Sharing templates using myExperiment

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About myExperiment and LabTrove

The myExperiment platform provides a repository for workflows in a collaborative environment. In the laboratory notebook context, a workflow is an explicit and precise description of a scientific process. LabTrove templates represent steps in a workflow. As such, LabTrove templates are potentially very useful objects to share between researchers working with similar procedures and protocols. This topic tells you how to link LabTrove with myExperiment, by exporting the XML description of a template, together with authorship details and a representative image of the template, then uploading the XML file to myExperiment. From there, other users can share or import the template and use it in their own LabTrove Notebook.

For more information about myExperiment, refer to the website and the following publication: Goble CA, et al. myExperiment: a repository and social network for the sharing of bioinformatics workflows. Nucl. Acids Res., 2010. doi:10.1093/nar/gkq429

Exporting a template from LabTrove

To create an XML package suitable for uploading to myExperiment, complete the following steps:

  1. Login to your Trove
  2. Select the Notebook that you want to work with
  3. Select the template post that you want to export
  4. Click PNG Image. LabTrove generates an image of the template as you view it in the LabTrove user interface, with a URI that includes the post identifier
  5. Click XML (With Files). LabTrove generates an XML representation of the template, with a URI that includes the post identifier

Uploading a LabTrove template to myExperiment

To upload the XML package you exported from LabTrove, complete the following steps:

  1. Login to myExperiment at http://www.myexperiment.org/
  2. In the New/Upload pane, select Workflow and Click Go
  3. Type the path to the XML file of the template, or click Browse to locate the XML file
  4. By default, myExperiment will try to obtain descriptive metadata from the LabTrove template. If you want to supply your own description, select Enter custom metadata and complete the appropriate fields
  5. If you want to supply Other metadata and settings, add tags to describe the LabTrove template and, if required, select the sharing and collaboration details
  6. Click Upload and Continue. The template appears in myExperiment

Finding LabTrove templates in myExperiment

To search for LabTrove templates, complete the following steps:

  1. Login to myExperiment at http://www.myexperiment.org/
  2. In the Search field, type kind: (LabTrove templates)
  3. Select Workflows from the drop-down menu
  4. Click Search. A list of LabTrove templates is displayed.

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