").appendTo(i),n=i.uniqueId().attr("id");return this._addClass(s,"ui-tooltip-content"),this._addClass(i,"ui-tooltip","ui-widget ui-widget-content"),i.appendTo(this._appendTo(e)),this.tooltips[n]={element:e,tooltip:i}},_find:function(t){var e=t.data("ui-tooltip-id");return e?this.tooltips[e]:null},_removeTooltip:function(t){t.remove(),delete this.tooltips[t.attr("id")]},_appendTo:function(t){var e=t.closest(".ui-front, dialog");return e.length||(e=this.document[0].body),e},_destroy:function(){var e=this;t.each(this.tooltips,function(i,s){var n=t.Event("blur"),o=s.element;n.target=n.currentTarget=o[0],e.close(n,!0),t("#"+i).remove(),o.data("ui-tooltip-title")&&(o.attr("title")||o.attr("title",o.data("ui-tooltip-title")),o.removeData("ui-tooltip-title"))}),this.liveRegion.remove()}}),t.uiBackCompat!==!1&&t.widget("ui.tooltip",t.ui.tooltip,{options:{tooltipClass:null},_tooltip:function(){var t=this._superApply(arguments);return this.options.tooltipClass&&t.tooltip.addClass(this.options.tooltipClass),t}}),t.ui.tooltip});
\ No newline at end of file
diff --git a/assets/preload/site-style.css b/assets/preload/site-style.css
new file mode 100644
index 0000000..5f4cc7a
--- /dev/null
+++ b/assets/preload/site-style.css
@@ -0,0 +1,25 @@
+:root {
+ --site-color: rgb(96,96,172);
+}
+
+#headband {
+ background-color: var(--site-color);
+}
+
+#logo_topleft {
+ float: left;
+ margin-top: 10px;
+ margin-left: 10px;
+}
+
+#logo_topright {
+ float: right;
+ margin-top: 10px;
+ margin-right: 10px;
+ width: 48px;
+}
+
+a {
+ color: var(--site-color);
+ text-decoration: none;
+}
diff --git a/categories/days-alpha-sorted.md b/categories/days-alpha-sorted.md
new file mode 100644
index 0000000..fa87e47
--- /dev/null
+++ b/categories/days-alpha-sorted.md
@@ -0,0 +1,103 @@
+---
+layout: default
+---
+
+{%- assign this_name = page.name | split: "." -%}
+{%- assign this_category = this_name[0] | replace: '-alpha-sorted', '' -%}
+{%- assign this_pagetitle = this_category | capitalize | replace: '_', ' ' -%}
+
+
+
+
+
{{ this_pagetitle }}
+
+
+
+{%- comment -%}
+ * collecting the pages
+{%- endcomment -%}
+
+{%- assign cat_posts = site.emptyArray -%}
+{%- for post in site.documents -%}
+ {%- if post.categories contains this_category -%}
+ {%- assign cat_posts = cat_posts | push: post -%}
+ {%- endif -%}
+{%- endfor -%}
+
+{%- assign cat_posts = cat_posts | sort: 'title' -%}
+
+{%- comment -%}
+ * special posts for prepending content to the listing pages
+ * they are processed first, so separate loops are needed
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {%- if post.tags contains '.prepend' -%}
+
+{{ post.content | markdownify }}
+
+ {%- endif -%}
+{%- endfor -%}
+
+{%- comment -%}
+ * featured posts on top, so new loop
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+
+ {%- if post.tags contains '.featured' -%}
+ {%- assign excerpt_link = post.url | relative_url -%}
+ {%- if post.excerpt_link contains '/' -%}
+ {%- assign excerpt_link = post.excerpt_link -%}
+ {%- endif -%}
+
+ {%- endif -%}
+{%- endfor -%}
+
+{%- comment -%}
+ * remaining normal posts, again new loop
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {% unless post.tags contains '.featured' or post.tags contains '.prepend' or post.tags contains '.append' %}
+ {%- assign excerpt_link = post.url | relative_url -%}
+ {%- if post.excerpt_link contains '/' -%}
+ {%- assign excerpt_link = post.excerpt_link -%}
+ {%- endif -%}
+
+ {% endunless %}
+{%- endfor -%}
+
+{%- comment -%}
+ * special posts for appending content to the listing pages
+ * they are processed last, so again a separate loop is needed
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {%- if post.tags contains '.append' -%}
+
+{{ post.content | markdownify }}
+
+ {%- endif -%}
+{%- endfor -%}
+
diff --git a/categories/days-date-sorted.md b/categories/days-date-sorted.md
new file mode 100644
index 0000000..082494b
--- /dev/null
+++ b/categories/days-date-sorted.md
@@ -0,0 +1,87 @@
+---
+layout: default
+---
+
+{%- assign this_name = page.name | split: "." -%}
+{%- assign this_category = this_name[0] | replace: '-date-sorted', '' -%}
+{%- assign this_pagetitle = this_category | capitalize | replace: '_', ' ' -%}
+
+
+
+
+
{{ this_pagetitle }}
+
+
+
+{%- comment -%}
+ * collecting the pages
+{%- endcomment -%}
+
+{%- assign cat_posts = site.emptyArray -%}
+{%- for post in site.documents -%}
+ {%- if post.categories contains this_category -%}
+ {%- assign cat_posts = cat_posts | push: post -%}
+ {%- endif -%}
+{%- endfor -%}
+
+{%- assign cat_posts = cat_posts | sort: 'date' | reverse -%}
+
+{%- comment -%}
+ * special posts for prepending content to the listing pages
+ * they are processed first, so separate loops are needed
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {%- if post.tags contains '.prepend' -%}
+
+{{ post.content | markdownify }}
+
+ {%- endif -%}
+{%- endfor -%}
+
+{%- comment -%}
+ * no separate treatment of featured posts
+{%- endcomment -%}
+
+{%- assign today = site.time | date: '%Y%m%d' -%}
+{%- assign page_tag = this_category | downcase -%}
+
+{%- for post in cat_posts -%}
+ {% unless post.tags contains '.prepend' or post.tags contains '.append' %}
+ {%- assign post_author = post.author | downcase -%}
+ {%- assign excerpt_link = post.url | relative_url -%}
+ {%- if post.excerpt_link contains '/' -%}
+ {%- assign excerpt_link = post.excerpt_link -%}
+ {%- endif -%}
+ {%- assign post_day = post.date | date: '%Y%m%d' -%}
+ {%- assign post_year = post.date | date: '%Y' -%}
+ {%- if post_day > today -%}
+ {%- assign post_year = 'Upcoming' -%}
+ {%- endif %}
+ {%- if current_year != post_year -%}
+ {% assign current_year = post_year %}
+
{{ current_year }}
+ {% endif %}
+
+ {%- if post_day > today -%}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {%- endif -%}
+
{{ post.excerpt }}
+
+
+ {% endunless %}
+{%- endfor -%}
+
+{%- for post in cat_posts -%}
+ {%- if post.tags contains '.append' -%}
+
+{{ post.content | markdownify }}
+
+ {%- endif -%}
+{%- endfor -%}
diff --git a/categories/days.md b/categories/days.md
new file mode 100644
index 0000000..fa87e47
--- /dev/null
+++ b/categories/days.md
@@ -0,0 +1,103 @@
+---
+layout: default
+---
+
+{%- assign this_name = page.name | split: "." -%}
+{%- assign this_category = this_name[0] | replace: '-alpha-sorted', '' -%}
+{%- assign this_pagetitle = this_category | capitalize | replace: '_', ' ' -%}
+
+
+
+
+
{{ this_pagetitle }}
+
+
+
+{%- comment -%}
+ * collecting the pages
+{%- endcomment -%}
+
+{%- assign cat_posts = site.emptyArray -%}
+{%- for post in site.documents -%}
+ {%- if post.categories contains this_category -%}
+ {%- assign cat_posts = cat_posts | push: post -%}
+ {%- endif -%}
+{%- endfor -%}
+
+{%- assign cat_posts = cat_posts | sort: 'title' -%}
+
+{%- comment -%}
+ * special posts for prepending content to the listing pages
+ * they are processed first, so separate loops are needed
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {%- if post.tags contains '.prepend' -%}
+
+{{ post.content | markdownify }}
+
+ {%- endif -%}
+{%- endfor -%}
+
+{%- comment -%}
+ * featured posts on top, so new loop
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+
+ {%- if post.tags contains '.featured' -%}
+ {%- assign excerpt_link = post.url | relative_url -%}
+ {%- if post.excerpt_link contains '/' -%}
+ {%- assign excerpt_link = post.excerpt_link -%}
+ {%- endif -%}
+
+ {%- endif -%}
+{%- endfor -%}
+
+{%- comment -%}
+ * remaining normal posts, again new loop
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {% unless post.tags contains '.featured' or post.tags contains '.prepend' or post.tags contains '.append' %}
+ {%- assign excerpt_link = post.url | relative_url -%}
+ {%- if post.excerpt_link contains '/' -%}
+ {%- assign excerpt_link = post.excerpt_link -%}
+ {%- endif -%}
+
+ {% endunless %}
+{%- endfor -%}
+
+{%- comment -%}
+ * special posts for appending content to the listing pages
+ * they are processed last, so again a separate loop is needed
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {%- if post.tags contains '.append' -%}
+
+{{ post.content | markdownify }}
+
+ {%- endif -%}
+{%- endfor -%}
+
diff --git a/categories/doc-alpha-sorted.md b/categories/doc-alpha-sorted.md
new file mode 100644
index 0000000..fa87e47
--- /dev/null
+++ b/categories/doc-alpha-sorted.md
@@ -0,0 +1,103 @@
+---
+layout: default
+---
+
+{%- assign this_name = page.name | split: "." -%}
+{%- assign this_category = this_name[0] | replace: '-alpha-sorted', '' -%}
+{%- assign this_pagetitle = this_category | capitalize | replace: '_', ' ' -%}
+
+
+
+
+
{{ this_pagetitle }}
+
+
+
+{%- comment -%}
+ * collecting the pages
+{%- endcomment -%}
+
+{%- assign cat_posts = site.emptyArray -%}
+{%- for post in site.documents -%}
