories</a>
       <a class="extra" href="{{ BASE_PATH }}{{ site.JB.tags_path }}">Tags</a>
     </div>
diff --git a/_layouts/default.html b/_layouts/default.html
index c175a7b..2d9be07 100644
--- a/_layouts/default.html
+++ b/_layouts/default.html
@@ -1,6 +1,6 @@
 ---
 theme :
-  name : tom
+  name : twitter
 ---
 {% include JB/setup %}
-{% include themes/tom/default.html %}
+{% include themes/twitter/default.html %}
diff --git a/_layouts/page.html b/_layouts/page.html
index 4a80f5e..a4a2d0b 100644
--- a/_layouts/page.html
+++ b/_layouts/page.html
@@ -2,4 +2,4 @@
 layout: default
 ---
 {% include JB/setup %}
-{% include themes/tom/page.html %}
+{% include themes/twitter/page.html %}
diff --git a/_layouts/post.html b/_layouts/post.html
index 47080b7..9971d7c 100644
--- a/_layouts/post.html
+++ b/_layouts/post.html
@@ -2,4 +2,4 @@
 layout: default
 ---
 {% include JB/setup %}
-{% include themes/tom/post.html %}
+{% include themes/twitter/post.html %}
diff --git a/_posts/2012-04-26-opentox-blogging.md b/_posts/2012-04-26-opentox-blogging.md
index 6de92a1..35b91f6 100644
--- a/_posts/2012-04-26-opentox-blogging.md
+++ b/_posts/2012-04-26-opentox-blogging.md
@@ -2,53 +2,41 @@
 layout: post
 title: "Blogging at opentox.github.com"
 description: ""
-category: meta
-tags: []
+category: Development
+tags: [Blogging]
 ---
 {% include JB/setup %}
 
-For OpenTox GitHub organization members only
-
 Install Jekyll
 --------------
-<br />
 
     gem install jekyll
 
-<br />
 Get opentox.github.com
 ----------------------
-<br />
 
     git clone git@github.com:opentox/opentox.github.com.git
 
-<br />
 Preview
 -------
-<br />
 
     cd opentox.github.com
     jekyll --server
 
 view at `http://localhost:4000`
 
-<br />
 Blog
 ----
-<br />
 
     rake post title="foo"
 
-Edit blog at `_posts/[...]foo.md. Use a [spell-checker](/linux/2012/05/18/using-vim/).
+Edit blog at `_posts/[...]foo.md`. Use a [spell-checker](/linux/2012/05/18/using-vim/).
 
-<br />
 Categories and tags
 -------------------
-<br />
 
-Categories should match github projects (e.g. client, server, algorithm, ...) or "general" for topics that apply to more than one project. 
-For larger collections of related documents that would go to "general", invent a new category to avoid crowding the "general" category.
-Use tags to refer to concepts (e.g REST, "support vector machines", ...). Please 
+Please choose one of the terms *Usage*, *Installation* or *Development* as a category for your post. 
+Use tags to refer to related concepts (e.g *REST*, *support vector machines*, ...). Please 
 
 - re-use existing tags as much as possible. 
 - when re-using, be sure to use the verbatim expression (e.g. capitalization).
@@ -57,13 +45,11 @@ This is important for the 'Related Posts' functionality (although it does not se
 
 Publish
 -------
-<br />
 
     git add .
     git commit -m "Add new content"
     git push 
 
-<br />
 Formatting
 -------
 * [Markdown Syntax Documentation](http://daringfireball.net/projects/markdown/syntax)
diff --git a/_posts/2012-05-01-services-tutorial---lazar-feature-generation-feature-selection-validation.md b/_posts/2012-05-01-services-tutorial---lazar-feature-generation-feature-selection-validation.md
index 5503c52..549998d 100644
--- a/_posts/2012-05-01-services-tutorial---lazar-feature-generation-feature-selection-validation.md
+++ b/_posts/2012-05-01-services-tutorial---lazar-feature-generation-feature-selection-validation.md
@@ -2,8 +2,8 @@
 layout: post
 title: "Lazar Feature Generation, Feature Selection, Validation"
 description: "This article illustrates feature generation, feature selection, and validation using opentox-ruby and the REST paradigm. As such, it may be useful as a high-level documentation."
-category: algorithm
-tags: [Feature Generation, Feature Selection, Validation, Tutorials]
+category: Usage
+tags: [Algorithm, Feature Generation, Feature Selection, Validation, Tutorials]
 ---
 {% include JB/setup %}
 
