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Drug Re-Purposing Workflow

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

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Workflow Components

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Titles (0)

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Inputs (5)

Name	Description
source_file
source_id
target_file
target_id
blast_file

Processors (8)

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 toEncode = contents_file; String encoded = java.net.URLEncoder.encode(toEncode, "UTF-8"); String url_string = "http://cypher001.ncl.ac.uk:8080/examples/servlets/servlet/HelloWorldExample?contents="+encoded;
get_target_url	beanshell	Script String toEncode = contents_file; String encoded = java.net.URLEncoder.encode(toEncode, "UTF-8"); String url_string = "http://cypher001.ncl.ac.uk:8080/examples/servlets/servlet/HelloWorldExample?contents="+encoded;
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;
KEGG_Pathways_and_Additional_Information	workflow

Beanshells (19)

Name	Inputs	Outputs
get_source_url	contents_file	url_string
get_target_url	contents_file	url_string
extract_blast_ids	xml_result	gi_lines_val
find_unique_proteins	gi_val tfasta_in	cfasta_out
String_to_list	in1	out1
get_identifiers_from_uniprot	parsed_uniprot identifier_name	out1
parse_embl_id	input	output
Extraction_of_info	xml_result	fastas_out
get_identifiers_from_uniprot_2_2	parsed_uniprot identifier_name	out1
GO_deXMLer	in1	out1
get_identifiers_from_uniprot_2_2	parsed_uniprot identifier_name	out1
to_Lower_Case_2	in1	out1
get_identifiers_from_uniprot_2_2	parsed_uniprot identifier_name	out1
deXMLer	in1	out1
extract_embl_from_blast	unique_identifiers	out1
remove_Nulls	input	output
extract_gene_ids	input	output
remove_nulls_2	input	output
uniprot_to_string	input	output

Outputs (7)

Name	Description
unique_identifiers
PubMed_Results
Interpro_results
GO_output
KEGG_Pathways_descriptions
KEGG_Pathways_URL
parsed_data

Datalinks (19)

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
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
Extract_unique_proteins_from_blast_results:unique_identifiers	KEGG_Pathways_and_Additional_Information:dgr
Extract_unique_proteins_from_blast_results:unique_identifiers	KEGG_Pathways_and_Additional_Information:BLAST_results
Extract_unique_proteins_from_blast_results:unique_identifiers	unique_identifiers
KEGG_Pathways_and_Additional_Information:PubMed_results	PubMed_Results
KEGG_Pathways_and_Additional_Information:InterPro_Results	Interpro_results
KEGG_Pathways_and_Additional_Information:GO_output	GO_output
KEGG_Pathways_and_Additional_Information:NCBIGitoKeggPathways_pathway_descriptions	KEGG_Pathways_descriptions
KEGG_Pathways_and_Additional_Information:NCBIGitoKeggPathways_URL	KEGG_Pathways_URL
KEGG_Pathways_and_Additional_Information:parsed_data	parsed_data

Coordinations (3)

Controller	Target
Workflow8	Extract_unique_proteins_from_blast_results
Extract_proteins_using_a_gi___output_as_fasta_file__2	get_target_url
Extract_proteins_using_a_gi___output_as_fasta_file_	get_source_url

Information Workflow Type

Taverna 2

Information Uploader

Morgan Taschuk

Information License

All versions of this Workflow are licensed under:

Information Version 4 (of 6)

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Information Shared with Groups (1)

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Information Favourited By (0)

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Information Statistics

4451 viewings

1820 downloads

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Citations (0)

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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)

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Taverna 2

Uploader

Morgan Taschuk

Vaccine Targets Workflow (3)

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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...