From 8b2621a44e417be835b80690b27f615e7806a205 Mon Sep 17 00:00:00 2001
From: PlushZ <55543056+PlushZ@users.noreply.github.com>
Date: Wed, 30 Jun 2021 15:31:39 +0200
Subject: [PATCH 1/7] Create beerDEcoded.yaml
---
tour/beerDEcoded.yaml | 188 ++++++++++++++++++++++++++++++++++++++++++
1 file changed, 188 insertions(+)
create mode 100644 tour/beerDEcoded.yaml
diff --git a/tour/beerDEcoded.yaml b/tour/beerDEcoded.yaml
new file mode 100644
index 00000000..4c76c98e
--- /dev/null
+++ b/tour/beerDEcoded.yaml
@@ -0,0 +1,188 @@
+id: beerDEcoded
+name: BeerDEcoded - StreetScienceCommunity
+description: BeerDEcoded - StreetScienceCommunity
+title_default: BeerDEcoded
+steps:
+ - title: BeerDEcoded - StreetScienceCommunity
+ content: >-
+ What is a beer microbiome? There are collections of small living
+ creatures. These small creatures are called bacteria and they are
+ everywhere. In our gut, in the soil, even on vending machines. Some of
+ these bacteria are actually very good for us. And some others can make us
+ very ill. Bacteria come in different shapes and sizes but they have the
+ same components. One crucial component is the DNA, the blueprint of life.
+ The DNA encodes the shape and size and many other things unique for a
+ bacterial species. Because of the encoding information the DNA can be used
+ to identify what kind of bacteria the DNA is from. Therefore, within a
+ sample form soil, our gut or beer one can specify what kind of species are
+ inside the sample. Follow this tour to learn more about this kind of
+ analysis.
Read and Follow the instructions before clicking
+ 'Next'.
Click 'Prev' in case you missed out on any
+ step."
+ backdrop: true
+ - title: Create a new history
+ element: '#history-new-button'
+ intro: >-
+ Let's start by creating a new history.
Click on the button 'Create
+ new history'
+ position: left
+ preclick:
+ - '#center-panel'
+ - title: Rename the history
+ element: '#current-history-panel > div.controls'
+ intro: Change the name of the new history to 'BeerDEcoded'.
+ position: left
+ - title: Uploading the input data
+ content: We need to upload data. We will start with a fastq file.
+ backdrop: true
+ - title: Uploading the input data
+ element: .upload-button
+ intro: >-
+ We will import fastq into the history we just created.
Click
+ 'Next' and the tour will open Galaxy Upload Manager and take you to
+ the Upload screen.
+ position: right
+ postclick:
+ - .upload-button
+ - title: Uploading the input data
+ intro: Upload the data by clicking the 'Paste/Fetch Data' button.
+ - title: Uploading the input data
+ content: >-
+ Load the data into your history by providing the links or choose your
+ fastq file from your computer.
Click on 'Start' to upload the
+ data into your Galaxy history.
+ - title: Uploading the input data
+ content: >-
+ The upload may take awhile.
Hit the Close button when you
+ see that the files are uploaded into your history.
+ - title: Uploading the input data Complete !
+ content: 'Now that your data is ready, let''s use some tools.
'
+ backdrop: true
+ - title: Assign taxonomic classifications
+ content: >-
+ One of the key steps in metagenomic data analysis is to identify the taxon
+ to which the individual reads belong. Taxonomic classification tools are
+ based on microbial genome databases to identify the origin of each
+ sequence.
+ backdrop: true
+ - title: Taxonomic classification with Kraken2
+ content: >-
+ To perform the taxonomic classification we will use Kraken2. This tool
+ uses the minimizer method to sample the k-mers (all the read’s
+ subsequences of length k) in a deterministic fashion in order to reduce
+ memory constumption and processing time. In addition, it masks
+ low-complexity sequences from reference sequences by using dustmasker.
