Pack: Taverna 2.1 beta 2 example workflows

Description:

Designed to show the use of EMBOSS based Soaplab services from Taverna, this workflow has no inputs as all initial values are specified as string constants. A sequence set is fetched using the seqret tool, then simultaneously scanned for predicted transmembrane regions and subjected to a multiple alignment using emma. This alignment is then plotted to a set of PNG images and also used to build a profile using the prophecy and prophet tools.

Description:

Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned.

Description:

This workflow shows the use of the iteration strategy editor to ensure that only relevant combinations of inputs are used during an implicit iteration.

Description:

Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default.

InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to the signatures are returned, which are annotated with the corresponding InterPro and GO term assignments for these signature matches.

checkStatus is executed repeatedly as long as the status is equal to RUNNING - check Details -> Advanced for loop condition.

Description:

Given an identifier such as '1crn' fetches the PDB format flatfile and returns the corresponding 3D image of the protein.

Description:

Use the local java plugins and some filtering operations to fetch the comic strip image from http://xkcd.com/

Based on the FetchDailyDilbert workflow.

Description:

This workflow retrieves nucleotide and protein sequences with the literature and references associated to them given a protein and a nucleotide id.

Description:

Perform multiple iterations of services in order to show pipelining

Description:

This workflow retrieves a sequence associated with its features in embl format