+ {%- if post.categories contains this_category -%}
+ {%- assign cat_posts = cat_posts | push: post -%}
+ {%- endif -%}
+{%- endfor -%}
+
+{%- assign cat_posts = cat_posts | sort: 'title' -%}
+
+{%- comment -%}
+ * special posts for prepending content to the listing pages
+ * they are processed first, so separate loops are needed
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {%- if post.tags contains '.prepend' -%}
+
+{{ post.content | markdownify }}
+
+ {%- endif -%}
+{%- endfor -%}
+
+{%- comment -%}
+ * featured posts on top, so new loop
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+
+ {%- if post.tags contains '.featured' -%}
+ {%- assign excerpt_link = post.url | relative_url -%}
+ {%- if post.excerpt_link contains '/' -%}
+ {%- assign excerpt_link = post.excerpt_link -%}
+ {%- endif -%}
+
+ {%- endif -%}
+{%- endfor -%}
+
+{%- comment -%}
+ * remaining normal posts, again new loop
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {% unless post.tags contains '.featured' or post.tags contains '.prepend' or post.tags contains '.append' %}
+ {%- assign excerpt_link = post.url | relative_url -%}
+ {%- if post.excerpt_link contains '/' -%}
+ {%- assign excerpt_link = post.excerpt_link -%}
+ {%- endif -%}
+
+ {% endunless %}
+{%- endfor -%}
+
+{%- comment -%}
+ * special posts for appending content to the listing pages
+ * they are processed last, so again a separate loop is needed
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {%- if post.tags contains '.append' -%}
+
+{{ post.content | markdownify }}
+
+ {%- endif -%}
+{%- endfor -%}
+
diff --git a/categories/doc-date-sorted.md b/categories/doc-date-sorted.md
new file mode 100644
index 0000000..082494b
--- /dev/null
+++ b/categories/doc-date-sorted.md
@@ -0,0 +1,87 @@
+---
+layout: default
+---
+
+{%- assign this_name = page.name | split: "." -%}
+{%- assign this_category = this_name[0] | replace: '-date-sorted', '' -%}
+{%- assign this_pagetitle = this_category | capitalize | replace: '_', ' ' -%}
+
+
+
+
+
{{ this_pagetitle }}
+
+
+
+{%- comment -%}
+ * collecting the pages
+{%- endcomment -%}
+
+{%- assign cat_posts = site.emptyArray -%}
+{%- for post in site.documents -%}
+ {%- if post.categories contains this_category -%}
+ {%- assign cat_posts = cat_posts | push: post -%}
+ {%- endif -%}
+{%- endfor -%}
+
+{%- assign cat_posts = cat_posts | sort: 'date' | reverse -%}
+
+{%- comment -%}
+ * special posts for prepending content to the listing pages
+ * they are processed first, so separate loops are needed
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {%- if post.tags contains '.prepend' -%}
+
+{{ post.content | markdownify }}
+
+ {%- endif -%}
+{%- endfor -%}
+
+{%- comment -%}
+ * no separate treatment of featured posts
+{%- endcomment -%}
+
+{%- assign today = site.time | date: '%Y%m%d' -%}
+{%- assign page_tag = this_category | downcase -%}
+
+{%- for post in cat_posts -%}
+ {% unless post.tags contains '.prepend' or post.tags contains '.append' %}
+ {%- assign post_author = post.author | downcase -%}
+ {%- assign excerpt_link = post.url | relative_url -%}
+ {%- if post.excerpt_link contains '/' -%}
+ {%- assign excerpt_link = post.excerpt_link -%}
+ {%- endif -%}
+ {%- assign post_day = post.date | date: '%Y%m%d' -%}
+ {%- assign post_year = post.date | date: '%Y' -%}
+ {%- if post_day > today -%}
+ {%- assign post_year = 'Upcoming' -%}
+ {%- endif %}
+ {%- if current_year != post_year -%}
+ {% assign current_year = post_year %}
+
{{ current_year }}
+ {% endif %}
+
+ {%- if post_day > today -%}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {%- endif -%}
+
{{ post.excerpt }}
+
+
+ {% endunless %}
+{%- endfor -%}
+
+{%- for post in cat_posts -%}
+ {%- if post.tags contains '.append' -%}
+
+{{ post.content | markdownify }}
+
+ {%- endif -%}
+{%- endfor -%}
diff --git a/categories/doc.md b/categories/doc.md
new file mode 100644
index 0000000..fa87e47
--- /dev/null
+++ b/categories/doc.md
@@ -0,0 +1,103 @@
+---
+layout: default
+---
+
+{%- assign this_name = page.name | split: "." -%}
+{%- assign this_category = this_name[0] | replace: '-alpha-sorted', '' -%}
+{%- assign this_pagetitle = this_category | capitalize | replace: '_', ' ' -%}
+
+
+
+
+
{{ this_pagetitle }}
+
+
+
+{%- comment -%}
+ * collecting the pages
+{%- endcomment -%}
+
+{%- assign cat_posts = site.emptyArray -%}
+{%- for post in site.documents -%}
+ {%- if post.categories contains this_category -%}
+ {%- assign cat_posts = cat_posts | push: post -%}
+ {%- endif -%}
+{%- endfor -%}
+
+{%- assign cat_posts = cat_posts | sort: 'title' -%}
+
+{%- comment -%}
+ * special posts for prepending content to the listing pages
+ * they are processed first, so separate loops are needed
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {%- if post.tags contains '.prepend' -%}
+
+{{ post.content | markdownify }}
+
+ {%- endif -%}
+{%- endfor -%}
+
+{%- comment -%}
+ * featured posts on top, so new loop
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+
+ {%- if post.tags contains '.featured' -%}
+ {%- assign excerpt_link = post.url | relative_url -%}
+ {%- if post.excerpt_link contains '/' -%}
+ {%- assign excerpt_link = post.excerpt_link -%}
+ {%- endif -%}
+
+ {%- endif -%}
+{%- endfor -%}
+
+{%- comment -%}
+ * remaining normal posts, again new loop
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {% unless post.tags contains '.featured' or post.tags contains '.prepend' or post.tags contains '.append' %}
+ {%- assign excerpt_link = post.url | relative_url -%}
+ {%- if post.excerpt_link contains '/' -%}
+ {%- assign excerpt_link = post.excerpt_link -%}
+ {%- endif -%}
+
+ {% endunless %}
+{%- endfor -%}
+
+{%- comment -%}
+ * special posts for appending content to the listing pages
+ * they are processed last, so again a separate loop is needed
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {%- if post.tags contains '.append' -%}
+
+{{ post.content | markdownify }}
+
+ {%- endif -%}
+{%- endfor -%}
+
diff --git a/categories/howto-alpha-sorted.md b/categories/howto-alpha-sorted.md
new file mode 100644
index 0000000..fa87e47
--- /dev/null
+++ b/categories/howto-alpha-sorted.md
@@ -0,0 +1,103 @@
+---
+layout: default
+---
+
+{%- assign this_name = page.name | split: "." -%}
+{%- assign this_category = this_name[0] | replace: '-alpha-sorted', '' -%}
+{%- assign this_pagetitle = this_category | capitalize | replace: '_', ' ' -%}
+
+
+
+
+
{{ this_pagetitle }}
+
+
+
+{%- comment -%}
+ * collecting the pages
+{%- endcomment -%}
+
+{%- assign cat_posts = site.emptyArray -%}
+{%- for post in site.documents -%}
+ {%- if post.categories contains this_category -%}
+ {%- assign cat_posts = cat_posts | push: post -%}
+ {%- endif -%}
+{%- endfor -%}
+
+{%- assign cat_posts = cat_posts | sort: 'title' -%}
+
+{%- comment -%}
+ * special posts for prepending content to the listing pages
+ * they are processed first, so separate loops are needed
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {%- if post.tags contains '.prepend' -%}
+
+{{ post.content | markdownify }}
+
+ {%- endif -%}
+{%- endfor -%}
+
+{%- comment -%}
+ * featured posts on top, so new loop
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+
+ {%- if post.tags contains '.featured' -%}
+ {%- assign excerpt_link = post.url | relative_url -%}
+ {%- if post.excerpt_link contains '/' -%}
+ {%- assign excerpt_link = post.excerpt_link -%}
+ {%- endif -%}
+
+ {%- endif -%}
+{%- endfor -%}
+
+{%- comment -%}
+ * remaining normal posts, again new loop
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {% unless post.tags contains '.featured' or post.tags contains '.prepend' or post.tags contains '.append' %}
+ {%- assign excerpt_link = post.url | relative_url -%}
+ {%- if post.excerpt_link contains '/' -%}
+ {%- assign excerpt_link = post.excerpt_link -%}
+ {%- endif -%}
+
+ {% endunless %}
+{%- endfor -%}
+
+{%- comment -%}
+ * special posts for appending content to the listing pages
+ * they are processed last, so again a separate loop is needed
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {%- if post.tags contains '.append' -%}
+
+{{ post.content | markdownify }}
+
+ {%- endif -%}
+{%- endfor -%}
+
diff --git a/categories/howto-date-sorted.md b/categories/howto-date-sorted.md
new file mode 100644
index 0000000..082494b
--- /dev/null
+++ b/categories/howto-date-sorted.md
@@ -0,0 +1,87 @@
+---
+layout: default
+---
+
+{%- assign this_name = page.name | split: "." -%}
+{%- assign this_category = this_name[0] | replace: '-date-sorted', '' -%}
+{%- assign this_pagetitle = this_category | capitalize | replace: '_', ' ' -%}
+
+
+
+
+
{{ this_pagetitle }}
+
+
+
+{%- comment -%}
+ * collecting the pages
+{%- endcomment -%}
+
+{%- assign cat_posts = site.emptyArray -%}
+{%- for post in site.documents -%}
+ {%- if post.categories contains this_category -%}