diff --git a/_posts/2012-05-02-bbrc-and-last-pm-usage.md b/_posts/2012-05-02-bbrc-and-last-pm-usage.md
index e9ec4ba..7edd79a 100644
--- a/_posts/2012-05-02-bbrc-and-last-pm-usage.md
+++ b/_posts/2012-05-02-bbrc-and-last-pm-usage.md
@@ -2,8 +2,8 @@
 layout: post
 title: "BBRC and LAST PM Usage"
 description: "This post provides a more 'how-to' like way to using BBRC and LAST-PM via REST than the usage informations for [BBRC](http://bbrc.maunz.de#usage) and for [LAST-PM](http://last-pm.maunz.de#usage)."
-category: algorithm
-tags: [Fminer, Feature Generation, BBRC, LAST-PM, Tutorials]
+category: Usage
+tags: [Algorithm, Fminer, Feature Generation, BBRC, LAST-PM, Tutorials]
 ---
 {% include JB/setup %}
 
diff --git a/_posts/2012-05-02-calculating-physico-chemical-descriptors-with-opentox-algorithm.md b/_posts/2012-05-02-calculating-physico-chemical-descriptors-with-opentox-algorithm.md
index 74737f7..b31cbdd 100644
--- a/_posts/2012-05-02-calculating-physico-chemical-descriptors-with-opentox-algorithm.md
+++ b/_posts/2012-05-02-calculating-physico-chemical-descriptors-with-opentox-algorithm.md
@@ -2,8 +2,8 @@
 layout: post
 title: "Calculating physico chemical descriptors with opentox algorithm"
 description: "Opentox-ruby has facilities to calculate more than 300 non-proprietary physico-chemical descriptors, whose calculation can be easily triggered with REST calls."
-category: algorithm
-tags: [Feature Generation, Feature Selection, Tutorials]
+category: Usage
+tags: [Algorithm, Feature Generation, Feature Selection, Tutorials]
 ---
 {% include JB/setup %}
 
diff --git a/_posts/2012-05-02-data-mining-and-machine-learning-algorithms-in-lazar.md b/_posts/2012-05-02-data-mining-and-machine-learning-algorithms-in-lazar.md
index f926e9b..8d3814c 100644
--- a/_posts/2012-05-02-data-mining-and-machine-learning-algorithms-in-lazar.md
+++ b/_posts/2012-05-02-data-mining-and-machine-learning-algorithms-in-lazar.md
@@ -2,8 +2,8 @@
 layout: post
 title: "Data Mining and Machine Learning Algorithms in Lazar"
 description: "Several statistical learners exist within Lazar. This page details important computational components."
-category: algorithm
-tags: [Lazar, Data Mining, Tutorials]
+category: Usage
+tags: [Algorithm, Lazar, Data Mining, Tutorials]
 ---
 {% include JB/setup %}
 
diff --git a/_posts/2012-05-02-lazar-models-and-how-to-trigger-them.md b/_posts/2012-05-02-lazar-models-and-how-to-trigger-them.md
index 17e2223..237047d 100644
--- a/_posts/2012-05-02-lazar-models-and-how-to-trigger-them.md
+++ b/_posts/2012-05-02-lazar-models-and-how-to-trigger-them.md
@@ -2,8 +2,8 @@
 layout: post
 title: "Lazar Models and how to trigger them"
 description: "I have implemented several underlying statistical learners within Lazar. There are kernel models for classification and regression. There are also facilities for physico-chemical descriptor calculation."
-category: algorithm
-tags: [Lazar, Algorithm Selection, Tutorials]
+category: Usage
+tags: [Lazar, Algorithm, Tutorials]
 ---
 {% include JB/setup %}
 
diff --git a/_posts/2012-05-02-multinomial-fminer.md b/_posts/2012-05-02-multinomial-fminer.md
index da60858..9b7f08a 100644
--- a/_posts/2012-05-02-multinomial-fminer.md
+++ b/_posts/2012-05-02-multinomial-fminer.md
@@ -2,8 +2,8 @@
 layout: post
 title: "Multinomial Fminer"
 description: "Both libraries (libbbrc and liblast) within the [Fminer2 package](http://github.com/amaunz/fminer2) are now usable in a multinomial context. The efficient pruning technique specific to libbbrc has been generalized to this setting."
-category: algorithm
-tags: [Fminer, Feature Generation, BBRC, LAST-PM, Tutorials]
+category: Usage
+tags: [Algorithm, Fminer, Feature Generation, BBRC, LAST-PM, Tutorials]
 ---
 {% include JB/setup %}
 
diff --git a/_posts/2012-05-02-parameter-selection-with-bbrc-and-last-pm.md b/_posts/2012-05-02-parameter-selection-with-bbrc-and-last-pm.md
index ef4ea2f..758df8f 100644
--- a/_posts/2012-05-02-parameter-selection-with-bbrc-and-last-pm.md
+++ b/_posts/2012-05-02-parameter-selection-with-bbrc-and-last-pm.md
@@ -2,8 +2,8 @@
 layout: post
 title: "Parameter Selection with BBRC and LAST PM"
 description: "This post gives some information on how parameters for BBRC and LAST could be selected, especially for the case of regression. Please see the [usage information](/algorithm/2012/05/02/bbrc-and-last-pm-usage) on how to apply the hints in your situation."
-category: algorithm
-tags: [Fminer, Feature Generation, BBRC, LAST-PM, Tutorials]
+category: Usage
+tags: [Algorithm, Fminer, Feature Generation, BBRC, LAST-PM, Tutorials]
 ---
 