+ backdrop: true
+ - title: Taxonomic classification with Kraken2
+ element: .toolMenuContainer
+ intro: Available tools appear here in the tool menu.
+ position: right
+ - title: Taxonomic classification with Kraken2
+ element: '#__BVID__106'
+ content: >-
+ You can use 'tool search' to locate tools.
Search for
+ 'Kraken2' and select it.
Tools may take a couple of moments
+ to load.
+ placement: right
+ - title: Taxonomic classification with Kraken2
+ element: .toolMenuContainer
+ intro: >-
+ Open 'Kraken2' tool
Click 'Next' to continue our
+ tour.
+ position: right
+ - title: Assign taxonomic labels with Kraken2
+ element: 'div[tour_id="use_names"]'
+ intro: Have a look at the tool's parameters of the 'Kraken2' tool.
+ placement: right
+ - title: Assign taxonomic labels with Kraken2
+ intro: >-
+ Please select the following parameters:
'Single or paired
+ reads': Single
'Input sequences': Uploaded dataset
+ 'Print scientific names instead of just taxids': Yes
+ 'Confidence': 0.0
'In “Create Report”':
+ 'Print a report with aggregrate counts/clade to
+ file': Yes
'Format report output like
+ Kraken 1’s kraken-mpa-report': Yes
'Select a Kraken2
+ database': fungi2019-03'
Click 'Next' and the tour will
+ 'Execute' the Kraken2 tool for you.'
+ postclick:
+ - '#execute'
+ - title: Assign taxonomic labels with Kraken2
+ element: '#current-history-panel > div.controls'
+ intro: >-
+ Congratulations, you have created two files. It contains Classification
+ and Report file.
It will remain stored in your history.
+ Click the 'eye' icon to view the data once the history item turns
+ green.
+ position: left
+ - title: Analyze taxonomic assigment
+ content: >-
+ Once we have assigned the corresponding taxa to the sequence, the next
+ step is to properly visualize the data, for which we will use the Krona
+ pie chart tool (Ondov
+ et al. 2011).
+ backdrop: true
+ - title: Adjust dataset format
+ element: '#__BVID__106'
+ intro: >-
+ But before that, we need to adjust the format of the data output from
+ Kraken2.
Search and select the 'Reverse' tool.
+ position: right
+ - title: Adjust dataset format
+ intro: >-
+ You have selected the Reverse tool.
Ensure that for 'Input tabular
+ dataset' you have selected the report output file from
+ Kraken2.
'Execute' the Reverse tool when you are ready.
+ position: right
+ - title: Adjust dataset format
+ element: '#__BVID__106'
+ intro: Search and select the 'Replace Text' tool.
+ position: right
+ - title: Adjust dataset format
+ intro: >-
+ You have selected the Replace Text tool.
Please select the
+ following parameters:
'File to process': Output dataset
+ 'out_file' from 'Reverse' tool
'In “Replacements”':
+ 'Replacement 1':
+ 'Find pattern':
+ \|
'Replace
+ with:': \t
'Replacement 2':
+ 'Find pattern':
+ [a-z]__
'Replace
+ with:': Empty
'Execute' the Reverse tool when you are
+ ready.
+ position: right
+ - title: Visualize the taxonomical classification with Krona
+ content: >-
+ Krona allows hierarchical data to be explored with zooming,
+ multi-layered pie charts. With this tool, we can easily visualize the
+ composition of the bacterial communities and compare how the populations
+ of microorganisms are modified according to the conditions of the
+ environment.
+ backdrop: true
+ - title: Visualize metagenomics analysis results
+ element: '#__BVID__106'
+ intro: Search and select the 'Krona pie chart' tool.
+ position: right
+ - title: Visualize metagenomics analysis results
+ intro: >-
+ You have selected the 'Krona pie chart' tool.
Please select the
+ following parameters:
'What is the type of your input
+ data': Tabular
'Input file': Output dataset 'out_file' from
+ 'Replace Text' tool
'Provide a name for the basal rank':
+ Root
'Combine data from multiple datasets?': No
+ 'Execute' the 'Krona pie chart' tool when you are ready.