+ {%- assign cat_posts = cat_posts | push: post -%}
+ {%- endif -%}
+{%- endfor -%}
+
+{%- assign cat_posts = cat_posts | sort: 'date' | reverse -%}
+
+{%- comment -%}
+ * special posts for prepending content to the listing pages
+ * they are processed first, so separate loops are needed
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {%- if post.tags contains '.prepend' -%}
+
+{{ post.content | markdownify }}
+
+ {%- endif -%}
+{%- endfor -%}
+
+{%- comment -%}
+ * no separate treatment of featured posts
+{%- endcomment -%}
+
+{%- assign today = site.time | date: '%Y%m%d' -%}
+{%- assign page_tag = this_category | downcase -%}
+
+{%- for post in cat_posts -%}
+ {% unless post.tags contains '.prepend' or post.tags contains '.append' %}
+ {%- assign post_author = post.author | downcase -%}
+ {%- assign excerpt_link = post.url | relative_url -%}
+ {%- if post.excerpt_link contains '/' -%}
+ {%- assign excerpt_link = post.excerpt_link -%}
+ {%- endif -%}
+ {%- assign post_day = post.date | date: '%Y%m%d' -%}
+ {%- assign post_year = post.date | date: '%Y' -%}
+ {%- if post_day > today -%}
+ {%- assign post_year = 'Upcoming' -%}
+ {%- endif %}
+ {%- if current_year != post_year -%}
+ {% assign current_year = post_year %}
+
{{ current_year }}
+ {% endif %}
+
+ {%- if post_day > today -%}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {%- endif -%}
+
{{ post.excerpt }}
+
+
+ {% endunless %}
+{%- endfor -%}
+
+{%- for post in cat_posts -%}
+ {%- if post.tags contains '.append' -%}
+
+{{ post.content | markdownify }}
+
+ {%- endif -%}
+{%- endfor -%}
diff --git a/categories/howto.md b/categories/howto.md
new file mode 100644
index 0000000..fa87e47
--- /dev/null
+++ b/categories/howto.md
@@ -0,0 +1,103 @@
+---
+layout: default
+---
+
+{%- assign this_name = page.name | split: "." -%}
+{%- assign this_category = this_name[0] | replace: '-alpha-sorted', '' -%}
+{%- assign this_pagetitle = this_category | capitalize | replace: '_', ' ' -%}
+
+
+
+
+
{{ this_pagetitle }}
+
+
+
+{%- comment -%}
+ * collecting the pages
+{%- endcomment -%}
+
+{%- assign cat_posts = site.emptyArray -%}
+{%- for post in site.documents -%}
+ {%- if post.categories contains this_category -%}
+ {%- assign cat_posts = cat_posts | push: post -%}
+ {%- endif -%}
+{%- endfor -%}
+
+{%- assign cat_posts = cat_posts | sort: 'title' -%}
+
+{%- comment -%}
+ * special posts for prepending content to the listing pages
+ * they are processed first, so separate loops are needed
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {%- if post.tags contains '.prepend' -%}
+
+{{ post.content | markdownify }}
+
+ {%- endif -%}
+{%- endfor -%}
+
+{%- comment -%}
+ * featured posts on top, so new loop
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+
+ {%- if post.tags contains '.featured' -%}
+ {%- assign excerpt_link = post.url | relative_url -%}
+ {%- if post.excerpt_link contains '/' -%}
+ {%- assign excerpt_link = post.excerpt_link -%}
+ {%- endif -%}
+
+ {%- endif -%}
+{%- endfor -%}
+
+{%- comment -%}
+ * remaining normal posts, again new loop
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {% unless post.tags contains '.featured' or post.tags contains '.prepend' or post.tags contains '.append' %}
+ {%- assign excerpt_link = post.url | relative_url -%}
+ {%- if post.excerpt_link contains '/' -%}
+ {%- assign excerpt_link = post.excerpt_link -%}
+ {%- endif -%}
+
+ {% endunless %}
+{%- endfor -%}
+
+{%- comment -%}
+ * special posts for appending content to the listing pages
+ * they are processed last, so again a separate loop is needed
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {%- if post.tags contains '.append' -%}
+
+{{ post.content | markdownify }}
+
+ {%- endif -%}
+{%- endfor -%}
+
diff --git a/categories/material-alpha-sorted.md b/categories/material-alpha-sorted.md
new file mode 100644
index 0000000..fa87e47
--- /dev/null
+++ b/categories/material-alpha-sorted.md
@@ -0,0 +1,103 @@
+---
+layout: default
+---
+
+{%- assign this_name = page.name | split: "." -%}
+{%- assign this_category = this_name[0] | replace: '-alpha-sorted', '' -%}
+{%- assign this_pagetitle = this_category | capitalize | replace: '_', ' ' -%}
+
+
+
+
+
{{ this_pagetitle }}
+
+
+
+{%- comment -%}
+ * collecting the pages
+{%- endcomment -%}
+
+{%- assign cat_posts = site.emptyArray -%}
+{%- for post in site.documents -%}
+ {%- if post.categories contains this_category -%}
+ {%- assign cat_posts = cat_posts | push: post -%}
+ {%- endif -%}
+{%- endfor -%}
+
+{%- assign cat_posts = cat_posts | sort: 'title' -%}
+
+{%- comment -%}
+ * special posts for prepending content to the listing pages
+ * they are processed first, so separate loops are needed
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {%- if post.tags contains '.prepend' -%}
+
+{{ post.content | markdownify }}
+
+ {%- endif -%}
+{%- endfor -%}
+
+{%- comment -%}
+ * featured posts on top, so new loop
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+
+ {%- if post.tags contains '.featured' -%}
+ {%- assign excerpt_link = post.url | relative_url -%}
+ {%- if post.excerpt_link contains '/' -%}
+ {%- assign excerpt_link = post.excerpt_link -%}
+ {%- endif -%}
+
+ {%- endif -%}
+{%- endfor -%}
+
+{%- comment -%}
+ * remaining normal posts, again new loop
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {% unless post.tags contains '.featured' or post.tags contains '.prepend' or post.tags contains '.append' %}
+ {%- assign excerpt_link = post.url | relative_url -%}
+ {%- if post.excerpt_link contains '/' -%}
+ {%- assign excerpt_link = post.excerpt_link -%}
+ {%- endif -%}
+
+ {% endunless %}
+{%- endfor -%}
+
+{%- comment -%}
+ * special posts for appending content to the listing pages
+ * they are processed last, so again a separate loop is needed
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {%- if post.tags contains '.append' -%}
+
+{{ post.content | markdownify }}
+
+ {%- endif -%}
+{%- endfor -%}
+
diff --git a/categories/material-date-sorted.md b/categories/material-date-sorted.md
new file mode 100644
index 0000000..082494b
--- /dev/null
+++ b/categories/material-date-sorted.md
@@ -0,0 +1,87 @@
+---
+layout: default
+---
+
+{%- assign this_name = page.name | split: "." -%}
+{%- assign this_category = this_name[0] | replace: '-date-sorted', '' -%}
+{%- assign this_pagetitle = this_category | capitalize | replace: '_', ' ' -%}
+
+
+
+
+
{{ this_pagetitle }}
+
+
+
+{%- comment -%}
+ * collecting the pages
+{%- endcomment -%}
+
+{%- assign cat_posts = site.emptyArray -%}
+{%- for post in site.documents -%}
+ {%- if post.categories contains this_category -%}
+ {%- assign cat_posts = cat_posts | push: post -%}
+ {%- endif -%}
+{%- endfor -%}
+
+{%- assign cat_posts = cat_posts | sort: 'date' | reverse -%}
+
+{%- comment -%}
+ * special posts for prepending content to the listing pages
+ * they are processed first, so separate loops are needed
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {%- if post.tags contains '.prepend' -%}
+
+{{ post.content | markdownify }}
+
+ {%- endif -%}
+{%- endfor -%}
+
+{%- comment -%}
+ * no separate treatment of featured posts
+{%- endcomment -%}
+
+{%- assign today = site.time | date: '%Y%m%d' -%}
+{%- assign page_tag = this_category | downcase -%}
+
+{%- for post in cat_posts -%}
+ {% unless post.tags contains '.prepend' or post.tags contains '.append' %}
+ {%- assign post_author = post.author | downcase -%}
+ {%- assign excerpt_link = post.url | relative_url -%}
+ {%- if post.excerpt_link contains '/' -%}
+ {%- assign excerpt_link = post.excerpt_link -%}
+ {%- endif -%}
+ {%- assign post_day = post.date | date: '%Y%m%d' -%}
+ {%- assign post_year = post.date | date: '%Y' -%}
+ {%- if post_day > today -%}
+ {%- assign post_year = 'Upcoming' -%}
+ {%- endif %}
+ {%- if current_year != post_year -%}
+ {% assign current_year = post_year %}
+
{{ current_year }}
+ {% endif %}
+
+ {%- if post_day > today -%}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {%- endif -%}
+
{{ post.excerpt }}
+
+
+ {% endunless %}
+{%- endfor -%}
+
+{%- for post in cat_posts -%}
+ {%- if post.tags contains '.append' -%}
+
+{{ post.content | markdownify }}
+
+ {%- endif -%}
+{%- endfor -%}
diff --git a/categories/material.md b/categories/material.md
new file mode 100644
index 0000000..fa87e47
--- /dev/null
+++ b/categories/material.md
@@ -0,0 +1,103 @@
+---
+layout: default
+---
+
+{%- assign this_name = page.name | split: "." -%}
+{%- assign this_category = this_name[0] | replace: '-alpha-sorted', '' -%}
+{%- assign this_pagetitle = this_category | capitalize | replace: '_', ' ' -%}
+
+
+
+
+
{{ this_pagetitle }}
+
+
+
+{%- comment -%}
+ * collecting the pages
+{%- endcomment -%}
+
+{%- assign cat_posts = site.emptyArray -%}
+{%- for post in site.documents -%}
