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.
   
   
2. Optionally, click the "Extracts" tab to view the results of the query.
   
   
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'.
   
   
4. Next, click Execute. The tool may take two to three minutes to complete.
   
   
5. After execution has completed, the 'View Results' and 'Save Result' buttons become enabled.
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.
7. Enter 'Aronaute_Arabidopsis.fa' for the file name and click 'OK'.
8. In the Tools tab, select the 'clustalo-lonestar' (Clustal Omega running on Lonestar) tool under the 'iPlant' node.
   
   
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
   
   
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.