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rnateam.viennarna.yaml
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rnateam.viennarna.yaml
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name: Galaxy RNA-workbench ViennaRNA Exercise
description: The Galaxy RNA-workbench introduces itself
title_default: "Galaxy RNA-workbench ViennaRNA Introduction Exercise"
tags:
- "RNA"
steps:
- title: "<b>Welcome to the Galaxy RNA-worbench ViennaRNA example!</b>"
content: "This tour will walk you through an exercise which guides you on how to use the Galaxy RNA-workbench. <br><br>
Read and Follow the instructions before clicking <b>'Next'</b>.<br><br>
Click <b>'Prev'</b> in case you missed out on any step"
backdrop: true
- title: "<b>Scenario</b>"
content: "We have a gene of interest and want to predict it's mRNA secondary structure. We also have a binding factor and want to see how interaction of this factor changes the secondary structure. Last but not least we have conservation information for this mRNA and want to see how the consensus structure of conserved RNAs looks like."
backdrop: true
- title: "<b>Goal</b>"
content: "The goal of this exercise is to <b>become familiar with some of the ViennaRNA tools</b>."
backdrop: true
- title: "<b>Overview</b>"
content: "Together we will go through the following:<br>
<b>Folding of single RNA sequence and alignment with and without constraints</b>
<dir>
<li>Step 1: Download fasta file with RNA sequence</li>
<li>Step 2: Fold sequence with default RNAfold settings</li>
<li>Step 3: Inspect structure and MFE</li>
<li>Step 4: Visualize structure</li>
<li>Step 5: Fold sequence with partition function output</li>
<li>Step 6: Inspect structure, ensembl MFE and ensembl population</li>
<li>Step 7: Visualize structure</li>
<li>Step 8: Use binding sites as constraint for folding</li>
<li>Step 9: Inspect structure, ensembl MFE and ensembl population of constrained sequence</li>
<li>Step 10: Download alignment of gene of interest</li>
<li>Step 11: Fold alignment and compare consesus structure to single sequence structure</li>
<li>Step 12: Name your history</li>
<li>Step 13: Make a workflow out of this steps</li>
<li>Step 14: Share workflow</li>
</dir>"
backdrop: true
- title: "<b>Step 1: Download fasta file with RNA sequence</b>"
# content: "We will now proceed to download the sequence of the gene of interest (the file <b>'Homo_sapiens_CXCL2_sequence.fa'</b>) from <a href=\"http://doi.org/10.5281/zenodo.212693\" target=\"_blank\">zenodo</a> to your computer and then <b>upload</b> the same file to Galaxy."
content: "We will now proceed to download the sequence of the gene of interest. Please downloas the file <b>'Homo_sapiens_CXCL2_sequence.fa'</b> from <a href=\"https://github.com/jfallmann/test-data/raw/master/viennarna-galaxy-tour/Homo_sapiens_CXCL2_sequence.fa\" target=\"_blank\">github</a> to your computer and will then <b>upload</b> the same file to Galaxy."
backdrop: true
- title: "<b>Step 1: Download fasta file with RNA sequence</b>"
element: ".upload-button"
intro: "Use the upload button to upload the file to Galaxy.<br><br>
Click <b>'Next'</b> and the tour will take you to the Upload screen"
position: "right"
postclick:
- ".upload-button"
- title: "<b>Step 1: Download fasta file with RNA sequence</b>"
element: "#btn-local"
intro: "This is the upload screen.<br><br>
Simply click <b>'Next'</b> and tour will open up your file directory for you to select the downloaded <b>'Homo_sapiens_CXCL2_sequence.fa'</b>."
position: "top"
postclick:
- "#btn-local"
- title: "<b>Step 1: Download fasta file with RNA sequence</b>"
element: "#btn-start"
intro: "Now that you've selected the file, select <b>'hg19'</b> as the genome
and fasta as file format.<br><br>
Click <b>'Next'</b> and the tour will <b>'Start'</b> the upload.<br>
Galaxy will automatically unpack the file."
position: "bottom"
postclick:
- "#btn-start"
- "#btn-close"
- title: "<b>Step 1: Download fasta file with RNA sequence</b>"
element: "#right"
intro: "This is your history!<br><br>
All <b>analysis steps will be recorded</b> and can be redone at any time.<br><br>
You should be able to see your uploaded file here in a few moments."