 {% include JB/setup %}
diff --git a/_posts/2012-05-02-selecting-features-with-opentox-algorithm.md b/_posts/2012-05-02-selecting-features-with-opentox-algorithm.md
index 3225966..e51c180 100644
--- a/_posts/2012-05-02-selecting-features-with-opentox-algorithm.md
+++ b/_posts/2012-05-02-selecting-features-with-opentox-algorithm.md
@@ -2,8 +2,8 @@
 layout: post
 title: "Selecting Features with opentox algorithm"
 description: ""
-category: algorithm
-tags: [Feature Generation, Feature Selection, Tutorials]
+category: Usage
+tags: [Algorithm, Feature Generation, Feature Selection, Tutorials]
 ---
 {% include JB/setup %}
 
diff --git a/_posts/2012-05-02-support-calculation-in-fminer.md b/_posts/2012-05-02-support-calculation-in-fminer.md
index b987eb4..c29a55b 100644
--- a/_posts/2012-05-02-support-calculation-in-fminer.md
+++ b/_posts/2012-05-02-support-calculation-in-fminer.md
@@ -2,8 +2,8 @@
 layout: post
 title: "Support Calculation in Fminer"
 description: "Fminer algorithms BBRC and LAST-PM can now be used for automatic support calculation. This post shows how to use it."
-category: algorithm
-tags: [Fminer, Feature Generation, BBRC, LAST-PM, Tutorials]
+category: Usage
+tags: [Algorithm, Fminer, Feature Generation, BBRC, LAST-PM, Tutorials]
 ---
 {% include JB/setup %}
 
diff --git a/_posts/2012-05-02-use-case-table-for-fminer.md b/_posts/2012-05-02-use-case-table-for-fminer.md
index 58fa6cd..4468e5b 100644
--- a/_posts/2012-05-02-use-case-table-for-fminer.md
+++ b/_posts/2012-05-02-use-case-table-for-fminer.md
@@ -2,8 +2,8 @@
 layout: post
 title: "Use Case Table for Fminer"
 description: "Important use-cases and command line arguments / web service switches are presented below. The list is not complete! See [fminer README](https://github.com/amaunz/fminer2/blob/master/fminer/README) and [web services README](http://github.com/opentox/algorithm) for a more complete overview."
-category: algorithm
-tags: [Fminer, Feature Generation, BBRC, LAST-PM, Tutorials]
+category: Usage
+tags: [Algorithm, Fminer, Feature Generation, BBRC, LAST-PM, Tutorials]
 ---
 {% include JB/setup %}
 
diff --git a/_posts/2012-05-02-using-ist-opentox-virtual-appliance.md b/_posts/2012-05-02-using-ist-opentox-virtual-appliance.md
index d2907c5..373880f 100644
--- a/_posts/2012-05-02-using-ist-opentox-virtual-appliance.md
+++ b/_posts/2012-05-02-using-ist-opentox-virtual-appliance.md
@@ -2,7 +2,7 @@
 layout: post
 title: "IST Opentox Virtual Appliance"
 description: "**The IST Opentox Virtual Appliance is a tool that facilitates using IST's developments.**"
-category: setup
+category: Installation
 tags: [Windows, Setup]
 ---
 
diff --git a/_posts/2012-05-07-release-with-git-flow.md b/_posts/2012-05-07-release-with-git-flow.md
index 4e3022d..5f12ea5 100644
--- a/_posts/2012-05-07-release-with-git-flow.md
+++ b/_posts/2012-05-07-release-with-git-flow.md
@@ -2,8 +2,8 @@
 layout: post
 title: "Release Development with Git Flow"
 description: "Release Development with Git Flow"
-category: development
-tags: [GIT, deployment]
+category: Development
+tags: [Git, Deployment]
 ---
 {% include JB/setup %}
 