+ {%- if post.categories contains this_category -%}
+ {%- assign cat_posts = cat_posts | push: post -%}
+ {%- endif -%}
+{%- endfor -%}
+
+{%- assign cat_posts = cat_posts | sort: 'title' -%}
+
+{%- comment -%}
+ * special posts for prepending content to the listing pages
+ * they are processed first, so separate loops are needed
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {%- if post.tags contains '.prepend' -%}
+
+{{ post.content | markdownify }}
+
+ {%- endif -%}
+{%- endfor -%}
+
+{%- comment -%}
+ * featured posts on top, so new loop
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+
+ {%- if post.tags contains '.featured' -%}
+ {%- assign excerpt_link = post.url | relative_url -%}
+ {%- if post.excerpt_link contains '/' -%}
+ {%- assign excerpt_link = post.excerpt_link -%}
+ {%- endif -%}
+
+ {%- endif -%}
+{%- endfor -%}
+
+{%- comment -%}
+ * remaining normal posts, again new loop
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {% unless post.tags contains '.featured' or post.tags contains '.prepend' or post.tags contains '.append' %}
+ {%- assign excerpt_link = post.url | relative_url -%}
+ {%- if post.excerpt_link contains '/' -%}
+ {%- assign excerpt_link = post.excerpt_link -%}
+ {%- endif -%}
+
+ {% endunless %}
+{%- endfor -%}
+
+{%- comment -%}
+ * special posts for appending content to the listing pages
+ * they are processed last, so again a separate loop is needed
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {%- if post.tags contains '.append' -%}
+
+{{ post.content | markdownify }}
+
+ {%- endif -%}
+{%- endfor -%}
+
diff --git a/categories/people-alpha-sorted.md b/categories/people-alpha-sorted.md
new file mode 100644
index 0000000..fa87e47
--- /dev/null
+++ b/categories/people-alpha-sorted.md
@@ -0,0 +1,103 @@
+---
+layout: default
+---
+
+{%- assign this_name = page.name | split: "." -%}
+{%- assign this_category = this_name[0] | replace: '-alpha-sorted', '' -%}
+{%- assign this_pagetitle = this_category | capitalize | replace: '_', ' ' -%}
+
+
+
+
+
{{ this_pagetitle }}
+
+
+
+{%- comment -%}
+ * collecting the pages
+{%- endcomment -%}
+
+{%- assign cat_posts = site.emptyArray -%}
+{%- for post in site.documents -%}
+ {%- if post.categories contains this_category -%}
+ {%- assign cat_posts = cat_posts | push: post -%}
+ {%- endif -%}
+{%- endfor -%}
+
+{%- assign cat_posts = cat_posts | sort: 'title' -%}
+
+{%- comment -%}
+ * special posts for prepending content to the listing pages
+ * they are processed first, so separate loops are needed
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {%- if post.tags contains '.prepend' -%}
+
+{{ post.content | markdownify }}
+
+ {%- endif -%}
+{%- endfor -%}
+
+{%- comment -%}
+ * featured posts on top, so new loop
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+
+ {%- if post.tags contains '.featured' -%}
+ {%- assign excerpt_link = post.url | relative_url -%}
+ {%- if post.excerpt_link contains '/' -%}
+ {%- assign excerpt_link = post.excerpt_link -%}
+ {%- endif -%}
+
+ {%- endif -%}
+{%- endfor -%}
+
+{%- comment -%}
+ * remaining normal posts, again new loop
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {% unless post.tags contains '.featured' or post.tags contains '.prepend' or post.tags contains '.append' %}
+ {%- assign excerpt_link = post.url | relative_url -%}
+ {%- if post.excerpt_link contains '/' -%}
+ {%- assign excerpt_link = post.excerpt_link -%}
+ {%- endif -%}
+
+ {% endunless %}
+{%- endfor -%}
+
+{%- comment -%}
+ * special posts for appending content to the listing pages
+ * they are processed last, so again a separate loop is needed
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {%- if post.tags contains '.append' -%}
+
+{{ post.content | markdownify }}
+
+ {%- endif -%}
+{%- endfor -%}
+
diff --git a/categories/people-date-sorted.md b/categories/people-date-sorted.md
new file mode 100644
index 0000000..082494b
--- /dev/null
+++ b/categories/people-date-sorted.md
@@ -0,0 +1,87 @@
+---
+layout: default
+---
+
+{%- assign this_name = page.name | split: "." -%}
+{%- assign this_category = this_name[0] | replace: '-date-sorted', '' -%}
+{%- assign this_pagetitle = this_category | capitalize | replace: '_', ' ' -%}
+
+
+
+
+
{{ this_pagetitle }}
+
+
+
+{%- comment -%}
+ * collecting the pages
+{%- endcomment -%}
+
+{%- assign cat_posts = site.emptyArray -%}
+{%- for post in site.documents -%}
+ {%- if post.categories contains this_category -%}
+ {%- assign cat_posts = cat_posts | push: post -%}
+ {%- endif -%}
+{%- endfor -%}
+
+{%- assign cat_posts = cat_posts | sort: 'date' | reverse -%}
+
+{%- comment -%}
+ * special posts for prepending content to the listing pages
+ * they are processed first, so separate loops are needed
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {%- if post.tags contains '.prepend' -%}
+
+{{ post.content | markdownify }}
+
+ {%- endif -%}
+{%- endfor -%}
+
+{%- comment -%}
+ * no separate treatment of featured posts
+{%- endcomment -%}
+
+{%- assign today = site.time | date: '%Y%m%d' -%}
+{%- assign page_tag = this_category | downcase -%}
+
+{%- for post in cat_posts -%}
+ {% unless post.tags contains '.prepend' or post.tags contains '.append' %}
+ {%- assign post_author = post.author | downcase -%}
+ {%- assign excerpt_link = post.url | relative_url -%}
+ {%- if post.excerpt_link contains '/' -%}
+ {%- assign excerpt_link = post.excerpt_link -%}
+ {%- endif -%}
+ {%- assign post_day = post.date | date: '%Y%m%d' -%}
+ {%- assign post_year = post.date | date: '%Y' -%}
+ {%- if post_day > today -%}
+ {%- assign post_year = 'Upcoming' -%}
+ {%- endif %}
+ {%- if current_year != post_year -%}
+ {% assign current_year = post_year %}
+
{{ current_year }}
+ {% endif %}
+
+ {%- if post_day > today -%}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {%- endif -%}
+
{{ post.excerpt }}
+
+
+ {% endunless %}
+{%- endfor -%}
+
+{%- for post in cat_posts -%}
+ {%- if post.tags contains '.append' -%}
+
+{{ post.content | markdownify }}
+
+ {%- endif -%}
+{%- endfor -%}
diff --git a/categories/people.md b/categories/people.md
new file mode 100644
index 0000000..fa87e47
--- /dev/null
+++ b/categories/people.md
@@ -0,0 +1,103 @@
+---
+layout: default
+---
+
+{%- assign this_name = page.name | split: "." -%}
+{%- assign this_category = this_name[0] | replace: '-alpha-sorted', '' -%}
+{%- assign this_pagetitle = this_category | capitalize | replace: '_', ' ' -%}
+
+
+
+
+
{{ this_pagetitle }}
+
+
+
+{%- comment -%}
+ * collecting the pages
+{%- endcomment -%}
+
+{%- assign cat_posts = site.emptyArray -%}
+{%- for post in site.documents -%}
+ {%- if post.categories contains this_category -%}
+ {%- assign cat_posts = cat_posts | push: post -%}
+ {%- endif -%}
+{%- endfor -%}
+
+{%- assign cat_posts = cat_posts | sort: 'title' -%}
+
+{%- comment -%}
+ * special posts for prepending content to the listing pages
+ * they are processed first, so separate loops are needed
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {%- if post.tags contains '.prepend' -%}
+
+{{ post.content | markdownify }}
+
+ {%- endif -%}
+{%- endfor -%}
+
+{%- comment -%}
+ * featured posts on top, so new loop
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+
+ {%- if post.tags contains '.featured' -%}
+ {%- assign excerpt_link = post.url | relative_url -%}
+ {%- if post.excerpt_link contains '/' -%}
+ {%- assign excerpt_link = post.excerpt_link -%}
+ {%- endif -%}
+
+ {%- endif -%}
+{%- endfor -%}
+
+{%- comment -%}
+ * remaining normal posts, again new loop
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {% unless post.tags contains '.featured' or post.tags contains '.prepend' or post.tags contains '.append' %}
+ {%- assign excerpt_link = post.url | relative_url -%}
+ {%- if post.excerpt_link contains '/' -%}
+ {%- assign excerpt_link = post.excerpt_link -%}
+ {%- endif -%}
+
+ {% endunless %}
+{%- endfor -%}
+
+{%- comment -%}
+ * special posts for appending content to the listing pages
+ * they are processed last, so again a separate loop is needed
+{%- endcomment -%}
+
+{%- for post in cat_posts -%}
+ {%- if post.tags contains '.append' -%}
+
+{{ post.content | markdownify }}
+
+ {%- endif -%}
+{%- endfor -%}
+
diff --git a/favicon.ico b/favicon.ico
new file mode 100644
index 0000000..76ec133
Binary files /dev/null and b/favicon.ico differ
diff --git a/index.md b/index.md
new file mode 100644
index 0000000..e0eec2a
--- /dev/null
+++ b/index.md
@@ -0,0 +1,42 @@
+---
+title: "UZH BIO390 - Introduction to Bioinformatics Lecture Series"
+layout: default
+date: 2019-08-27
+permalink: /index.html
+author: "@mbaudis"
+category:
+ - doc
+tags:
+ - documentation
+ - FAQ
+---
+
+## {{ page.title }}
+
+This is a repository for materials related to the BIO390 _Introduction to Bioinformatics_ lecture series at the University of Zürich.
