iPlant Collaborative Tools

iPlant Collaborative provides access to a wide variety of biological applications determined by their science advisors and staff to be fundamental to the science infrastructure, and which directly supports specific scientific objectives. These applications are installed, supported, and maintained by iPlant staff. These applications are deployed directly on high-performance cluster systems or high-performance VMs. Deployments of these applications are tuned for optimal performance and scalability in a collaborative effort between the primary software author and iPlant staff. These applications are discoverable and usable by all authenticated users of the iPlant Cyberinfrastructure (CI).

The BioExtract Server team has deployed additional application to the iPlant CI and made them available to BioExtract Server researchs. Also, when you login to the BioExtract Server, any of the tools that you have deployed to iPlant are added to the list.

The iPlant Tool Interface

The BioExtract Server's iPlant interface does not differ from the majority of other tools in the list. Select an iPlant Tool by clicking its entry in the Available Tools list in the left panel. The interface for the selected tool appears in the right panel.

Clicking the Execute button will execute the tool. Once execution has been completed, the View Results button is enabled. Clicking it will display the output files associated with the tool execution. Clicking on the name of an output file will display the contents of the file.

Example using Clustal Omega. - a fast and scalable alignment tool(can align hundreds of thousands of sequences in hours)

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 clustalo-lonestar iPlant tool. Specify that the tool should "use records on the Extracts page formatted as FASTA" as the input data. Select 'fasta' for the 'Force sequence input file format' parameter and 'Protein' for 'Force a sequence type' parameter.
   
   
4. Next, click Execute. The tool may take two to three minutes to complete.
   
   
5. After execution has completed, the "View Results" button becomes enabled.
6. To view output, select the desired output file from the drop-down list and click the "View Results" button.