+ position: right
+ - title: Visualize metagenomics analysis results
+ element: '#current-history-panel > div.controls'
+ intro: >-
+ Let’s take a look at the result by clicking eye icon. Using the search bar
+ we can check if certain taxa are present.
+ position: left
+ preclick:
+ - '#center-panel'
+ - title: A tour BeerDEcoded
+ intro: >-
+ You have reached the end of the tour.
Thank you for going through
+ our tutorial.
+ backdrop: true
From 464a318977b41d2eec9ab1fc844570b6ff0afeb8 Mon Sep 17 00:00:00 2001
From: PlushZ <55543056+PlushZ@users.noreply.github.com>
Date: Thu, 22 Jul 2021 22:11:55 +0200
Subject: [PATCH 2/7] Update beerDEcoded.yaml
---
tour/beerDEcoded.yaml | 40 +++++++++++-----------------------------
1 file changed, 11 insertions(+), 29 deletions(-)
diff --git a/tour/beerDEcoded.yaml b/tour/beerDEcoded.yaml
index 4c76c98e..9a40695b 100644
--- a/tour/beerDEcoded.yaml
+++ b/tour/beerDEcoded.yaml
@@ -1,24 +1,13 @@
id: beerDEcoded
name: BeerDEcoded - StreetScienceCommunity
-description: BeerDEcoded - StreetScienceCommunity
+description: Workflow finds yeast strains contained in a sequenced beer sample.
title_default: BeerDEcoded
steps:
- title: BeerDEcoded - StreetScienceCommunity
content: >-
- What is a beer microbiome? There are collections of small living
- creatures. These small creatures are called bacteria and they are
- everywhere. In our gut, in the soil, even on vending machines. Some of
- these bacteria are actually very good for us. And some others can make us
- very ill. Bacteria come in different shapes and sizes but they have the
- same components. One crucial component is the DNA, the blueprint of life.
- The DNA encodes the shape and size and many other things unique for a
- bacterial species. Because of the encoding information the DNA can be used
- to identify what kind of bacteria the DNA is from. Therefore, within a
- sample form soil, our gut or beer one can specify what kind of species are
- inside the sample. Follow this tour to learn more about this kind of
- analysis.
Read and Follow the instructions before clicking
- 'Next'.
Click 'Prev' in case you missed out on any
- step."
+ Beer contains DNA that comes from its ingredients (hops, malts, yeast) and some hundred microbes. There are 1,000+ yeasts used for brewing and 200+ hop varieties, each one bearing a different DNA and contributing to differentiate its properties.
+ It is easier now to explore the potential of genome sequencing to understand the contribution of various species to product characteristics. The sequencing of the full genome of 157 brewing yeast strains was, for example, recently reported (Gallone B, Steensels J, Prahl T, et al. 2016).
+ Based on the identification of strains present in beer with desired characteristics, controlled experiments in which the microbial composition of the brew is altered could allow us to investigate if the presence of specific microorganisms affects flavour. The origin of each yeast species can be investigated; i.e. whether they come with the ingredients or from the environment at the production site. Furthermore, plant DNA, such as malt and hop varieties, can be found in beer samples, and the bacterial diversity can be mapped.
backdrop: true
- title: Create a new history
element: '#history-new-button'
@@ -33,7 +22,7 @@ steps:
intro: Change the name of the new history to 'BeerDEcoded'.
position: left
- title: Uploading the input data
- content: We need to upload data. We will start with a fastq file.
+ content: We need to upload data. We will start with a fastq file.
FASTQ format is a text-based format for storing both a biological sequence and its corresponding quality scores. Both the sequence letter and the quality score are encoded with a single ASCII character for brevity.
