Recording a Workflow

The steps to create a workflow in the BioExtract Server system are easy:

  1. Create a user account and sign in.
  2. Start recording.
  3. Perform a series of tasks.
  4. Save your tasks into a workflow.
  5. Test the workflow by running it.

At the top right corner of every BioExtract Server page, select register. Fill in the required fields and click Add User. Your account will be created immediately. Return to the BioExtract Server and sign in by clicking the sign in link in the upper right corner of every page.

Turn recording on, so the BioExtract Server can record what you do. To start recording:

  1. Click the Workflows tab.
  2. At the top of the left panel, select Create and Import Workflows. The Create and Import Workflows form opens in the right panel.
  3. In Create Workflow at the top of the form, click the Record Workflow button. Now perform the tasks you want to turn into a workflow and the BioExtract Server will record your actions in the background.

As an example, we will create a simple workflow that performs a BLAST analysis of a Gallus Gallus nucleotide sequence. To start creating this workflow:

  1. Click the Query tab. The left panel displays the Available Data Sources.
  2. In Available Data Sources, open Nucleotide Sequences > NCBI Nucleotide Databases and click the Nucleotide check box. The data source Nucleotide will appear in the adjacent box.
  3. In the Query Form at the bottom of the page, open the Search Field drop-down menu and select Accession.
  4. In the Search Term box, enter the accession number, in this case ef608155 and click Submit Query. The Extracts page opens displaying information about that sequence.
  5. Click the Tools tab. The left panel displays the Available Tools.
  6. In Available Tools, open Similarity Search Tools and select blastn. The blastn tool form opens in the right panel.
  7. In Input Data at the top of the form, select Use records on Extracts page formatted as FASTA and click the Execute button at the bottom of the form. Now wait for the tool to complete.

Once the tool executes, you can save your tasks into a workflow. To do so:

  1. Click the Workflows tab.
  2. At the top of the left panel, select Create and Import Workflows. The Create and Import Workflows form opens in the right panel.
  3. In Save Workflow enter a name and a description for this new workflow. For this example, enter test workflow for both items.
  4. Click the Save button. You'll see your new workflow in the Workflows list in the left panel. The workflow is now ready to be tested.

Test the workflow to make sure things are running smoothly. To do so:

  1. In the Workflows list, click the new workflow's name. The workflow graph and its control buttons will open in the right panel. In this example, you'll see two workflow nodes. The top node represents the query performed and the bottom node represents the execution of the tool, blastn.
  2. In the title of the workflow panel, click the Start button to the right of the workflow's name. The workflow begins to run. Now wait until all of the workflow nodes turn green, indicating successful completion.
  3. Once all of the nodes in the workflow complete, check the workflow provenance report for errors. To do so, click the Provenance button located below the workflow graph. The workflow provenance report will open.
  4. Read through the report checking for errors. View the input and output files to make sure things are running smoothly. If errors occurred, troubleshoot and re-create the workflow. If it still doesn't work, contact us through BioExtract Server feedback! located in the top right corner of every page.

After verifying that the workflow is correct, you can execute it, modify it, and share it with others.

Other important information