This workflow uses one or more services that are deprecated as of 31st December 2012 (over 11 years ago), and may no longer function. Show details...

Drug Re-Purposing Workflow

Created: 2011-03-25 20:06:13 Last updated: 2011-04-01 12:40:56

Download Workflow

No description has been set

Preview

Download as scalable diagram (SVG)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/1984/download?version=2
[ More Info Expand ]

Workflow Components

Authors (0)

Titles (0)

Descriptions (0)

Dependencies (0)

Inputs (5)

Name	Description
source_file
source_id
target_file
target_id
blast_file

Processors (7)

Name	Type	Description
Extract_proteins_using_a_gi___output_as_fasta_file_	workflow
Extract_proteins_using_a_gi___output_as_fasta_file__2	workflow
get_source_url	beanshell	Script String url_string = "http://cypher001.ncl.ac.uk:8080/examples/servlets/servlet/HelloWorldExample";
get_target_url	beanshell	Script String url_string = "http://cypher001.ncl.ac.uk:8080/examples/servlets/servlet/RequestInfoExample";
Workflow8	workflow
Extract_unique_proteins_from_blast_results	workflow
Write_Text_File	localworker	Script BufferedWriter out = new BufferedWriter(new FileWriter(outputFile)); out.write(filecontents); out.close(); outputFile = filecontents;

Beanshells (5)

Name	Inputs	Outputs
get_source_url	fasta	url_string
get_target_url	fasta	url_string
extract_blast_ids	xml_result	gi_lines_val
find_unique_proteins	gi_val tfasta_in	cfasta_out
Extraction_of_info	xml_result	fastas_out

Outputs (4)

Name	Description
finalStatus
blasted_identifiers
unique_identifiers
BlastReport

Datalinks (16)

Source	Sink
source_id	Extract_proteins_using_a_gi___output_as_fasta_file_:id
source_file	Extract_proteins_using_a_gi___output_as_fasta_file_:fasta_file_path
target_id	Extract_proteins_using_a_gi___output_as_fasta_file__2:id
target_file	Extract_proteins_using_a_gi___output_as_fasta_file__2:fasta_file_path
Extract_proteins_using_a_gi___output_as_fasta_file_:file_output	get_source_url:fasta
Extract_proteins_using_a_gi___output_as_fasta_file__2:file_output	get_target_url:fasta
get_source_url:url_string	Workflow8:subjectURL
get_target_url:url_string	Workflow8:queryURL
blast_file	Extract_unique_proteins_from_blast_results:blastFile
Extract_proteins_using_a_gi___output_as_fasta_file__2:file_output	Extract_unique_proteins_from_blast_results:tfasta
Workflow8:BlastReport	Write_Text_File:filecontents
blast_file	Write_Text_File:outputFile
Workflow8:FinalStatus	finalStatus
Extract_unique_proteins_from_blast_results:blasted_identifiers	blasted_identifiers
Extract_unique_proteins_from_blast_results:unique_identifiers	unique_identifiers
Write_Text_File:outputFile	BlastReport

Coordinations (1)

Controller	Target
Workflow8	Extract_unique_proteins_from_blast_results

Information Workflow Type

Taverna 2

Information Uploader

Morgan Taschuk

Information License

All versions of this Workflow are licensed under:

Information Version 2 (of 6)

Information Credits (2)

(People/Groups)

Information Attributions (0)

(Workflows/Files)

None

Information Tags (7)

Uploader tags

Log in to add Tags

Information Shared with Groups (1)

A Team

Information Featured In Packs (0)

None

Log in to add to one of your Packs

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

4247 viewings

1730 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

Vaccine Target Workflow

Created by Morgan Taschuk on Friday 25 March 2011 20:06:13 (UTC)

Last edited by Morgan Taschuk on Friday 25 March 2011 20:11:45 (UTC)
Vaccine Targets

Created by Morgan Taschuk on Monday 28 March 2011 11:21:44 (UTC)

Last edited by Morgan Taschuk on Monday 28 March 2011 11:27:02 (UTC)

Revision comment:

Edited the unique protein finder to be more efficient.
Vaccine Targets

Created by Morgan Taschuk on Tuesday 29 March 2011 13:28:19 (UTC)
Vaccine Targets

Created by Morgan Taschuk on Wednesday 30 March 2011 19:58:58 (UTC)

Last edited by Morgan Taschuk on Wednesday 30 March 2011 20:06:02 (UTC)

Revision comment:

new dynamic HttpServlet call

better workflows for GO, PubMed, Interpro
Drug Re-Purposing Workflow

Created by Morgan Taschuk on Friday 01 April 2011 02:47:59 (UTC)

Revision comment:

All workin
Drug Re-Purposing Workflow

Created by Morgan Taschuk on Friday 01 April 2011 12:40:48 (UTC)

Reviews (0)

No reviews yet

Be the first to review!

Comments (0)

View Timeline

No comments yet

Log in to make a comment

Other workflows that use similar services (101)

Only the first 2 workflows that use similar services are shown. View all workflows that use these services.

Taverna 2

Uploader

Morgan Taschuk

Vaccine Targets Workflow (3)

Download

Comparison of the genome of Bacillus anthracis to closely related strains will allow the discovery of proteins which may be involved in pathogenicity. Based on the biochemical pathways where the protein interacts, vaccines can be designed for these unique proteins. By gaining insight into the biochemical pathways that the unique proteins are involved in, the proteins can also be assessed for potential quality as vaccines. The key components of the vaccine finding system are the following: T...