A FASTQ file normally uses four lines per sequence.
backdrop: true
- title: Taxonomic classification with Kraken2
element: .toolMenuContainer
From fd93de0c485cddcf8077c4f38540cc4226dd3df7 Mon Sep 17 00:00:00 2001
From: PlushZ <55543056+PlushZ@users.noreply.github.com>
Date: Fri, 3 Sep 2021 10:58:41 +0200
Subject: [PATCH 4/7] Update beerDEcoded.yaml
---
tour/beerDEcoded.yaml | 88 ++++++++++++++++++++++++++-----------------
1 file changed, 54 insertions(+), 34 deletions(-)
diff --git a/tour/beerDEcoded.yaml b/tour/beerDEcoded.yaml
index 7ede5764..a2a0a679 100644
--- a/tour/beerDEcoded.yaml
+++ b/tour/beerDEcoded.yaml
@@ -3,16 +3,23 @@ name: BeerDEcoded - StreetScienceCommunity
description: Workflow finds yeast strains contained in a sequenced beer sample.
title_default: BeerDEcoded
steps:
- - title: BeerDEcoded - StreetScienceCommunity
+ - title: [INFO] DNA in beer
content: >-
Beer contains DNA that comes from its ingredients and some hundred microbes. There are 1,000+ yeasts used for brewing and 200+ hop varieties, each one bearing a different DNA and contributing to differentiate its properties.
+ - title: [ACTION] Create a new history
element: '#history-new-button'
intro: >-
Let's start by creating a new history.
backdrop: true
- - title: Taxonomic classification with Kraken2
+ - title: [ACTION] Go to the tool menu
element: .toolMenuContainer
intro: Available tools appear here in the tool menu.
position: right
- - title: Taxonomic classification with Kraken2
+ - title: [ACTION] Search for 'Kraken2' tool
element: '#__BVID__106'
content: >-
You can use 'tool search' to locate tools.
+ The beerDeCoded process contains 3 consistent steps. The first step is DNA extraction from beer. Then, this DNA can be sequenced. That means that we can obtain the sequence of nucleotides for this specific DNA. Finally, we have to analyze received data in order to know which organisms this DNA is from.
- title: [ACTION] Create a new history
element: '#history-new-button'
intro: >-
@@ -64,7 +64,7 @@ steps:
- title: [INFO] Process of taxonomic classification with Kraken2
content: >-
To perform the taxonomic classification we will use Kraken2. This tool uses k-mers (the read’s subsequences of length k) to assign a taxonomic label to the sequence (if possible).
+
backdrop: true
- title: [ACTION] Go to the tool menu
element: .toolMenuContainer
From 9f102afaf4bf2af7a15a2a3a3382924700b8a977 Mon Sep 17 00:00:00 2001
From: PlushZ <55543056+PlushZ@users.noreply.github.com>
Date: Thu, 9 Sep 2021 19:23:22 +0200
Subject: [PATCH 6/7] Create readme
---
tour/images/readme | 1 +
1 file changed, 1 insertion(+)
create mode 100644 tour/images/readme
diff --git a/tour/images/readme b/tour/images/readme
new file mode 100644
index 00000000..cc3a9807
--- /dev/null
+++ b/tour/images/readme
@@ -0,0 +1 @@
+ This folder is created for images for BeerDeCoded Tour
From 53a8253334ba57e690b304663c7a90aa70c7fad3 Mon Sep 17 00:00:00 2001
From: PlushZ <55543056+PlushZ@users.noreply.github.com>
Date: Thu, 9 Sep 2021 19:24:43 +0200
Subject: [PATCH 7/7] Add files via upload
---
tour/images/kraken2_simlified.jpg | Bin 0 -> 750477 bytes
tour/images/workflow-of-beerDeCoded.png | Bin 0 -> 43097 bytes
2 files changed, 0 insertions(+), 0 deletions(-)
create mode 100644 tour/images/kraken2_simlified.jpg
create mode 100644 tour/images/workflow-of-beerDeCoded.png
diff --git a/tour/images/kraken2_simlified.jpg b/tour/images/kraken2_simlified.jpg
new file mode 100644
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