diff --git a/_posts/2012-05-08-how-to-solve-cannot-load-such-file----opentoxserver-errors.md b/_posts/2012-05-08-how-to-solve-cannot-load-such-file----opentoxserver-errors.md
index 0905958..71cca2b 100644
--- a/_posts/2012-05-08-how-to-solve-cannot-load-such-file----opentoxserver-errors.md
+++ b/_posts/2012-05-08-how-to-solve-cannot-load-such-file----opentoxserver-errors.md
@@ -2,7 +2,7 @@
 layout: post
 title: "How to solve 'cannot load such file opentox/server' errors whens starting unicorn"
 description: ""
-category: server
+category: Installation
 tags: ["Debugging"]
 ---
 {% include JB/setup %}
diff --git a/_posts/2012-05-08-toxbank-investigation-configuration.md b/_posts/2012-05-08-toxbank-investigation-configuration.md
index 72fbd38..fa47ed4 100644
--- a/_posts/2012-05-08-toxbank-investigation-configuration.md
+++ b/_posts/2012-05-08-toxbank-investigation-configuration.md
@@ -2,7 +2,7 @@
 layout: post
 title: "OpenTox/ToxBank Webservices Configuration"
 description: "Example Configuration for OpenTox/ToxBank webservices"
-category: server
+category: Installation
 tags: [Setup]
 ---
 {% include JB/setup %}
diff --git a/_posts/2012-05-18-improved-ubuntu-terminal.md b/_posts/2012-05-18-improved-ubuntu-terminal.md
index dd43bc0..7df5bc4 100644
--- a/_posts/2012-05-18-improved-ubuntu-terminal.md
+++ b/_posts/2012-05-18-improved-ubuntu-terminal.md
@@ -2,8 +2,8 @@
 layout: post
 title: "Improved Ubuntu Terminal"
 description: "Some techniques to improve user experience on Ubuntu terminal sessions"
-category: linux
-tags: [Ubuntu, Debian, Terminal, Thinkpad, Setup]
+category: Development
+tags: [Ubuntu, Debian, Terminal, Thinkpad, Setup, Linux]
 ---
 {% include JB/setup %}
 
diff --git a/_posts/2012-05-18-using-vim.md b/_posts/2012-05-18-using-vim.md
index e78d828..0e0cd29 100644
--- a/_posts/2012-05-18-using-vim.md
+++ b/_posts/2012-05-18-using-vim.md
@@ -2,8 +2,8 @@
 layout: post
 title: "Using Vim on Linux"
 description: "Using Vim on Linux"
-category: linux
-tags: [Ubuntu, Debian, Terminal, VIM, GIT, Setup]
+category: Development
+tags: [Ubuntu, Debian, Terminal, Vim, Git, Setup, Linux]
 ---
 {% include JB/setup %}
 
diff --git a/_posts/2012-05-20-installing-ubuntu-on-thinkpads.md b/_posts/2012-05-20-installing-ubuntu-on-thinkpads.md
index 79edd8d..adfcfc7 100644
--- a/_posts/2012-05-20-installing-ubuntu-on-thinkpads.md
+++ b/_posts/2012-05-20-installing-ubuntu-on-thinkpads.md
@@ -2,8 +2,8 @@
 layout: post
 title: "Installing Ubuntu on Thinkpads"
 description: ""
-category: linux
-tags: [Ubuntu, Debian, Thinkpad, Setup]
+category: Development
+tags: [Ubuntu, Debian, Thinkpad, Setup, Linux]
 ---
 {% include JB/setup %}
 
diff --git a/_posts/2012-05-25-installation-issues.md b/_posts/2012-05-25-installation-issues.md
index 7f2bb6b..3da4ef4 100644
--- a/_posts/2012-05-25-installation-issues.md
+++ b/_posts/2012-05-25-installation-issues.md
@@ -2,7 +2,7 @@
 layout: post
 title: "Installer issues"
 description: ""
-category: setup
+category: Installation
 tags: [Ubuntu, Debian, Setup]
 ---
 {% include JB/setup %}
diff --git a/_posts/2012-06-29-useful-git-tricks.md b/_posts/2012-06-29-useful-git-tricks.md
index 91d1383..b9dfa89 100644
--- a/_posts/2012-06-29-useful-git-tricks.md
+++ b/_posts/2012-06-29-useful-git-tricks.md
@@ -2,8 +2,8 @@
 layout: post
 title: "Useful git tricks"
 description: "A collection of helpful commands for the SCM system git"
-category: development
-tags: [Linux, Ubuntu, Debian, Terminal, GIT]
+category: Development
+tags: [Linux, Ubuntu, Debian, Terminal, Git]
 ---
 {% include JB/setup %}
 
diff --git a/_posts/2012-07-16-example-webservice-configuration-file.md b/_posts/2012-07-16-example-webservice-configuration-file.md
index ece65b2..1c74f2c 100644
--- a/_posts/2012-07-16-example-webservice-configuration-file.md
+++ b/_posts/2012-07-16-example-webservice-configuration-file.md
@@ -2,8 +2,8 @@
 layout: post
 title: "Example Webservice Configuration File"
 description: ""
-category: server
-tags: [Setup, webservices]
+category: Installation
+tags: [Setup, Webservices]
 ---
 {% include JB/setup %}
 
