Using an iPlant Discovery Environment (DE) File as Input

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.

Using an iPlant Discovery Environment (DE) File as Input into a BioExtract Server tool

If you have synchronized your BioExtract Server user credentials with iPlant (see iPlant User Credential Synchronization), you have the option of using a file you have stored in your iPlant DE as input into a BioExtract Server tool.

  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 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
  7. Enter 'Aronaute_Arabidopsis.fa' for the file name and click 'OK'. iPlant tool execution
  8. In the Tools tab, select the 'clustalo-lonestar' (Clustal Omega running on Lonestar) tool under the 'iPlant' node.

    iPlant tool selection
  9. Next, select the 'Import a file from iPlant' radio button and click the adjacent 'Select File' button. Select the 'Aronaute_Arabidopsis.fa' file from your iPlant DE

    iPlant tool execution
  10. Before executing the tool, verify that the 'Force sequence input file format' is set to 'fasta' and the 'Force a sequence type' is 'Protein' . Click the 'Execute' button. iPlant tool execution