+
+#### Summary
+
+The handling and analysis of biological data using computational methods has become an essential part in most areas of biology. In this lecture, students will be introduced to the use of bioinformatics tools and methods in different topics, such as molecular resources and databases, standards and ontologies, sequence and high performance genome analysis, biological networks, molecular dynamics, proteomics, evolutionary biology and gene regulation. Additionally, the use of low level tools (e.g. Programming and scripting languages) and specialized applications will be demonstrated. Another topic will be the visualization of quantitative and qualitative biological data and analysis results.
+
+#### [Schedule]({{ "/categories/days.html" | relative_url }})
+
+#### Learning Goals
+
+The overall learning goals - especially the (limited) set necessary for passing the test - will be updated throughout the semester.
+
+* Core [__Learning Goals__]({{ "/doc/learning-goals.html" | relative_url }})
+
+This list is not exhaustive; additional information about "need to know" topics
+will be provided during the individual lectures.
+
+#### Literature and Resources
+
+* [Literature links]({{ "/doc/literature-links.html" | relative_url }}) and recommendations
+* [Resource links]({{ "/doc/resource-links.html" | relative_url }}) (browsers and online repositories)
+
+#### Links
+
+* BIO390 HS 2019 in the [UZH OLAT](https://lms.uzh.ch/auth/RepositoryEntry/16616980617) system
+* BIO390 HS 2019 in the [UZH directory](https://studentservices.uzh.ch/uzh/anonym/vvz/index.html#/details/2019/003/SM/50858977)
+
diff --git a/pages/_days/2019-09-17-Michael-Baudis.md b/pages/_days/2019-09-17-Michael-Baudis.md
new file mode 100644
index 0000000..2c25ae5
--- /dev/null
+++ b/pages/_days/2019-09-17-Michael-Baudis.md
@@ -0,0 +1,22 @@
+---
+title: 'Michael Baudis - Introducing Bioinformatics'
+layout: default
+author:
+ - "@mbaudis"
+excerpt_separator:
+www_link:
+www_links_formatted:
+ - '
[2018 lecture slides]'
+categories:
+ - days
+tags:
+ - material
+ - lectures
+---
+
+## {{ page.title }}
+
+The first day of the "Introduction to Bioinformatics" lecture series starts with a general introduction into the field and a description of the lecture topics, timeline and procedures.
+
+
+
diff --git a/pages/_days/2019-09-24-Christian-von-Mering.md b/pages/_days/2019-09-24-Christian-von-Mering.md
new file mode 100644
index 0000000..0384fb4
--- /dev/null
+++ b/pages/_days/2019-09-24-Christian-von-Mering.md
@@ -0,0 +1,21 @@
+---
+title: 'Christian von Mering - Sequence Bioinformatics'
+layout: default
+author:
+ - ""
+excerpt_separator:
+www_link: # web address, e.g. https://www.ga4gh.org; auto-linked
+pdf_file_name: # name of PDF (no path) somewhere in "assets"; auto-linked
+www_links_formatted: # one or more formatted html links
+ - '
[UZH-BIO390]'
+categories:
+ - days
+tags:
+ - material
+ - lectures
+---
+
+## {{ page.title }}
+
+
+
diff --git a/pages/_days/2019-10-01-Shinichi-Sunagawa.md b/pages/_days/2019-10-01-Shinichi-Sunagawa.md
new file mode 100644
index 0000000..9d54955
--- /dev/null
+++ b/pages/_days/2019-10-01-Shinichi-Sunagawa.md
@@ -0,0 +1,21 @@
+---
+title: 'Shinichi Sunagawa - Metagenomics'
+layout: default
+author:
+ - ""
+excerpt_separator:
+www_link: # web address, e.g. https://www.ga4gh.org; auto-linked
+pdf_file_name: # name of PDF (no path) somewhere in "assets"; auto-linked
+www_links_formatted: # one or more formatted html links
+ - '
[UZH-BIO390]'
+categories:
+ - days
+tags:
+ - material
+ - lectures
+---
+
+## {{ page.title }}
+
+
+
diff --git a/pages/_days/2019-10-08-Mark-Robinson.md b/pages/_days/2019-10-08-Mark-Robinson.md
new file mode 100644
index 0000000..11a9b27
--- /dev/null
+++ b/pages/_days/2019-10-08-Mark-Robinson.md
@@ -0,0 +1,21 @@
+---
+title: 'Mark Robinson - Statistical Bioinformatics'
+layout: default
+author:
+ - ""
+excerpt_separator:
+www_link: # web address, e.g. https://www.ga4gh.org; auto-linked
+pdf_file_name: # name of PDF (no path) somewhere in "assets"; auto-linked
+www_links_formatted: # one or more formatted html links
+ - '
[UZH-BIO390]'
+categories:
+ - days
+tags:
+ - material
+ - lectures
+---
+
+## {{ page.title }}
+
+
+
diff --git a/pages/_days/2019-10-15-Izaskun-Mallona.md b/pages/_days/2019-10-15-Izaskun-Mallona.md
new file mode 100644
index 0000000..a9f36d8
--- /dev/null
+++ b/pages/_days/2019-10-15-Izaskun-Mallona.md
@@ -0,0 +1,21 @@
+---
+title: ' Izaskun Mallona - Regulatory Genomics and Epigenomics'
+layout: default
+author:
+ - ""
+excerpt_separator:
+www_link: # web address, e.g. https://www.ga4gh.org; auto-linked
+pdf_file_name: # name of PDF (no path) somewhere in "assets"; auto-linked
+www_links_formatted: # one or more formatted html links
+ - '
[UZH-BIO390]'
+categories:
+ - days
+tags:
+ - material
+ - lectures
+---
+
+## {{ page.title }}
+
+
+
diff --git a/pages/_days/2019-10-22-Abdullah-Kahraman.md b/pages/_days/2019-10-22-Abdullah-Kahraman.md
new file mode 100644
index 0000000..ac0a12a
--- /dev/null
+++ b/pages/_days/2019-10-22-Abdullah-Kahraman.md
@@ -0,0 +1,21 @@
+---
+title: 'Abdullah Kahraman - Molecular Interaction Networks'
+layout: default
+author:
+ - ""
+excerpt_separator:
+www_link: # web address, e.g. https://www.ga4gh.org; auto-linked
+pdf_file_name: # name of PDF (no path) somewhere in "assets"; auto-linked
+www_links_formatted: # one or more formatted html links
+ - '
[UZH-BIO390]'
+categories:
+ - days
+tags:
+ - material
+ - lectures
+---
+
+## {{ page.title }}
+
+
+
diff --git a/pages/_days/2019-10-29-Katja-Baerenfaller.md b/pages/_days/2019-10-29-Katja-Baerenfaller.md
new file mode 100644
index 0000000..b89f86a
--- /dev/null
+++ b/pages/_days/2019-10-29-Katja-Baerenfaller.md
@@ -0,0 +1,21 @@
+---
+title: 'Katja Baerenfaller - Proteomics'
+layout: default
+author:
+ - ""
+excerpt_separator:
+www_link: # web address, e.g. https://www.ga4gh.org; auto-linked
+pdf_file_name: # name of PDF (no path) somewhere in "assets"; auto-linked
+www_links_formatted: # one or more formatted html links
+ - '
[UZH-BIO390]'
+categories:
+ - days
+tags:
+ - material
+ - lectures
+---
+
+## {{ page.title }}
+
+
+
diff --git a/pages/_days/2019-11-05-Amedeo-Caflisch.md b/pages/_days/2019-11-05-Amedeo-Caflisch.md
new file mode 100644
index 0000000..59d58fa
--- /dev/null
+++ b/pages/_days/2019-11-05-Amedeo-Caflisch.md
@@ -0,0 +1,21 @@
+---
+title: 'Amedeo Caflisch - Molecular Dynamics'
+layout: default
+author:
+ - ""
+excerpt_separator:
+www_link: # web address, e.g. https://www.ga4gh.org; auto-linked
+pdf_file_name: # name of PDF (no path) somewhere in "assets"; auto-linked
+www_links_formatted: # one or more formatted html links
+ - '
[UZH-BIO390]'
+categories:
+ - days
+tags:
+ - material
+ - lectures
+---
+
+## {{ page.title }}
+
+
+
diff --git a/pages/_days/2019-11-12-Elif-Ozkirimli.md b/pages/_days/2019-11-12-Elif-Ozkirimli.md
new file mode 100644
index 0000000..76e13f9
--- /dev/null
+++ b/pages/_days/2019-11-12-Elif-Ozkirimli.md
@@ -0,0 +1,21 @@
+---
+title: 'Elif Ozkirimli - Protein Structure and Interactions'
+layout: default
+author:
+ - ""
+excerpt_separator:
+www_link: # web address, e.g. https://www.ga4gh.org; auto-linked
+pdf_file_name: # name of PDF (no path) somewhere in "assets"; auto-linked
+www_links_formatted: # one or more formatted html links
+ - '
[UZH-BIO390]'
+categories:
+ - days
+tags:
+ - material
+ - lectures
+---
+
+## {{ page.title }}
+
+
+
diff --git a/pages/_days/2019-11-19-Valerie-Barbie.md b/pages/_days/2019-11-19-Valerie-Barbie.md
new file mode 100644
index 0000000..e7e7999
--- /dev/null
+++ b/pages/_days/2019-11-19-Valerie-Barbie.md
@@ -0,0 +1,21 @@
+---
+title: 'Christophe Dessimoz - Sequence Evolution and Phylogenetics'
+layout: default
+author:
+ - ""
+excerpt_separator:
+www_link: # web address, e.g. https://www.ga4gh.org; auto-linked
+pdf_file_name: # name of PDF (no path) somewhere in "assets"; auto-linked
+www_links_formatted: # one or more formatted html links
+ - '
[UZH-BIO390]'
+categories:
+ - days
+tags:
+ - material
+ - lectures
+---
+
+## {{ page.title }}
+
+
+
diff --git a/pages/_days/2019-11-26-Christophe-Dessimoz.md b/pages/_days/2019-11-26-Christophe-Dessimoz.md
new file mode 100644
index 0000000..dc47948
--- /dev/null
+++ b/pages/_days/2019-11-26-Christophe-Dessimoz.md
@@ -0,0 +1,21 @@
+---
+title: 'Valerie Barbie - Clinical Bioinformatics'
+layout: default
+author:
+ - ""
+excerpt_separator:
+www_link: # web address, e.g. https://www.ga4gh.org; auto-linked
+pdf_file_name: # name of PDF (no path) somewhere in "assets"; auto-linked
+www_links_formatted: # one or more formatted html links
+ - '
[UZH-BIO390]'
+categories:
+ - days
+tags:
+ - material
+ - lectures
+---
+
+## {{ page.title }}
+
+
+
diff --git a/pages/_days/2019-12-03-Andreas-Wagner.md b/pages/_days/2019-12-03-Andreas-Wagner.md
new file mode 100644
index 0000000..a492145
--- /dev/null
+++ b/pages/_days/2019-12-03-Andreas-Wagner.md
@@ -0,0 +1,21 @@
+---
+title: 'Andreas Wagner - Biological Networks'
+layout: default
+author:
+ - ""
+excerpt_separator:
+www_link: # web address, e.g. https://www.ga4gh.org; auto-linked
+pdf_file_name: # name of PDF (no path) somewhere in "assets"; auto-linked
+www_links_formatted: # one or more formatted html links
+ - '
[UZH-BIO390]'
+categories:
+ - days
+tags:
+ - material
+ - lectures
+---
+
+## {{ page.title }}
+
+
+
diff --git a/pages/_days/2019-12-10-Alex-H-Wagner.md b/pages/_days/2019-12-10-Alex-H-Wagner.md
new file mode 100644
index 0000000..b267bfe
--- /dev/null
+++ b/pages/_days/2019-12-10-Alex-H-Wagner.md
@@ -0,0 +1,21 @@
+---
+title: 'Alex Handler Wagner- Human Genome Variation'
+layout: default
+author:
+ - ""
+excerpt_separator:
+www_link: # web address, e.g. https://www.ga4gh.org; auto-linked
+pdf_file_name: # name of PDF (no path) somewhere in "assets"; auto-linked
+www_links_formatted: # one or more formatted html links
+ - '
[UZH-BIO390]'
+categories:
+ - days
+tags:
+ - material
+ - lectures
+---
+
+## {{ page.title }}
+
+
+
diff --git a/pages/_days/2019-12-17-Michael-Baudis-Exam.md b/pages/_days/2019-12-17-Michael-Baudis-Exam.md
new file mode 100644
index 0000000..f13ece3
--- /dev/null
+++ b/pages/_days/2019-12-17-Michael-Baudis-Exam.md
@@ -0,0 +1,21 @@
+---
+title: 'Exam'
+layout: default
+author:
+ - ""
+excerpt_separator:
+www_link: # web address, e.g. https://www.ga4gh.org; auto-linked
+pdf_file_name: # name of PDF (no path) somewhere in "assets"; auto-linked
+www_links_formatted: # one or more formatted html links
+ - '
[UZH-BIO390]'
+categories:
+ - days
+tags:
+ - material
+ - lectures
+---
+
+## {{ page.title }}
+
+
+
diff --git a/pages/_doc/+generated-podmd-doc-ProgenetixTemplate-bootstrap_site.md b/pages/_doc/+generated-podmd-doc-ProgenetixTemplate-bootstrap_site.md
new file mode 100644
index 0000000..5d0d23a
--- /dev/null
+++ b/pages/_doc/+generated-podmd-doc-ProgenetixTemplate-bootstrap_site.md
@@ -0,0 +1,44 @@
+---
+title: "ProgenetixTemplate::bootstrap_site.pl Perl Code Documentation"
+layout: default
+www_link:
+excerpt_separator:
+date: 2019-07-10
+category:
+ - howto
+tags:
+ - Perl
+ - ProgenetixTemplate
+ - code
+ - documentation
+---
+
+## {{ page.title }}
+
+
+
+
+The bootstrap_site is a utility for creating the structure of __Progenetix
+Jekyll Website Template__ based websites. The current functions are:
+
+* create list pages for all categories defined in `_config.yml`, separate for
+standard (alphabetically sorted) and reverse date sorted categories
+* as for categories, do the same for tags
+* check/add collections directories
+
+Additional options:
+
+* with the argument `-update y`, users will be prompted if they want to download
+the newest `style.css` and `layout.css` files from the "Progenetix :: Template"
+repository - this will overwrite the existing files!
+
+For `categories` and `tags` annotated in the `_config.yml` file, 3 listing pages
+will be generated:
+
+* (tag/category).md
+ - the standard landing page, which will be either date or alphabetically
+ sorted, depending on the label in the config (default alphabetic)
+* (tag/category)-date-sorted.md, (tag/category)-alpha-sorted.md
+ - separate date or alpha sorted landing pages, to switch to
+
+
diff --git a/pages/_doc/+generated-podmd-doc-ProgenetixTemplate-podmd.md b/pages/_doc/+generated-podmd-doc-ProgenetixTemplate-podmd.md
new file mode 100644
index 0000000..27c4140
--- /dev/null
+++ b/pages/_doc/+generated-podmd-doc-ProgenetixTemplate-podmd.md
@@ -0,0 +1,103 @@
+---
+title: "ProgenetixTemplate::podmd.pl Perl Code Documentation"
+layout: default
+www_link:
+excerpt_separator:
+date: 2019-07-10
+category:
+ - howto
+tags:
+ - Perl
+ - ProgenetixTemplate
+ - code
+ - documentation
+---
+
+## {{ page.title }}
+
+
+
+
+The "podmd.pl" script parses inline documentation from - now various - code files
+and writes it to a given output directory, in the format of Jekyll-compatible
+Markdown files, i.e. including a YAML header.
+
+* location: `__Jekyll_site_directory__/_tools/`
+
+Processing the input files is based on parameters provided in the "podmd.yaml"
+configuration file. Please have a look for examples there.
+
+For now, the functions of the script are optimised for use in the
+[Progenetix](http://info.progenetix.org) documentation environment but may be
+adapted for other purposes.
+
+The script itself contains an inline predefined minimal processing configuration
+which should be overridden from a `./podmd.yaml` file:
+
+```
+my $here_path = File::Basename::dirname( eval { ( caller() )[1] } );
+my $conf_yaml = $here_path.'/podmd.yaml';
+my $config = {
+ output_dir => '../pages/_doc',
+ output_pre => '+generated-podmd-doc',
+ category => 'howto',
+ tags => [ qw(code documentation) ],
+ md_starts => [ '^=podmd', '\/\*podmd', '^# podmd' ],
+ md_stops => [ '^=cut', 'end_podmd\*\/', '^# end_podmd' ],
+ packages => {
+ ProgenetixTemplate => {
+ input => '.',
+ extensions => [ '.pl' ],
+ language => 'Perl',
+ },
+ },
+};
+
+if (-f $conf_yaml) {
+ $config = LoadFile($here_path.'/podmd.yaml') }
+```
+For the scanned files, comment lines are read in if they are between one of the
+`md_starts` and `md_stops` markers, which can be defined as global parameters
+or package specific.