diff --git a/_posts/2012-07-17-client-server-synchronisation.md b/_posts/2012-07-17-client-server-synchronisation.md
index ecf2d66..71b305c 100644
--- a/_posts/2012-07-17-client-server-synchronisation.md
+++ b/_posts/2012-07-17-client-server-synchronisation.md
@@ -2,7 +2,7 @@
 layout: post
 title: "Client - server synchronisation"
 description: ""
-category: client
+category: Usage
 tags: []
 ---
 {% include JB/setup %}
diff --git a/_posts/2012-07-18-4store-setup.md b/_posts/2012-07-18-4store-setup.md
index 76c23d5..bd20776 100644
--- a/_posts/2012-07-18-4store-setup.md
+++ b/_posts/2012-07-18-4store-setup.md
@@ -2,7 +2,7 @@
 layout: post
 title: "4store setup"
 description: ""
-category: setup
+category: Installation
 tags: [4store]
 ---
 {% include JB/setup %}
diff --git a/_posts/2012-07-20-error-handling.md b/_posts/2012-07-20-error-handling.md
index f54e01d..55033e0 100644
--- a/_posts/2012-07-20-error-handling.md
+++ b/_posts/2012-07-20-error-handling.md
@@ -2,8 +2,8 @@
 layout: post
 title: "Error handling"
 description: ""
-category: development
-tags: [development]
+category: Development
+tags: [Error handling]
 ---
 {% include JB/setup %}
 For developers only.
diff --git a/_posts/2012-07-22-opentox-object-internals.md b/_posts/2012-07-22-opentox-object-internals.md
index 4ddb339..9870432 100644
--- a/_posts/2012-07-22-opentox-object-internals.md
+++ b/_posts/2012-07-22-opentox-object-internals.md
@@ -2,8 +2,8 @@
 layout: post
 title: "OpenTox object internals"
 description: ""
-category: client
-tags: [development]
+category: Usage
+tags: [OpenTox objects, Metadata]
 ---
 {% include JB/setup %}
 Default OpenTox objects are defined in `opentox-client/lib/opentox.rb`. They contain metadata as `RDF::Graph` in the `@rdf` variable.
diff --git a/_posts/2012-07-23-how-to-run-services-behind-a-proxy.md b/_posts/2012-07-23-how-to-run-services-behind-a-proxy.md
index 50e6485..9251240 100644
--- a/_posts/2012-07-23-how-to-run-services-behind-a-proxy.md
+++ b/_posts/2012-07-23-how-to-run-services-behind-a-proxy.md
@@ -2,8 +2,8 @@
 layout: post
 title: "How to run webservices behind a proxy"
 description: ""
-category: setup
-tags: [installation, configuration]
+category: Installation
+tags: [Configuration]
 ---
 {% include JB/setup %}
 Assigning a IP address to the full hostame in `etc/hosts` may cause uri problems when a proxy rewrites http to https. The solution is to remove all full hostname entries from `/etc/hosts` - after that all requests will have to pass the proxy.
diff --git a/_posts/2012-07-28-working-on-a-server-via-ssh.md b/_posts/2012-07-28-working-on-a-server-via-ssh.md
index 15eb38c..7ab9596 100644
--- a/_posts/2012-07-28-working-on-a-server-via-ssh.md
+++ b/_posts/2012-07-28-working-on-a-server-via-ssh.md
@@ -2,8 +2,8 @@
 layout: post
 title: "Working on a server via SSH"
 description: "Working on a server via SSH"
-category: linux
-tags: [Linux, Ubuntu, Debian, Terminal, SSH]
+category: Development
+tags: [Linux, Ubuntu, Debian, Terminal, SSH, Linux]
 ---
 {% include JB/setup %}
 
diff --git a/_posts/2012-07-30-how-to-run-4store-without-internet-connection.md b/_posts/2012-07-30-how-to-run-4store-without-internet-connection.md
index 614c033..29d14e8 100644
--- a/_posts/2012-07-30-how-to-run-4store-without-internet-connection.md
+++ b/_posts/2012-07-30-how-to-run-4store-without-internet-connection.md
@@ -2,8 +2,8 @@
 layout: post
 title: "How to run 4store without internet connection"
 description: ""
-category: setup
-tags: [4store, installation]
+category: Installation
+tags: [4store]
 ---
 {% include JB/setup %}
 
