added discussed changes of the last sequencing round to the protokoll

Makefile

@@ -69,6 +69,22 @@ pdf: detached-serve ## generate the PDF of the protocols
             "$(SITE_URL)/protocols/$$t?without-details" \
             2> /dev/null ; \
 	done
+
+	${CHROME} \
+		--headless \
+		--disable-gpu \
+		--print-to-pdf="$(PDF_DIR)/beer-dna-sequencing-flongle-instructor.pdf" \
+		"$(SITE_URL)/protocols/beer-dna-sequencing?flongle" \
+		2> /dev/null
+
+	${CHROME} \
+		--headless \
+		--disable-gpu \
+		--print-to-pdf="$(PDF_DIR)/beer-dna-sequencing-flongle-learners.pdf" \
+		"$(SITE_URL)/protocols/beer-dna-sequencing?flongle?without-details" \
+		2> /dev/null
+
+
 	pkill -f jekyll
 .PHONY: pdf
 

README.md

@@ -90,3 +90,8 @@ In the sequel, we assume you use miniconda.
 
 7. Open the website in your favorite browser at:
    [http://127.0.0.1:4000/](http://127.0.0.1:4000/)
+
+
+## How can I generate the PDFs for the protocols locally?
+
+The protocols can be extracted to PDFs in 2 versions: one for participants/pupils with only the instructions, one for the instructors/teachers with instructions and details

_config.yml

@@ -13,6 +13,8 @@ repository: StreetScienceCommunity/StreetScienceCommunity.github.io
 participation_form: https://docs.google.com/forms/d/e/1FAIpQLScNgEDWoftccrUHXhsAOgLCFiG1FAQzQxsSW44uDTrEKwZ7_A/viewform
 google_group: https://groups.google.com/forum/#!forum/streetsciencecommunity
 
+includes_dir: .
+
 collections:
   events:
     permalink: /events/:path/

_events/2018-11-10-first_workshop.md

@@ -31,7 +31,7 @@ the initial feedback is overwhelming. It was a blast to do some wet-lab work,
 specially as most of us, as bioinformaticians and computer scientists, are not
 used to it!
 
-{% include event-images.html images="
+{% include _includes/event-images.html images="
   /images/events/2018-11-10-first_workshop/DSC_6931.jpg
   /images/events/2018-11-10-first_workshop/DSC_6878.jpg
   /images/events/2018-11-10-first_workshop/DSC_6852.jpg
@@ -46,7 +46,7 @@ DNA of the yeast inside this beer. To do so, we:
 
 - Extracted the yeast from the beer with several centrifuge runs
 
-{% include event-images.html images="
+{% include _includes/event-images.html images="
   /images/events/2018-11-10-first_workshop/DSC_6863.jpg
   /images/events/2018-11-10-first_workshop/DSC_6867.jpg
   /images/events/2018-11-10-first_workshop/DSC_6889.jpg
@@ -55,7 +55,7 @@ DNA of the yeast inside this beer. To do so, we:
 
 - Broke the cell membranes of the yeasts using an ethanol bath and a lysis buffer
 
-{% include event-images.html images="
+{% include _includes/event-images.html images="
   /images/events/2018-11-10-first_workshop/DSC_6900.jpg
   /images/events/2018-11-10-first_workshop/DSC_6919.jpg
   /images/events/2018-11-10-first_workshop/DSC_6938.jpg
@@ -64,7 +64,7 @@ DNA of the yeast inside this beer. To do so, we:
 
 - Extracted the DNA from the cell using magnetic beads and a MinElute Reaction Kit 50 from Qiagen
 
-{% include event-images.html images="
+{% include _includes/event-images.html images="
   /images/events/2018-11-10-first_workshop/DSC_7003.jpg
   /images/events/2018-11-10-first_workshop/DSC_6993.jpg
   /images/events/2018-11-10-first_workshop/DSC_6994.jpg
@@ -87,7 +87,7 @@ During the DNA extracted, we started to play with the MinION with the
 installation of the Nanopore software and ran a functional test of the flowcell.
 We then did the library preparation: preparation of the DNA for sequencing.
 
-{% include event-images.html images="
+{% include _includes/event-images.html images="
   /images/events/2018-11-10-first_workshop/DSC_6857.jpg
   /images/events/2018-11-10-first_workshop/DSC_6954.jpg
   /images/events/2018-11-10-first_workshop/DSC_6853.jpg
@@ -96,7 +96,7 @@ We then did the library preparation: preparation of the DNA for sequencing.
 