position: "left"
- title: "<b>Step 2: Fold sequence with default RNAfold settings</b>"
element: '#tool-search-query'
intro: "We now want to predict the secondary structure of our gene of interest using <b>RNAfold</b> from the ViennaRNA package.<br><br>
This Galaxy instance has the ViennaRNA package already integrated, so we don't need to install them.<br><br>
<b>Note:</b> You can use 'tool search' to locate tools. Tools may take a couple of moments to load, please bear with us."
position: "right"
- title: "<b>Step 2: Fold sequence with default RNAfold settings</b>"
element: "#tool-search-query"
intro: "You can now type and select <b>'RNAfold'</b>.<br><br>"
- title: "<b>Step 2: Fold sequence with default RNAfold settings</b>"
intro: "<b>Follow this set of instructions once the tool was loaded:</b><br>
<ol>
<li>Input from FASTA file</li>
<li>Sequence to fold: Homo_sapiens_CXCL2_sequence.fa</li>
<li>Keep the rest of the options at their default values.</li>
<li>Click button 'Execute' and wait for the tool to finish.</li>
</ol>"
position: "bottom"
- title: "<b>Step 3: Inspect structure and MFE</b>"
element: '#current-history-panel'
intro: "To inspect the resulting folded sequence as dot-bracket string just<br><br>
<dir>
<li>Click on the <b>eye icon</b> of the latest dataset and scroll to the right</li>
</dir>"
position: "left"
- title: "<b>Step 4: Visualize structure</b>"
element: "#tool-search-query"
intro: "You can now type and select <b>'RNAplot'</b>."
- title: "<b>Step 4: Visualize structure</b>"
intro: "<b>Follow this set of instructions once the tool was loaded:</b><br>
<ol>
<li>Input from RNAfold on data</li>
<li>Keep the rest of the options at their default values.</li>
<li>Click button 'Execute' and wait for the tool to finish.</li>
</ol>"
position: "bottom"
- title: "<b>Step 4: Visualize structure</b>"
element: '#current-history-panel'
intro: "<b>To inspect the output of <b>RNAplot</b>:</b><br>
<dir>
<li>Click on the <b>'eye icon'</b> of the corresponding dataset</li>
<li>Download the file to disk</li>
<li>untar the file (e.g. with tar -xvf) and view the ps file.</li>
</dir>"
position: "left"
- title: "<b>Step 5: Fold sequence with partition function output</b>"
element: "#tool-search-query"
intro: "You can now type and select <b>'RNAfold'</b>.<br><br>"
- title: "<b>Step 5: Fold sequence with partition function output</b>"
intro: "<b>Follow this set of instructions once the tool was loaded:</b><br>
<ol>
<li>Input from FASTA file, same as before</li>
<li>Sequence to fold: Homo_sapiens_CXCL2_sequence.fa</li>
<li>Keep the rest of the options at their default values.</li>
<li><b>BUT</b> this time set the 'Calculate Partition Function' option to 'Yes'</li>
<li>Click button 'Execute' and wait for the tool to finish.</li>
</ol>"
position: "bottom"
- title: "<b>Step 6: Inspect structure, ensembl MFE and ensembl population</b>"
element: '#current-history-panel'
intro: "To inspect the resulting folded sequence as dot-bracket string just<br><br>
<dir>
<li>Click on the <b>eye icon</b> of the latest dataset and scroll to the right</li>
<li>Note the extra lines in the dot-bracket output and the new MFEs at the end</li>
<li>The first new line shows a condensed representation of the pair probabilities, similar to the bracket notation, followed by the ensemble free energy in kcal/mol. This notation makes use of the letters \" . , | { } ( ) \" denoting bases that are essentially unpaired, weakly paired, strongly paired without preference, weakly upstream (downstream) paired, or strongly up− (down−)stream paired bases, respectively. On the next line the centroid structure as derived from the pair probabilities together with its free energy and distance to the ensemble is shown. The last line shows the frequency of the mfe structure, and the structural diversity (mean distance between the structures in the ensemble).</li>
</dir>"
position: "left"
- title: "<b>Step 7: Visualize structure</b>"
element: '#current-history-panel'
intro: "This time we do not use <b>RNAplot</b> to generate a ps, but we use the extra ouput that is being generated by <b>RNAfold</b>.<br><br>
<b>Click on the newly generated dataset in rna_eps format:</b><br>
<ol>
<li>Click the <b>'eye icon'</b> and open the eps image with your eps viewer of choice.</li>
<li>Compare this plots with the one generated by <b>RNAplot</b> (You should not see any differences).</li>
</ol>"
position: "left"
- title: "<b>Step 7: Visualize structure</b>"