+
+Similarly, code is read in between the `md_code_starts` and `md_code_stops`
+markers, but is wrapped in source quote tags.
+
+If per-line commenting is uses between the markers (Python "# " line starts),
+these comment tags a re removed. However, this will also remove Markdown H1
+tags - so either use HTML for those or pre-pend them with a space.
+
+No file is created if there isn't any content in the text buffer.
+
+If documentation has been found, the YAML-prefixed markdown file is created in
+the `output_dir` target directory.
+
+The [YAML header](https://progenetix.github.io/progenetix-site-template/howto/yamlheader/)
+contains directives and parameters for the processing of the page through the
+[__Jekyll__](https://jekyllrb.com) website generation engine.
+
+The following code shows how the header is generated through injecting some
+file dependent parameters into a standard _Jekyll_ YAML header:
+
+```
+ my $mdFtxt = <
{language} Code Documentation"
+layout: default
+www_link: $package->{web_project_link}
+excerpt_separator:
+date: $today
+category:
+ - $config->{category}
+tags:
+ - $package->{language}
+ - $scope
+$addTags
+---
+
+## {{ page.title }}
+
+
+
+END
+```
diff --git a/pages/_doc/learning-goals.md b/pages/_doc/learning-goals.md
new file mode 100644
index 0000000..ec6b213
--- /dev/null
+++ b/pages/_doc/learning-goals.md
@@ -0,0 +1,130 @@
+---
+title: "UZH BIO390 - Learning Goals"
+layout: default
+date: 2019-09-10
+permalink: /doc/learning-goals.html
+author: "@mbaudis"
+category:
+ - doc
+tags:
+ - documentation
+ - FAQ
+ - material
+---
+
+## {{page.title}}
+
+This page indicates some of the learning goals, as emphasised by the different lecturers. Some points will have been discussed in different lectures; accordingly, exam questions may not refer to information of one specific presentation.
+
+#### Bioinformatics: Definition & Concepts
+
+* definition of "Bioinformatics" (cf. Anna Tramontano)
+* categories of informatics tools used in bioinformatics
+* hypothesis versus data driven science
+* areas of bioinformatics/bioinformaticians, in contrast to ("pure" modelling, statistics etc.)
+* 3 main categories of biological data, and example resources
+* definition of API
+* common sequence related file formats
+* hierarchies and relationships as 2 main principles of ontologies
+* areas of "not-bioinformatics", and why
+
+#### Sequence Analysis
+
+* substitution matrices
+* BLAST
+
+#### Statistical Bioinformatics
+
+* statistical evidence for a change in the means
+* usage of gene expression profiling
+* dimensionality reduction
+* central limit theorem
+* multiple testing correction
+* parameters for hierarchical clustering
+
+#### Bioinformatics tools: Statistics & Graphics in R & BioConductor
+
+* What is tidy data?
+* ideas behind ggplot: components of a ggplot, arrangement of input data ... (no actual code writing needed)
+* interpret common types of plots, e.g. barplot, boxplot, histogram
+* effect of data transformation (e.g. log) on common types of plots
+
+#### Regulatory Genomics and Epigenomics
+
+* secondary/tertiary human genome structure
+* functional genome content
+* transcription factors & genome interaction
+* chemical genome modifications, their effectors and results
+* Chip-Seq
+
+#### Metagenomics
+
+* Students can explain the concept of taxonomic diversity
+* Students can explain the concept microbial community dissimilarity
+* Students know how sequences are used to derive an adopted species concept for prokaryotes
+* Students are familiar with the principle steps for 16S rRNA-based taxonomic composition analysis
+* Students can recapitulate the essential steps of short sequencing read assembly into contigs and scaffolds
+* Students can describe the basic steps of metagenomic analysis: from raw reads to the reconstruction of genomic scaffolds
+
+#### Proteomics
+
+* principles of proteome organization in the cell
+* key experimental and computational concepts for the collection and analysis of high confidence protein-protein interaction data
+
+#### Molecular Dynamics
+
+* atomistic model
+* force field (potential energy function)
+* treatment of solvent
+* molecular dynamics (Newton equation of motion; Langevin equation)
+* simulations of peptides and proteins
+* statistical error and systematic error
+
+#### Clinical Bioinformatics & Personalized Medicine
+
+* genomic variants (types, numbers)
+* genomic privacy and re-identification (concepts)
+* Beacon example
+* long range familial searches
+* main bottlenecks of molecular diagnostics in the clinical setting
+* goals of many personalized health initiatives
+* direct-to-consumer genetic testing -> what, how
+* currently favoured clinical NGS technology
+* clinical trial participation
+
+#### Text Mining
+
+* text mining pipelines & (current) common programs/applications
+* article/literature repositories (with focus on accessibility)
+* processing steps in text mining
+* common problems in text mining
+
+#### Biological Networks
+
+* Protein interaction and metabolic networks
+* the two-hybrid assay and its limitations
+* detection of protein complexes
+* graphs, nodes, edges, paths
+* geodesics, graph diameter
+* common types of degree distributions
+* adjacency matrix
+* shortest path matrix
+* degree correlations
+* assortative and disassortative graphs
+* clustering coefficient
+* community (module) detection
+* modularity Q
+* Girvan-Newman algorithm
+* cliques
+* small world graphs
+* motifs, graph representations of metabolic networks
+* stoichiometry matrices
+* null space
+* flux balance analysis
+
+#### Gene regulation and epigenetics
+
+* read mapping
+* peak calling
+* sequence compression algorithms
+
diff --git a/pages/_doc/literature-links.md b/pages/_doc/literature-links.md
new file mode 100644
index 0000000..ec3c41d
--- /dev/null
+++ b/pages/_doc/literature-links.md
@@ -0,0 +1,29 @@
+---
+title: "UZH BIO390 - Literature"
+layout: default
+date: 2019-09-10
+permalink: /doc/literature-links.html
+www_links_formatted:
+ - '[BIO392 Course Literature]'
+author: "@mbaudis"
+category:
+ - doc
+tags:
+ - documentation
+ - FAQ
+ - material
+ - links
+ - articles
+---
+
+## {{page.title}}
+
+#### Books
+
+* Anna Tramontano: Introduction to Bioinformatics
+* Susan Holmes and Wolfgang Huber: Statistics for Biology
+* Robert Gentleman: R Programming for Bioinformatics
+* John Maindonald & W. John Braun: Data Analysis and Graphics Using R
+* Neil C. Jones & Pavel A. Pevzner: Bioinformatics Algorithms
+* Edward Tufte: The Visual Display of Quantitative Information
+* Uri Alon: An Introduction to Systems Biology
diff --git a/pages/_doc/resource-links.md b/pages/_doc/resource-links.md
new file mode 100644
index 0000000..66148a2
--- /dev/null
+++ b/pages/_doc/resource-links.md
@@ -0,0 +1,48 @@
+---
+title: "UZH BIO390 - Resource Links"
+layout: default
+date: 2019-09-10
+permalink: /doc/resource-links.html
+author: "@mbaudis"
+category:
+ - doc
+tags:
+ - documentation
+ - FAQ
+ - material
+ - links
+---
+
+## {{page.title}}
+
+This page shows some links to bioinformatics online resources, mostly related to (human) genome variants and/or genome interpretation.
+
+Please feel free to improve this page by submitting your own resource links and comments about those resources (content, purpose, criticism).