diff --git a/_posts/2012-08-02-converting-ova-images-to-kvm.md b/_posts/2012-08-02-converting-ova-images-to-kvm.md
index 24c9b10..1d2e766 100644
--- a/_posts/2012-08-02-converting-ova-images-to-kvm.md
+++ b/_posts/2012-08-02-converting-ova-images-to-kvm.md
@@ -2,7 +2,7 @@
 layout: post
 title: "Converting OVA images to KVM"
 description: "Converting an Open Virtual Appliance OVA-File to use in KVM"
-category: server
+category: Installation
 tags: [Linux, Ubuntu, Debian, OVA, Virtual Appliance]
 ---
 {% include JB/setup %}
diff --git a/_posts/2012-08-07-opentox-development-in-tmux.md b/_posts/2012-08-07-opentox-development-in-tmux.md
index 241a9e1..c547262 100644
--- a/_posts/2012-08-07-opentox-development-in-tmux.md
+++ b/_posts/2012-08-07-opentox-development-in-tmux.md
@@ -2,8 +2,8 @@
 layout: post
 title: "Opentox development in tmux"
 description: ""
-category: development
-tags: [development]
+category: Development
+tags: [Tmux]
 ---
 {% include JB/setup %}
 
diff --git a/_posts/2012-08-09-install-opentox-development-environment.md b/_posts/2012-08-09-install-opentox-development-environment.md
index c7fee0b..02946bb 100644
--- a/_posts/2012-08-09-install-opentox-development-environment.md
+++ b/_posts/2012-08-09-install-opentox-development-environment.md
@@ -2,8 +2,8 @@
 layout: post
 title: "Install opentox development environment"
 description: ""
-category: setup
-tags: [deployment, installation, Ubuntu, Debian, Setup]
+category: Installation
+tags: [Deployment, Ubuntu, Debian, Setup]
 ---
 {% include JB/setup %}
 
diff --git a/_posts/2012-08-15-how-to-add-data-entries-to-opentox-datasets.md b/_posts/2012-08-15-how-to-add-data-entries-to-opentox-datasets.md
index 4ded4dc..78e4e18 100644
--- a/_posts/2012-08-15-how-to-add-data-entries-to-opentox-datasets.md
+++ b/_posts/2012-08-15-how-to-add-data-entries-to-opentox-datasets.md
@@ -2,8 +2,8 @@
 layout: post
 title: "How to add data entries to OpenTox datasets"
 description: ""
-category: dataset
-tags: [dataset]
+category: Usage
+tags: [Dataset]
 ---
 {% include JB/setup %}
 
diff --git a/_posts/2012-08-20-how-to-grant-gemcutter-permissions.md b/_posts/2012-08-20-how-to-grant-gemcutter-permissions.md
index e8a0b46..bdafd17 100644
--- a/_posts/2012-08-20-how-to-grant-gemcutter-permissions.md
+++ b/_posts/2012-08-20-how-to-grant-gemcutter-permissions.md
@@ -2,8 +2,8 @@
 layout: post
 title: "How to grant gemcutter permissions"
 description: ""
-category: general
-tags: [development]
+category: Development
+tags: [Gemcutter, Gem]
 ---
 {% include JB/setup %}
 
diff --git a/_posts/2012-08-23-install-production-webservice-gems.md b/_posts/2012-08-23-install-production-webservice-gems.md
index 890184f..c139af3 100644
--- a/_posts/2012-08-23-install-production-webservice-gems.md
+++ b/_posts/2012-08-23-install-production-webservice-gems.md
@@ -2,8 +2,8 @@
 layout: post
 title: "Install production webservice gems"
 description: ""
-category: general
-tags: [installation, gem]
+category: Installation
+tags: [Gem]
 ---
 {% include JB/setup %}
 The installation of opentox-webservices is straightforward with the `gem` command, e.g.
diff --git a/_posts/2012-08-27-testing-website-with-capybara-webkit-and-testunit.md b/_posts/2012-08-27-testing-website-with-capybara-webkit-and-testunit.md
index c06503c..a360e39 100644
--- a/_posts/2012-08-27-testing-website-with-capybara-webkit-and-testunit.md
+++ b/_posts/2012-08-27-testing-website-with-capybara-webkit-and-testunit.md
@@ -2,7 +2,7 @@
 layout: post
 title: "Testing website with capybara-webkit and test/unit"
 description: ""
-category: testing 
+category: Development
 tags: [Headless browser, Testing]
 ---
 {% include JB/setup %}
diff --git a/_posts/2012-09-03-authorization--authentication-flow-and-configuration.md b/_posts/2012-09-03-authorization--authentication-flow-and-configuration.md
index 0451227..a3ab743 100644
--- a/_posts/2012-09-03-authorization--authentication-flow-and-configuration.md
+++ b/_posts/2012-09-03-authorization--authentication-flow-and-configuration.md
@@ -2,8 +2,8 @@
 layout: post
 title: "Authorization &#38; Authentication Flow and Configuration"
 description: "Authorization & Authentication flow for webservices using the opentox-ruby gem"
-category: server
-tags: [Setup, webservices]
+category: Installation
+tags: [Setup, Webservices]
 ---
 {% include JB/setup %}
 