 We then loaded the MinION with our DNA and launched the sequencing
 
-{% include event-images.html images="
+{% include _includes/event-images.html images="
   /images/events/2018-11-10-first_workshop/DSC_6951.jpg
   /images/events/2018-11-10-first_workshop/DSC_6946.jpg
   /images/events/2018-11-10-first_workshop/DSC_6973.jpg
@@ -113,7 +113,7 @@ _protocols/beer-dna-sequencing.md %}).*
 Milad then analyzed the generated sequences and extracted some *Saccharomyces
 cerevisae*.
 
-{% include event-images.html images="/images/events/2018-11-10-first_workshop/analysis_taxonomy.png" %}
+{% include _includes/event-images.html images="/images/events/2018-11-10-first_workshop/analysis_taxonomy.png" %}
 
 Very promising results (given we stoped the sequencing)!
 

_events/2019-03-10-first_public_workshop.md

@@ -21,13 +21,13 @@ photos:
 
 On the 31st of March, we hold our first public workshop for the [BeerDEcoded project]({% link _projects/beerdecoded.md %}) in Freiburg. Some students and external people participated to this event: 16 peoples in total, including us.
 
-{% include event-images.html images="
+{% include _includes/event-images.html images="
   /images/events/2019-03-10-first_public_workshop/DSC_9661.jpg"
 %}
 
 We started the day with a short introduction to beer, yeast, DNA and of course lab safety. Then all participants took part in some fun games on pipetting and centrifuging to make them more comfortable with both.
 
-{% include event-images.html images="
+{% include _includes/event-images.html images="
   /images/events/2019-03-10-first_public_workshop/DSC_9563.jpg
   /images/events/2019-03-10-first_public_workshop/DSC_9575.jpg
   /images/events/2019-03-10-first_public_workshop/DSC_9583.jpg
@@ -36,7 +36,7 @@ We started the day with a short introduction to beer, yeast, DNA and of course l
 
 We extracted yeast DNA of the not filtered Waldhaus, a local Black Forest beer.
 
-{% include event-images.html images="
+{% include _includes/event-images.html images="
   /images/events/2019-03-10-first_public_workshop/DSC_9644.jpg
   /images/events/2019-03-10-first_public_workshop/DSC_9596.jpg
   /images/events/2019-03-10-first_public_workshop/DSC_9598.jpg
@@ -47,7 +47,7 @@ We extracted yeast DNA of the not filtered Waldhaus, a local Black Forest beer.
 
 Then DNA extraction went well. In parallel, we started our DNA sequencing protocol using a previously extracted DNA from Rothaus, another local beer. Here we encountered several problems during the library preparation and the sequencing likely due to mistakes in the protocols and reuse of old flowcell. We will improve the protocol to fix the issues.
 
-{% include event-images.html images="
+{% include _includes/event-images.html images="
   /images/events/2019-03-10-first_public_workshop/DSC_9623.jpg
   /images/events/2019-03-10-first_public_workshop/DSC_9622.jpg
   /images/events/2019-03-10-first_public_workshop/DSC_9628.jpg
@@ -59,7 +59,7 @@ Then DNA extraction went well. In parallel, we started our DNA sequencing protoc
 
 We then analyzed the data using Galaxy.
 
-{% include event-images.html images="
+{% include _includes/event-images.html images="
   /images/events/2019-03-10-first_public_workshop/DSC_9613.jpg
   /images/events/2019-03-10-first_public_workshop/DSC_9656.jpg
   /images/events/2019-03-10-first_public_workshop/DSC_9538.jpg"

_events/2019-06-13-gcc.md

@@ -23,7 +23,7 @@ The [Galaxy Community Conference](https://galaxyproject.org/events/gcc2019/) was
 
 During the first day of GCC, we demonstrated how to sequence the DNA of beer (["Beer Decoded, Here and Now!"](https://gcc2019.sched.com/event/QZyL/beer-decoded-here-and-now)):
 
-{% include event-images.html images="
+{% include _includes/event-images.html images="
   /images/events/2019-06-13-gcc/48386951316_c278327495_c.jpg
   /images/events/2019-06-13-gcc/48387072522_9ae093edc0_c.jpg
   /images/events/2019-06-13-gcc/48386951631_c764e1cdd8_c.jpg
@@ -33,7 +33,7 @@ During the first day of GCC, we demonstrated how to sequence the DNA of beer (["
 
 Teresa gave also a talk about ["Street Science Community: make science tangible & accessible by bringing it to the 'street' with open science workshops"](https://gcc2019.sched.com/event/PSfv/street-science-community-make-science-tangible-accessible-by-bringing-it-to-the-street-with-open-science-workshops) during the plenary session of Wednesday afternoon.
 
-{% include event-images.html images="
+{% include _includes/event-images.html images="
   /images/events/2019-06-13-gcc/48387082312_d3124973e5_c.jpg
   /images/events/2019-06-13-gcc/48386941691_5bbfdebe67_c.jpg"
 %}

_events/2019-07-22-pupils_workshop.md

@@ -21,20 +21,20 @@ photos:
 
 On the 22st to 23rd of March, we held our first workshop with high school pupils for the [BeerDEcoded project]({% link _projects/beerdecoded.md %}) in Freiburg. Four pupils and one external participant made us a group of 10 people in total.
 
