This workflow uses one or more services that are deprecated as of 31st December 2012 (almost 12 years ago), and may no longer function. Show details...

Vaccine Targets Workflow

Created: 2011-03-30 20:45:57 Last updated: 2011-04-01 12:45:26

Download Workflow

Drug re-purposing workflow

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/2004/download?version=1
[ More Info Expand ]

Workflow Components

Authors (0)

Titles (0)

Descriptions (0)

Dependencies (0)

Inputs (4)

Name	Description
Drug_Target_Protein_FASTA
Target_Proteomes_GI
Target_Proteomes_Fasta_file
thresholdIdentity

Processors (6)

Name	Type	Description
Extract_proteins_using_a_gi___output_as_fasta_file_	workflow
Workflow8	workflow
Get_DrugTarget_Fasta_Url	beanshell	Script String encoded = java.net.URLEncoder.encode(contents_file, "UTF-8"); String url_string = "http://cypher001.ncl.ac.uk:8080/examples/servlets/servlet/HelloWorldExample?contents="+encoded;
Get_Target_Fasta_Url	beanshell	Script String encoded = java.net.URLEncoder.encode(contents_file, "UTF-8"); String url_string = "http://cypher001.ncl.ac.uk:8080/examples/servlets/servlet/HelloWorldExample?contents="+encoded;
Workflow27	workflow
KEGG_Pathways_and_Additional_Information	workflow

Beanshells (18)

Name	Inputs	Outputs
Get_DrugTarget_Fasta_Url	contents_file	url_string
Get_Target_Fasta_Url	contents_file	url_string
get_identifiers_from_uniprot_2_2	parsed_uniprot identifier_name	out1
to_Lower_Case_2	in1	out1
threshold_BLAST_results	blast_file thresholdIdentity	out1
Extraction_of_info	xml_result	fastas_out
remove_Nulls	input	output
extract_gene_ids	input	output
remove_nulls_2	input	output
uniprot_to_string	input	output
get_identifiers_from_uniprot_2_2	parsed_uniprot identifier_name	out1
GO_deXMLer	in1	out1
extract_embl_from_blast	unique_identifiers	out1
get_identifiers_from_uniprot_2_2	parsed_uniprot identifier_name	out1
deXMLer	in1	out1
parse_embl_id	input	output
String_to_list	in1	out1
get_identifiers_from_uniprot	parsed_uniprot identifier_name	out1

Outputs (6)

Name	Description
pathway_descriptions
Pathways_URL
GO_output
PubMed_results
InterPro_Results
protein_ids

Datalinks (15)

Source	Sink
Target_Proteomes_GI	Extract_proteins_using_a_gi___output_as_fasta_file_:id
Target_Proteomes_Fasta_file	Extract_proteins_using_a_gi___output_as_fasta_file_:fasta_file_path
Get_DrugTarget_Fasta_Url:url_string	Workflow8:subjectURL
Get_Target_Fasta_Url:url_string	Workflow8:queryURL
Drug_Target_Protein_FASTA	Get_DrugTarget_Fasta_Url:contents_file
Target_Proteomes_Fasta_file	Get_Target_Fasta_Url:contents_file
Workflow8:BlastReport	Workflow27:blast_file
thresholdIdentity	Workflow27:thresholdIdentity
Workflow27:thresholdedBlastResults	KEGG_Pathways_and_Additional_Information:BLAST_results
KEGG_Pathways_and_Additional_Information:NCBIGitoKeggPathways_pathway_descriptions	pathway_descriptions
KEGG_Pathways_and_Additional_Information:NCBIGitoKeggPathways_URL	Pathways_URL
KEGG_Pathways_and_Additional_Information:GO_output	GO_output
KEGG_Pathways_and_Additional_Information:PubMed_results	PubMed_results
KEGG_Pathways_and_Additional_Information:InterPro_Results	InterPro_Results
KEGG_Pathways_and_Additional_Information:parsed_data	protein_ids

Coordinations (1)

Controller	Target
Extract_proteins_using_a_gi___output_as_fasta_file_	Get_Target_Fasta_Url

Information Workflow Type

Taverna 2

Information Uploader

Morgan Taschuk

Information License

All versions of this Workflow are licensed under:

Information Version 1 (earliest) (of 3)

Information Credits (2)

(People/Groups)

Information Attributions (0)

(Workflows/Files)

None

Information Tags (0)

None

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

2343 viewings

1482 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

Drug Re-Purposing Workflow

Created by Morgan Taschuk on Wednesday 30 March 2011 20:45:56 (UTC)

Last edited by Morgan Taschuk on Wednesday 30 March 2011 20:46:58 (UTC)
Drug Re-Purposing Workflow

Created by Morgan Taschuk on Thursday 31 March 2011 22:54:35 (UTC)

Revision comment:

Added HTML integration
Vaccine Targets Workflow

Created by Morgan Taschuk on Friday 01 April 2011 12:43:48 (UTC)

Last edited by Morgan Taschuk on Friday 01 April 2011 12:45:26 (UTC)

Revision comment:

Final version

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

Drug Re-Purposing Workflow (6)

Download

The drug repurposing workflow system screens at least 20 bacterial proteomes against this set of proteins that are already being treated against using established drugs. By screening the bacterial proteomes it will be possible to find proteins of highly similar structure to those that are existing drug protein targets and so this will infer that it is highly likely that the drugs can be used as antimicrobials against these proteins of highly similar structure. Proteomes that will be screene...