@@ -101,4 +101,4 @@ Configuration-file example
           - "http://SERVER/validation"
           - !ruby/regexp /http\:\/\/SERVER\/validation\/[a-z,A-Z,\/,_\-]*$/
 
-   
\ No newline at end of file
+   
diff --git a/_posts/2012-09-10-error-message-segmentation-faults.md b/_posts/2012-09-10-error-message-segmentation-faults.md
index 95248a0..9114905 100644
--- a/_posts/2012-09-10-error-message-segmentation-faults.md
+++ b/_posts/2012-09-10-error-message-segmentation-faults.md
@@ -1,8 +1,8 @@
 ---
 layout: post
-title: "error message segmentation faults"
+title: "Error message segmentation faults"
 description: "sometimes error messge appears about segmentation faults"
-category: client 
+category: Installation
 tags: [Debugging]
 ---
 {% include JB/setup %}
diff --git a/_posts/2012-09-11-development-vanilla-version.md b/_posts/2012-09-11-development-vanilla-version.md
index d6cc87f..055a731 100644
--- a/_posts/2012-09-11-development-vanilla-version.md
+++ b/_posts/2012-09-11-development-vanilla-version.md
@@ -2,7 +2,7 @@
 layout: post
 title: "Development: Vanilla Version"
 description: ""
-category: development
+category: Development
 tags: [Lazar, Fminer, 4store, BBRC, LAST-PM, Tutorials]
 ---
 {% include JB/setup %}
diff --git a/_posts/2012-10-08-set-up-virtual-machine-in-proxmox-virtual-environment.md b/_posts/2012-10-08-set-up-virtual-machine-in-proxmox-virtual-environment.md
index 5d0f394..151e95a 100644
--- a/_posts/2012-10-08-set-up-virtual-machine-in-proxmox-virtual-environment.md
+++ b/_posts/2012-10-08-set-up-virtual-machine-in-proxmox-virtual-environment.md
@@ -2,7 +2,7 @@
 layout: post
 title: "Set Up Virtual Machine in Proxmox Virtual Environment"
 description: "Short description of a scenario "
-category: server 
+category: Installation
 tags: [Setup]
 ---
 {% include JB/setup %}
diff --git a/_posts/2012-11-07-unicorn-init-script-with-restart-and-upgrade.md b/_posts/2012-11-07-unicorn-init-script-with-restart-and-upgrade.md
index 833bbde..8823ca6 100644
--- a/_posts/2012-11-07-unicorn-init-script-with-restart-and-upgrade.md
+++ b/_posts/2012-11-07-unicorn-init-script-with-restart-and-upgrade.md
@@ -2,7 +2,7 @@
 layout: post
 title: "Unicorn Init Script with restart and upgrade"
 description: ""
-category: server
+category: Installation
 tags: [Setup]
 ---
 {% include JB/setup %}
diff --git a/_posts/2012-11-19-clever-feature-creation-keeps-your-database-small.md b/_posts/2012-11-19-clever-feature-creation-keeps-your-database-small.md
index 849e636..31504d1 100644
--- a/_posts/2012-11-19-clever-feature-creation-keeps-your-database-small.md
+++ b/_posts/2012-11-19-clever-feature-creation-keeps-your-database-small.md
@@ -2,8 +2,8 @@
 layout: post
 title: "Clever Feature Creation Keeps Your Database Small"
 description: ""
-category: development
-tags: [development,dataset, Feature Generation, Fminer]
+category: Development
+tags: [Dataset, Feature Generation, Fminer]
 ---
 {% include JB/setup %}
 
