Saving Tool Output to iPlant Discovery Environment

iPlant Discovery Environment (DE) is a system of software and hardware that provides a modern web interface and platform for powerful computing, data, and application resources. The DE facilitates data exploration and scientific discovery by integrating powerful, community-recommended software tools into a system that is robust enough to handle data while utilizing high performance computing resources like XSEDE (formerly known as TeraGrid) and others as needed to perform these tasks much more quickly.

As a register iPlant user, you are offered the ability to manage personal data on your DE platform. The Discovery Environment uses iRODS, which is also used by and accessible by other iPlant services. Your data is safe, easy for you to access, and not locked in to only one method.

Saving output from BioExtract Server tool execution to the iPlant DE

If you have synchronized your BioExtract Server user credentials with iPlant (see iPlant User Credential Synchronization), you have the option of storing the output from any executed BioExtract Server analytic tool to your iPlant DE account.

  1. In the Query tab, search NCBI for all Arabidopsis 'Argonaute' proteins.

    iPlant Query
  2. Optionally, click the "Extracts" tab to view the results of the query.

    iPlant tool selection
  3. In the Tools tab, select the 'Fetch Sequence Records' tool under the 'Information' node. Specify that the tool should 'Use records on the Extracts page' as input and the database parameter should be set to 'ncbi'.

    iPlant tool selection
  4. Next, click Execute. The tool may take two to three minutes to complete.

    iPlant tool execution
  5. After execution has completed, the 'View Results' and 'Save Result' buttons become enabled. iPlant tool execution
  6. To view output, select the 'result.txt' file from the drop-down list and click the "View Results" button. iPlant tool execution
  7. To save the output to your iPlant DE, select the 'result.txt' file from the drop-down list and click the "Save Result" button. Select the desired directory in which to store the file, then click the 'Create File' button. iPlant tool execution
  8. Enter the desired file name and click 'OK'. iPlant tool execution
  9. View the results of the operation by logging into your iPlant DE. iPlant tool execution