element: '#current-history-panel'
intro: "In addition to the structure ps file, <b>RNAfold</b> also generates a dotplot. This dotplot shows the pair probabilities within the equilibrium ensemble as n×n matrix, and is an excellent way to visualize structural alternatives. A square at row i and column j indicates a base pair. The area of a square in the upper right half of the matrix is proportional to the probability of the base pair (i,j) within the equilibrium ensemble. The lower left half shows all pairs belonging to the MFE structure. <br><br>
<b>Click on the second newly generated dataset in rna_eps format:</b><br>
<ol>
<li>Click the <b>'eye icon'</b> and open the eps image with your eps viewer of choice.</li>
<li>Compare the ensembl structure basepairs (upper right) with the MFE structure basepairs (lower left).<br>Do you see that the frequency of the MFE structure in the ensemble is low and the ensemble diversity is high?</li>
</ol>"
position: "left"
- title: "<b>Step 8: Use binding sites as constraint for folding</b>"
content: "Now imagine we have a binding factor of interest that is interacting with our RNA. We are interested in finding out how this is influencing the base-pairing of our mRNA molecule."
backdrop: true
- title: "<b>Step 8: Use binding sites as constraint for folding</b>"
element: ".upload-button"
content: "We will now upload the file containing constraints (the file <b>'Homo_sapiens_CXCL2_constraints.fa'</b>) from <a href=\"https://github.com/jfallmann/test-data/blob/master/viennarna-galaxy-tour\" target=\"_blank\">github</a> to Galaxy. In contrast to the beginning of this tour, this will be done automatically this time" #, set the file type to txt."
postclick:
- ".upload-button"
- "#btn-new"
- title: "<b>Step 8: Use binding sites as constraint for folding</b>"
element: ".upload-text-content"
content: "We will now upload the file containing constraints (the file <b>'Homo_sapiens_CXCL2_constraints.fa'</b>) from <a href=\"https://github.com/jfallmann/test-data/blob/master/viennarna-galaxy-tour\" target=\"_blank\">github</a> to Galaxy."
textinsert: |
https://github.com/jfallmann/test-data/raw/master/viennarna-galaxy-tour/Homo_sapiens_CXCL2_constraints.fa
- title: "<b>Step 8: Use binding sites as constraint for folding</b>"
element: "#btn-start"
content: "Click next to start the upload.<br>"
postclick:
- "#btn-start"
- title: "<b>Step 8: Use binding sites as constraint for folding</b>"
element: ".upload-box"
content: "Set filetype and genome accordingly and click next to proceed.<br>"
postclick:
- "#btn-close"
- title: "<b>Step 8: Use binding sites as constraint for folding</b>"
element: "#tool-search-query"
intro: "You can now type and select <b>'RNAfold'</b> again.<br><br>"
- title: "<b>Step 8: Use binding sites as constraint for folding</b>"
content: "<b>Follow this set of instructions once the tool was loaded:</b><br>
<ol>
<li>Input from FASTA file, same as before</li>
<li>Sequence to fold: Homo_sapiens_CXCL2_constraints.fa</li>
<li>Keep the first options at their default values.</li>
<li>Set the 'Calculate Partition Function' option to 'Yes'</li>
<li>Click on <b>'Structure constraints'</b></li>
<li>Select 'Constraints'-'The constraints are in the fasta input file'</b></li>
<li>Click button 'Execute' and wait for the tool to finish.</li>
</ol>"
position: "right"
- title: "<b>Step 9: Inspect structure, ensembl MFE and ensembl population of constrained sequence</b>"
element: '#current-history-panel'
intro: "To inspect the resulting folded sequence as dot-bracket string just<br><br>
<dir>
<li>Click on the <b>eye icon</b> of the latest dataset and scroll to the right</li>
<li>Note that the constraints led to changes in the predicted MFE structure as well as the ensembl. This can be used to predict the influence of interacting agents on RNA secondary structure. You can also inspect the additional output, similar to the last <b>RNAfold</b> runs.</li>
</dir>"
position: "left"
- title: "<b>Step 10: Download alignment of gene of interest</b>"
backdrop: true
element: ".upload-text-content:first"
content: "Now we upload a file containing a multiple alignment of the gene of interest across 8 primate species (the file <b>'CXCL2_8_primates_EPO.aln'</b>) from <a href=\"https://github.com/jfallmann/test-data/blob/master/viennarna-galaxy-tour\" target=\"_blank\">github</a> to Galaxy, this will be done automatically this time" #, set the file type to txt."