-{% include event-images.html images="
+{% include _includes/event-images.html images="
   /images/events/2019-07-22-pupils_workshop/1st-beerdecoded-workshop-with-pupils_48358150687_o.jpg"
 %}
 
 We started the day in the biology department at the University of Freiburg with a short introduction to beer, yeast, DNA and of course lab safety. We split the participants into two groups to bring in some competition: Who will extract and purify DNA the best? With some games the pupils learned to pipette accurately, organize the space in a centrifuge correctly and to enjoy the stimulation of a vortex mixer.
 
-{% include event-images.html images="
+{% include _includes/event-images.html images="
   /images/events/2019-07-22-pupils_workshop/1st-beerdecoded-workshop-with-pupils_48358152257_o.jpg
   /images/events/2019-07-22-pupils_workshop/1st-beerdecoded-workshop-with-pupils_48358151967_o.jpg"
 %}
 
 These skills combined allowed us to reduce 2 bottles of beer to a drop of liquid, hopefully containing as much DNA as possible and minimal contamination. Remember the two groups? Well, at the end of the day we definitely learned something: Disciplined lab work does make a difference, we had a clear winner!
 
-{% include event-images.html images="
+{% include _includes/event-images.html images="
   /images/events/2019-07-22-pupils_workshop/1st-beerdecoded-workshop-with-pupils_48358151462_o.jpg
   /images/events/2019-07-22-pupils_workshop/1st-beerdecoded-workshop-with-pupils_48358152152_o.jpg
   /images/events/2019-07-22-pupils_workshop/1st-beerdecoded-workshop-with-pupils_48358150612_o.jpg
@@ -43,7 +43,7 @@ These skills combined allowed us to reduce 2 bottles of beer to a drop of liquid
 
 At the following day we met again for the bioinformatics part - analyzing the data. Unfortunately, this had to be done with data from a different DNA extraction as we were lacking some necessary consumables. Looking at a mysterious FASTQ file, we worked together the decipher what was in front of us, benefiting from the crisp knowledge that pupils bring from school. The analysis with a Galaxy workflow not only allowed to identify a familiar sounding "Saccharomyces cerevisiae" among other species of yeast, but also to introduce the pupils in the work of a bioinformatician and the greater picture of the science behind BeerDeCoded.
 
-{% include event-images.html images="
+{% include _includes/event-images.html images="
   /images/events/2019-07-22-pupils_workshop/1st-beerdecoded-workshop-with-pupils_48358151272_o.jpg
   /images/events/2019-07-22-pupils_workshop/1st-beerdecoded-workshop-with-pupils_48358017231_o.jpg
   /images/events/2019-07-22-pupils_workshop/1st-beerdecoded-workshop-with-pupils_48358017361_o.jpg

_includes/beer-dna-sequencing-flowcell-select.html

@@ -0,0 +1,10 @@
+<div class="control">
+    Flow cell:
+    <label class="radio">
+        <input type="radio" name="flowcell" id="minion-flowcell" checked>
+        MinION Flow Cell
+    </label>
+    <label class="radio">
+        <input type="radio" name="flowcell" id="flongle-flowcell">
+        Flongle Flow Cell
+    </label>

_layouts/base.html

@@ -11,16 +11,21 @@
     <link rel="stylesheet" media="print" href="/css/print.css" />
   </head>
   <body>
-    {% include default-header.html %}
+    {% include _includes/default-header.html %}
 
     {{ content }}
 
-    {% include default-footer.html %}
+    {% include _includes/default-footer.html %}
 
     <script defer src="https://use.fontawesome.com/releases/v5.3.1/js/all.js"></script>
     <script src="/js/scripts.js"></script>
     {% if page.twitter_moment %}
       <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
     {% endif %}
+
+    {% if page.flowcell-select %}
+      <script src="/js/flowcell-select-scripts.js"></script>
+    {% endif %}
+
   </body>
 </html>

_projects/beerdecoded.md

@@ -38,7 +38,7 @@ description: An immersion into biology, bioinformatics & sciences via beer and t
 ## Previous workshops
 
 We already organized several BeerDEcoded workshops over the last year. You can read more about
- them by checking our [events]({% link events.md %}).
+them by checking our [events]({% link events.md %}).
 
 ## Why?
 
@@ -68,4 +68,4 @@ web-based platform for computational biology and bioinformatics.
 
 ## Some pictures
 
-{% include projects/beerdecoded.html %}
+{% include _includes/projects/beerdecoded.html %}