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Interactive Analyses

learning-objectives

• Request VICE access.

• Launch and access VICE application.

• Configure the VICE application and run an analysis.

• Save the outputs of a VICE application to your Data Store.

Description:

The Visual Interactive Computing Environment (VICE) allows you to work with popular interactive data science applications such JupyterLab, RStudio, Linux shell and others. In this exercise we will cover a simple introductory use case that allows us to complete our goal of visualizing a phylogenetic tree.

In this exercise we will:

1. Launch an RStudio session, loading the sequence alignments created earlier in the course.

2. Install an R package and create a phylogenetic tree from the alignment, saving it to a file.

3. Save our work to the Data Store and terminate the application.

Tip

Why use VICE?

The Discovery Environment excels at running compute intensive analyses non- interactively. In other words, once you launch a job in the DE, you get an output, but to start a new analysis (for example to tweak parameters), you need to relaunch that job, and await new results. This style of computing allows you to run large jobs that require lots of resources. However, several analyses we’d like to do are interactive – we need to visualize and manipulate parameters on the fly – for example, creating a figure where you need to see and adjust the results of an upstream analysis. This kind of work is often done using tools like R and RStudio, or other programing tools such as Jupyter. Hence VICE!

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Input Data:

Input	Description	Example
A folder of logs clstalw.aln fasta.aln phylip_interleaved.aln phylip_sequential.aln	The logs folder are log files returned with every Discovery Environment analyses. These can be useful for diagnosing failed analyses. All other files are outputs of the Muscle software and contain multiple sequence alignments in a variety of common formats.	View the example muscle_output folder.

Getting VICE Access

To minimize inappropriate use, VICE is a restricted service, currently accessible from CyVerse US. You must request access to use.

1. Visit the CyVerse User Portal and access the services panel; look for DE – VICE and select the REQUST ACCESS link.

   Tip

   Ensure that your CyVerse account is associated with an ORCID and a valid email address from an organization (i.e., .org, an educational institution with the .edu ending, or a government .gov). We will not grant access to commercial email addresses, e.g., @gmail.com @yahoo.com @msn.com etc.

Launching a VICE application

1. If necessary, log into the CyVerse Discovery Environment.

2. Click the (Data Icon) and navigate to your results folder in the tutorial_folder; click the (Add Folder button) and create a folder called rocker_output inside your tutorial folder.

3. Use this quicklaunch link or click on (Apps icon) to launch the Rocker RStudio Latest App. You can also use the DE search bar to search for this application in the Apps category.

   Tip

   We provide and maintain the latest versions of R and RStudio made available by the Rocker Project.

4. Launch the application and adjust the following:

   1. Under “Analysis Info”, for Output Folder click Browse and navigate to and select the rocker_output created above. click Next;

   2. For “Parameters”, under “Input Folder” click Browse and navigate to the tutorial_folder, then the results folder and select the muscle_output folder where your Muscle analysis results should be located; click Select Current Folder; then Next;

   3. Click Next to skip Advanced Settings;

   4. Click Launch Analysis to launch your application

5. In the navigation, click on the (Analyses) view. Your application will be listed as “Submitted” for a few minutes (usually just a few, but more depending on both the size of the application software and any imported datasets).

6. When the Status of the launch is Running, click on the (link out icon); a new tab where your VICE application will run should open in your browser.

   Tip

   Even when the application is in the ‘Running’ status, you may still have to wait some additional time if data is being transferred.

Completing our analysis in R

Once you have your RStudio session, it will largely behave as would an RStudio session running on your local Desktop. Some potential benefits of running RStudio in VICE include more processing power (especially if you choose additional resources at launch – see the Advanced Settings). Since this session is running on CyVerse hardware, transferring large data will also happen at increased speed. To complete our analyses, we will install the ape package and compute a phylogenetic tree.

Tip

While you don’t need to be an expert R user to complete this section, familiarity with R will help since we won’t be going into specific detail about this example.

Tip

The data we loaded at launch of the VICE application will be in the ‘work’ directory at ‘home’.

1. From the R console, enter the following commands:

   # install and load the needed R library
   install.packages("ape")
   library(ape)
   
   #Read in the aligned DNA fasta file
   alignment <- read.FASTA ("~/work/data/input/muscle_output/fasta.aln", type="DNA")
   
   # Create a distance matrix for the sequences
   dist_mtrx <- dist.dna(alignment)
   
   #Compute a neighbor-joining tree
   nj_tree <- nj(dist_mtrx)
   
   # plot the tree
   plot.phylo(nj_tree)
   
   # save the tree to a file
   write.tree(nj_tree, file = "~/work/data/output/tree.newick")
   
   #OR save to your CyVerse Data Store directly in the file browser
   write.tree(nj_tree, file = "~/work/home/YOUR_CYVERSE_USERNAME/tutorial_folder/rocker_output/tree.newick")
   

2. You should have visualized the resulting tree and also created the file ‘tree.newick’ in your work directory.

Terminating your VICE session and saving work to the Data Store

Once you have completed your work, you can save your work to the Data Store and terminate your VICE application.

Tip

VICE applications typically have a 48-hour run time. Unless you request an extension, your application will automatically save outputs. It is recommended that you save your work to the Data Store before time expires.

1. In the Analyses pane of the Discovery Environment, select your running RStudio VICE application.

2. Under More Actions, select Terminate; confirm Termination on the pop-up notice.

3. When the VICE application has the status completed, click the folder icon to view the folder on your data store where results will be written. It may take time for all outputs to be saved depending on the size of the data generated.

   Tip

   You don’t have to terminate your analyses to save your work to the Data Store. From within the RStudio environment using the terminal, you can use iCommands to transfer data (See Data Store Guide on iCommands). RStudio itself allows you to download files and plots directly to your local computer. Use the Export features present in the file pane.

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Output/Results

Output	Description	Example
‘tree.newick’	A Newick-formatted phylogenetic tree file which can visualized using your choice of tools.	Rstudio output

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Self Assessment Questions

Question

Q1. What kind of applications are supported in VICE?

1. Applications with their own graphical interface

2. Open-source applications

3. Applications that have interactive visualizations

4. All of the above

Answer

Correct answer is D

Question

Q2. Which of the following are restrictions on using VICE?

1. You must request access on the CyVerse user portal

2. VICE applications have a 48-hour runtime limit

3. You must install VICE applications yourself

4. A and B

5. C only

Answer

Correct answer is D, you must request separate access to use VICE at the services panel. There is a default 48-hour run time but you can extend your time by requesting this in the Analysis view for the launched application.

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Fix or improve this documentation

• Search for an answer: CyVerse Learning Center

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• Report an issue or submit a change: Github Repo Link

• Send feedback: learning@CyVerse.org

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