iMicrobe leverages the existing CyVerse cyberinfrastructure to take advantage of data sharing, common compute resources, and access to Apps and data processing pipelines.  All protocols and information on Apps are now available in protocols.io.  Check out our group at protocols.io for more information.

In order to access these resources, you need to create an CyVerse account.

  • note that CyVerse was formerly known as iPlant Collaborative, but now serves the entire life science community.

Check out the video on what the CyVerse Cyberinfrastructure is.  Or, browse the CyVerse Collaborative YouTube Channel.

Sign up for an CyVerse account

  1. To register for a CyVerse account
  2. Complete the information on the form
  3. The CyVerse support team will create your user account and send you a confirmation email
  4. Click on the validation link within the email to confirm and begin using your CyVerse account

Getting to CyVerse

Navigate to CyVerse and “Launch” under the Discovery Environment. This will take you to its login page. Once there, select the “Log in with your CyVerse ID” button, which will take you to the CyVerse authentication page. Enter your user name and password.

Discovery Environment Interface

Once logged in, you’ll see the following screen:
Discovery Environment Start Page

The Discovery Environment is divided into three components – Data, Apps, and Analyses.

Data: Serves as a file browser and allows you to upload, download, and view files and folders. You can also “Share” your files with fellow users, such as collaborators, graduate students, post docs and PIs (see the video). Through data sharing, data avoids duplication for each user, simultaneously minimizing disk space impact and maximizing collaboration by guaranteeing the same file is used by all involved.  See the 1 minute video on the iPlant Data Store

Note: advanced users can upload large datasets to iPlant using iRods file transfer protocol.  See the video.

Apps: An application browser, with applications functionally organized to allow easy finding. Here, you can find apps and run them on your data.

Analyses: A historical view of apps run in the past or present. You can check the status of your running apps, view parameters of the run or navigate to the output folders.

You can also check out the Discovery Environment 1 minute video or Tutorial for more information.

Accessing iMicrobe Datasets in the CyVerse Data Store
All of the Projects that you can see and search for on the interactive iMicrobe Data Website are also available in CyVerse in the iMicrobe Community Data folder. To access data in CyVerse, you first search for data in iMicrobe. For example, I would like to find all datasets from Antarctica. I can search using:
Map search: To find all datasets by selecting a region on a map.
Metadata search: To find all datasets by selecting metadata ranges.

Using the map search, I can select sampling sites of interest:
Screen Shot 2015-09-25 at 10.14.46 AM

When I scroll through the list of 20 samples, I select the Whale Fall metagenome.  This take me to the project:
Screen Shot 2015-09-25 at 10.17.25 AM

I then click on “Downloads” and click on “Reads” :
Screen Shot 2015-09-25 at 10.17.40 AM

I can then see the location of the Reads file in the iPlant’s Data Store:
Screen Shot 2015-09-25 at 10.17.52 AM

Running your Own Analyses

Let’s say you have your own microbial metagenome and would like to know if it contains viruses. We’ll use VirSorter, a freely available iMicrobe App in CyVerse. The first thing you need to do is upload your data (see the video on uploading data).

Navigate to “Data” -> “Upload” -> “Simple Upload from Desktop”

Discovery-Environment-Nagivate-Upload

You’ll be presented with an upload dialog window. Find your microbial data file and upload it. Once uploaded, you’ll need to run the VirSorter app on your new data.

Navigate to “Apps” -> “Public Apps” -> “Experimental” -> “iVirus” and select VIRSorter

Once selected, a VirSorter dialog window will appear, allowing you to select your input file, output directory, and the database to search VirSorter against. Go ahead and select your uploaded file, navigating to the location where you uploaded the file. Once done, click on “Launch Analyses” to begin.

Depending on the size of your dataset, VirSorter can take anywhere from a few minutes to days to complete. You’ll be notified when the job is submitted, running, and finished. To find your results, navigate to “Analyses” and select the VirSorter results. A Data window will pop up containing the analysis’ output directory. Check out the VirSorter wiki for information on the output files and protocols in protocols.io.

You can now download the results to your computer by checking the folder and navigating to “Download.”

And you’re finished!

For further support on CyVerse, check out the CyVerse Questions Forum.