+
+### Genome Browsers
+
+* [UCSC Genome Browser](https://genome.ucsc.edu/)
+
+### Variant Resources
+
+* [Cancer Genome Interpreter (CGI)](https://www.cancergenomeinterpreter.org/home)
+* [Clinical Interpretation of Variants in Cancer (CIViC)](https://civicdb.org/home)
+* [JAX Clinical Knowledgebase (CKB)](https://ckb.jax.org/)
+* [Molecular Match](https://app.molecularmatch.com/)
+* [OncoKB](http://oncokb.org/#/)
+* [Precision Medicine Knowledgebase (PMKB)](https://pmkb.weill.cornell.edu/)
+* [BRCA exchange](http://brcaexchange.org/)
+* [Cancer Driver Log (CanDL)](https://candl.osu.edu/)
+* [Gene Drug Knowledge Database](https://www.synapse.org/#!Synapse:syn2370773/wiki/62707)
+* [MatchMiner](http://bcb.dfci.harvard.edu/knowledge-systems/)
+* [COSMIC Drug Resistance Curation](http://cancer.sanger.ac.uk/cosmic/drug_resistance)
+* [My Cancer Genome](https://www.mycancergenome.org/)
+* [NCI Clinical Trials](https://www.cancer.gov/about-cancer/treatment/clinical-trials)
+* [Personalized Cancer Therapy Database](https://pct.mdanderson.org/#/home)
+* [ClinGen Knowledge Base](https://www.clinicalgenome.org/resources-tools/)
+* [ClinVar](http://www.ncbi.nlm.nih.gov/clinvar/)
+* [Pharmacogenomics Knowledgebase (PharmGKB)](https://www.pharmgkb.org/)
+* [The Human Gene Mutation Database (HGMD)](http://www.hgmd.cf.ac.uk)
+* [arrayMap](http://arraymap.org)
+* [Progenetix](http://progenetix.org)
+* [Beacon+](http://beacon.progenetix.org)
diff --git a/pages/_people/Caflisch-Amedeo.md b/pages/_people/Caflisch-Amedeo.md
new file mode 100644
index 0000000..fe11c13
--- /dev/null
+++ b/pages/_people/Caflisch-Amedeo.md
@@ -0,0 +1,27 @@
+---
+title: "Amedeo Caflisch"
+layout: default
+date: 1996-07-01
+excerpt_separator:
+excerpt_link: 'http://www.biochem-caflisch.uzh.ch'
+image_file: 'Caflisch.png'
+category:
+ - people
+tags:
+ - UZH
+---
+
+{% for static_file in site.static_files %}
+ {% if static_file.path contains page.image_file %}
+
+ {% endif %}
+{% endfor %}
+
+## {{ page.title }}
+
+* Professor of Computational Structural Biology
+* Department of Biochemistry
+* University of Zürich
+
+
+
diff --git a/pages/_people/Michael-Baudis.md b/pages/_people/Michael-Baudis.md
new file mode 100644
index 0000000..76e6948
--- /dev/null
+++ b/pages/_people/Michael-Baudis.md
@@ -0,0 +1,73 @@
+---
+title: "Michael Baudis"
+permalink: /group/Michael_Baudis/
+excerpt_link: https://info.baudisgroup.org/group/Michael_Baudis/
+layout: default
+excerpt_separator:
+date: 2007-08-01
+category:
+ - people
+tags:
+ - .featured
+ - group
+---
+
+## Michael Baudis
+#### Professor of Bioinformatics, Institute of Molecular Life Sciences, University of Zurich & Swiss Institute of Bioinformatics **SIB**
+
+
+
+| | |
+| ---: | --- |
+| __Contact__ | |
+| Address| 
Prof. Dr. Michael Baudis
Institute of Molecular Life Sciences
University of Zurich
Winterthurerstrasse 190
Y-13F-01
CH-8057 Zurich
Switzerland |
+| ORCID | [0000-0002-9903-4248](https://orcid.org/0000-0002-9903-4248) |
+| email | [mbaudis@imls.uzh.ch](mailto:mbaudis@imls.uzh.ch) |
+| github | [@mbaudis](http://github.com/mbaudis/) :: [@progenetix](http://github.com/progenetix/) :: [@baudisgroup](http://github.com/baudisgroup/) |
+| web | [UZH IMLS](http://www.imls.uzh.ch/en/research/baudis/) :: [SIB](http://sib.swiss/baudis-michael/) |
+| __Personal__ | |
+| Date of birth | 1967-11-11 |
+| Nationality | Germany |
+| Family | Married since 1991, two children |
+| email | [m@baud.is](mailto:m@baud.is) |
+| __Education__ | |
+| 2001 – 2003 | Postdoctoral Research Fellow, Pathology Department, Stanford University, U.S.A. |
+| 1994 – 1998 | Research thesis in molecular cytogenetics, German Cancer Research Center (DKFZ) & University of Heidelberg, Germany |
+| 1992 – 1998 | Student of Medicine, University of Heidelberg, Germany |
+| __Employment__ | |
+| 2015 – current | Professor of Bioinformatics, Institute of Molecular Life Sciences, University of Zurich, Switzerland |
+| 2007 – 2015 | Research Group Leader, Institute of Molecular Life Sciences, University of Zurich, Switzerland |
+| 2006 – 2007 | Research Group Leader, Genetics Department, RWTH Aachen University Hospital, Germany |
+| 2003 – 2006 | Research Assistant Professor, Department of Pediatric Oncology, University of Florida, Gainesville, U.S.A. |
+| 1998 – 2000 | Attending Physician, Faculty of Internal Medicine V, University of Heidelberg, Germany |
+
+
+### Biosketch
+
+
+
+Michael Baudis is a Professor of Bioinformatics at the Institute of Molecular Life Sciences, University of Zurich, and a group leader at the Swiss Institute of Bioinformatics.
+
+
+Michael studied Medicine at Heidelberg University from which he graduated in 1998 and received his German medical license after internships at Heidelberg University Hospital. 
Between 1994 - 1998, he performed his research thesis in Molecular Cytogenetics in the group of Peter Lichter at the German Cancer Research Center (DKFZ) Heidelberg, on the genomic analysis of malignant lymphomas, in the context of a multi-center clinical trial. He received his doctorate of the Medical Faculty of the Ruprecht-Karls Universität Heidelberg in 1999.
+
+
+While working as an attending physician in Hematology & Oncology at Heidelberg University Hospital between 1998 and the end of 2000, Dr. Baudis pursued research projects in molecular cytogenetics and biology of hematologic neoplasias, and started to collect genomic profiling data from Comparative Genomic Hybridization (CGH) experiments. 
In January 2000, he began a postdoctoral research project at Stanford University, in the group of Prof. Michael Cleary (Department of Pathology) with focus on the functional characterisation of E2A-HLF and E2A-PBX1 fusion genes in acute lymphoblastic leukemias, using in vitro cell line models with inducible constructs and array based gene expression analysis as well as murine essays. This work was extended during the following faculty position at the University of Florida.
+
+
+Already during his thesis at the DKFZ, Michael became interested in the systematic collection of genome screening data, then from the CGH experiments performed at the Lichter lab. Supported by an internal grant from the University of Heidelberg's Medical School, he was able to create a database of original and publication derived genomic copy number data from malignant lymphomas. 
The website of the progenetix.net molecular cancer cytogenetics website was launched in early 2001, accompanied by a publication in Bioinformatics.
+
+
+Following a brief stay at the RWTH Aachen (Human Genetics; 2006-2007), since August 2007 Michael has been a group leader and Professor of Bionformatics (2015) at the Institute of Molecular Life Sciences of the University of Zürich, as well as associated with the Swiss Institute of Bioinformatics SIB.
+
+
+The work of his Computational Oncogenomics group is centered on the comparative analysis of genomic profiling data in cancer, with a focus on somatic copy number variations (CNV, CNA). With the Progenetix and arrayMap repositories, the group provides some of the largest reference resources of curated genomic profiling and associated metadata covering the majority of cancer types.
+
+
+Apart from the analysis of cancer genome data, in recent years Michael has been involved in efforts to facilitate the access to genomic data for research on a global scale. 
Since its founding in 2014, Michael has been a member of the Global Alliance for Genomics and Health GA4GH, currently serving in the steering committee and as co-lead of its "Discovery" workstream. Related to the work in the Global Alliance, Michael also co-chairs the ELIXIR Beacon project, which develops APIs to query genomic data collections in a privacy-protecting manner. 
Here, the main focus on the group is in prototyping protocol extensions with demonstrator implementation in the Beacon+ project, connected to the Progenetix and arrayMap repositories.
+
+
+In the Swiss context, Michael has been involved in advising the Swiss Personalized Health Network (SPHN) initiative and currently leads its "Bioinformatics and Data Analytics" working group.
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
{{ current_year }}
+ {% endif %}
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
{{ current_year }}
+ {% endif %}
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
{{ current_year }}
+ {% endif %}
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
{{ current_year }}
+ {% endif %}
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
{{ current_year }}
+ {% endif %}
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
{{ current_year }}
+ {% endif %}
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
{{ current_year }}
+ {% endif %}
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
{{ current_year }}
+ {% endif %}
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
{{ current_year }}
+ {% endif %}
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
{{ current_year }}
+ {% endif %}
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
{{ current_year }}
+ {% endif %}
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
{{ current_year }}
+ {% endif %}
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
{{ current_year }}
+ {% endif %}
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+
+
+
Pages tagged "{{ this_pagetitle }}"
+
+
+ {% if post_day > today %}
+
{{ post.date | date: "%Y-%m-%d" }}
+ {% endif %}
+
{{ post.excerpt }}
+
+
+{%- endif -%}{%- endfor -%}
+{%- for static_file in site.static_files -%}{%- if static_file.path contains 'site-specific/site-logo-topright.png' -%}
+ 
+{%- endif -%}{%- endfor -%}
+
+ {%- elsif site.source_path contains '/' -%}
+
+
+
+
+
+
+ {%- endif -%}
+{%- endunless -%}
+
+{%- comment -%}
+ * / editing
+{%- endcomment -%}
+
+{%- if site.google_analytics -%}
+
+{%- endif -%}
+
+
+
diff --git a/_templates/2019-01-01-post.md b/_templates/2019-01-01-post.md
new file mode 100644
index 0000000..fc4c087
--- /dev/null
+++ b/_templates/2019-01-01-post.md
@@ -0,0 +1,27 @@
+---
+title: 'Post Template'
+date: 2019-01-01
+layout: default
+author: # quoted "@Github" shortname recommended
+excerpt_separator:
+excerpt_link: # an optional link to different page when clicking the excerpt
+www_link: # a simple web address related to the post, e.g. https://www.ga4gh.org
+www_links_formatted: # one or multiple complete links
+# - '[biorXiv]'
+pdf_file_name: # the name of a PDF (no path) somewhere in "assets", which will be auto-linked
+categories: # please adjust
+# - news
+# - minutes
+tags: # please adjust
+# - press
+# - faq
+# - contacts
+---
+
+## {{ page.title }}
+
+Some content which will shows up in the excerpt on listing pages...
+
+
+
+More content for the full page...
diff --git a/_templates/_categories-alpha-sorted.md b/_templates/_categories-alpha-sorted.md
new file mode 100644
index 0000000..fa87e47
--- /dev/null
+++ b/_templates/_categories-alpha-sorted.md
@@ -0,0 +1,103 @@
+---
+layout: default
+---
+
+{%- assign this_name = page.name | split: "." -%}
+{%- assign this_category = this_name[0] | replace: '-alpha-sorted', '' -%}
+{%- assign this_pagetitle = this_category | capitalize | replace: '_', ' ' -%}
+
+