diff --git a/_posts/2013-02-07-architecture-overview.md b/_posts/2013-02-07-architecture-overview.md
new file mode 100644
index 0000000..81683f3
--- /dev/null
+++ b/_posts/2013-02-07-architecture-overview.md
@@ -0,0 +1,50 @@
+---
+layout: post
+title: "Architecture overview"
+description: "High level oeverview about the IST OpenTox architecture"
+category: Development
+tags: [Architecture]
+---
+{% include JB/setup %}
+
+The IST OpenTox architecture consists of 3 main layers. [OpenTox](http://opentox.org) compliant **[webservices](https://en.wikipedia.org/wiki/Web_service)** are the core layer, that provide the functionality for OpenTox [classes](http://opentox.org/dev/apis). **Clients** (e.g. libraries for various programming languages and command line/graphical user interfaces) interact with webservices and provide interfaces for end users. Webservices may depend on **backends** for special purposes (e.g. databases, A+A servers, number crunching). Clients should **never** interact with backends directly.
+
+Clients:
+--------
+
+- use the OpenTox/ToxBank REST [API](http://opentox.org/dev/apis) to communicate with webservices 
+
+### Examples:   
+
+  **GUIs**: [ToxCreate](http://toxcreate.org), [ToxPredict](http://toxpredict.org), [lazar](http://lazar.in-silico.ch), toxbank protocol and investigation GUIs, [Bioclipse](http://www.bioclipse.net/), ...    
+  **CLIs and scripts**: validation scripts for algorithm model development, irb using [opentox-client](http://github.com/opentox/opentox-client), [curl](http://curl.haxx.se/), [opentox-test](http://github.com/opentox/opentox-test), ...    
+  **Libraries**: e.g. the [opentox-client](http://github.com/opentox/opentox-client) Ruby library
+
+Webservices:
+------------
+
+- use the OpenTox/ToxBank REST [API](http://opentox.org/dev/apis) to communicate with other webservices 
+- use application specific protocols to communicate with backends (implementation specific and optional)
+
+### Examples:    
+
+  **IST**: compound, feature, dataset, investigation, algorithm, model, task, a+a    
+  **ALU**: validation    
+  **IDEA**: dataset (AMBIT), algorithm, protocol    
+  **TUM**: algorithm, model    
+  **NTUA**: algorithm, model    
+
+Backends: 
+---------
+
+- optimized for particular purposes (data storage and retrieval, number crunching, ...)
+- never addressed directly from clients or 3rd party webservices
+- one backend may be used for multiple services
+
+### Examples:    
+
+  **IST**: {Redis}, [4store](http://www.4store.org/), \[Rserve\], [OpenSSO](https://en.wikipedia.org/wiki/OpenSSO)    
+  **External**: [CACTVS](http://cactus.nci.nih.gov/), [PubChem](https://pubchem.ncbi.nlm.nih.gov/)    
+    {} IST services that may be removed in the future    
+    \[\] IST services that may be added in the future    
+
diff --git a/_posts/2013-02-07-development-guidelines.md b/_posts/2013-02-07-development-guidelines.md
new file mode 100644
index 0000000..d6663fe
--- /dev/null
+++ b/_posts/2013-02-07-development-guidelines.md
@@ -0,0 +1,21 @@
+---
+layout: post
+title: "Development guidelines"
+description: ""
+category: Development
+tags: []
+---
+{% include JB/setup %}
+
+- Read and understand the [Architecture overview](/Development/2013/02/07/architecture-overview)
+- Follow the guidelines for [Error handling](/Development/2012/07/20/error-handling)
+- Add tests to [opentox-test](http://github.com/opentox/opentox-test) for your new features
+- Make sure that *all* tests in [opentox-test](http://github.com/opentox/opentox-test) pass before committing to an official branch (development, master)
+
+Try to reduce complexity in order to keep the system maintainable and stable:
+- Follow the [DRY](http://en.wikipedia.org/wiki/Don%27t_repeat_yourself) principle
+- Avoid dependencies (e.g. gems, backends), but don\'t reinvent the wheel
+- Implement only required/requested features, avoid features that "might be needed someday"
+- Avoid workarounds imposed/requested by other webservice developers. Get in contact with them and convince them to adhere to agreed API standards. Make recommendations to improve APIs if they lead to overly complicated implementations.
+- Revise design decisions and refactor if you observe that code is accumulating due to former decisions
+- Write clear, self documenting code
diff --git a/index.md b/index.md
index 43d5b06..d3af84c 100644
--- a/index.md
+++ b/index.md
@@ -1,12 +1,9 @@
 ---
 layout: page
-title: Articles
+title: OpenTox webservices 
 tagline: 
 ---
 {% include JB/setup %}
 
-<ul class="posts">
-  {% for post in site.posts %}
-    <li><span>{{ post.date | date_to_string }}</span> &raquo; <a href="{{ BASE_PATH }}{{ post.url }}">{{ post.title }}</a></li>
-  {% endfor %}
-</ul>
+These pages contain random notes about the development, installation and usage of [OpenTox](http://opentox.org) and [ToxBank](http://toxbank.net) webservices. The primary documentation is embedded in code at our [github repositories](http://github.com/opentox) which can be browsed at [RubyDoc.info](http://rubydoc.info/).
+
diff --git a/pages.html b/pages.html
deleted file mode 100644
index bde1a32..0000000
--- a/pages.html
+++ /dev/null
@@ -1,13 +0,0 @@
----
-layout: page
-title: Pages 
-header: Pages
-group: navigation
----
-{% include JB/setup %}
-
-<h2>All Pages</h2>
-<ul>
-{% assign pages_list = site.pages %}
-{% include JB/pages_list %}
-</ul>