preclick:
- ".upload-button"
- "#btn-new"
textinsert: |
https://github.com/jfallmann/test-data/raw/master/viennarna-galaxy-tour/CXCL2_8_primates_EPO.aln
- title: "<b>Step 10: Download alignment of gene of interest</b>"
element: "#btn-start"
content: "Click next to start the upload.<br>"
postclick:
- "#btn-start"
- "#btn-close"
- title: "<b>Step 11: Fold alignment and compare consesus structure to single sequence structure</b>"
element: "#tool-search-query"
intro: "You can now type and select <b>'RNAalifold'</b> from the tool list."
- title: "<b>Step 11: Fold alignment and compare consesus structure to single sequence structure</b>"
intro: "<b>Follow this set of instructions once the tool was loaded:</b><br>
<ol>
<li>Input from FASTA file</li>
<li>Sequence to fold: CXCL2_8_primates_EPO.fa</li>
<li>Keep the rest of the options at their default values.</li>
<li>Click button 'Execute' and wait for the tool to finish.</li>
<li>Then inspect the consensus structure predicted by <b>RNAalifold</b> and compare it to the <b>RNAfold</b> structures with and without constraints.</li>
</ol>"
position: "bottom"
- title: "<b>Step 12: Name your history</b>"
element: "#current-history-panel > div.controls > div.title > div"
intro: "Change the name of your history."
position: "bottom"
- title: "<b>Step 13: Make a workflow out of steps 5 to 9</b>"
element: '#history-options-button'
intro: "Please extract your history to a workflow.<br>
<b>(History options :: Extract workflow)</b><br><br>
<b>Do not include:</b> 'RNAplot'<br><br>
Click <b>'Create Workflow'</b>."
position: "left"
- title: "<b>Step 13: Make a workflow out of steps 5 to 9</b>"
element: '#history-options-button'
intro: "To make sure the workflow is correct, check it in the editor and make some small adjustments.<br><br>
<dir>
<li>Click on the name of your new workflow and select <b>'Edit'</b></li>
<li>The individual steps are displayed as boxes, their <b>outputs and inputs are connected through lines</b></li>
<li>When you click on a box you see the tool options on the right. Besides the tools, you should see two additional boxes titled <b>'Input dataset'</b>. These represent the data we want to feed into our workflow.</li>
</dir>"
position: "left"
- title: "<b>Step 13: Make a workflow out of steps 5 to 9</b>"
element: '#history-options-button'
intro: "To make sure our workflow is correct, we look at it in the editor and make some small adjustments.<br><br>
<dir>
<li>You can <b>change the names</b> of the input datasets to remember what they are used for. Don't forget to save it in the end by clicking on <b>'Options'</b> (top right) and selecting <b>'Save'</b></li>
</dir>"
position: "left"
- title: "<b>Step 14: Sharing workflow</b>"
element: 'a[href$="/workflow/list_for_run"]'
intro: "You can share your new workflow.<br>
<dir>
<li>Click on your workflow's name and select <b>'Share or publish'</b></li>
<li>Click <b>'Share with a user'</b></li>
<li>Enter the email address of the person you wish to share your workflow with.(the same as he/she uses to login to Galaxy)</li>
<li>Hit <b>'Share'</b></li>
</dir>"
position: "top"
- title: "<b>Step 14: Sharing workflow</b>"
element: '#center-panel'
intro: "If a workflow has been shared with you, you can find it under <b>'Workflows shared with you by others'</b>:<br>
<dir>
<li>Click on a workflow name and select <b>'View'</b></li>
<li>You can compare the workflows of others with your workflow</li>
</dir>"
position: "right"
- title: "<b>Enjoy the Galaxy RNA-workbench</b>"
intro: "Thanks for taking this tour! Happy research with Galaxy!"