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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

Authors (0)

Titles (1)

Descriptions (0)

Dependencies (0)

Inputs (7)

Name	Description
source_file
source_id
target_file
target_id
blast_file
fg_input
bg_input

Processors (10)

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";
Cloud_BLAST	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;
Workflow27	workflow
Workflow36	workflow
NCBIGitoKeggPathways	workflow

Beanshells (11)

Name	Inputs	Outputs
get_source_url	fasta	url_string
get_target_url	fasta	url_string
remove_Nulls	input	output
extract_kegg_ids	input	output
remove_nulls_2	input	output
add_ncbi_to_string	input	output
extract_blast_ids	xml_result	gi_lines_val
find_unique_proteins	gi_val tfasta_in	cfasta_out
average_identity	blast_file	out1
Extraction_of_info	xml_result	fastas_out
extract_gis_from_blast	unique_identifiers	out1

Outputs (12)

Name	Description
finalStatus
blasted_identifiers
unique_identifiers
BlastReport
overallSimilarity
gi_numbers
KEGGID
kegg_description
pathway_description
pathway_by_genes
image
url

Datalinks (29)

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	Cloud_BLAST:subjectURL
get_target_url:url_string	Cloud_BLAST: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
Cloud_BLAST:BlastReport	Write_Text_File:filecontents
blast_file	Write_Text_File:outputFile
Cloud_BLAST:BlastReport	Workflow27:blast_file
Extract_unique_proteins_from_blast_results:unique_identifiers	Workflow36:thresholded_blast
Workflow36:gi_numbers	NCBIGitoKeggPathways:Gi_numbers
fg_input	NCBIGitoKeggPathways:fg_color
bg_input	NCBIGitoKeggPathways:bg_color
Cloud_BLAST: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
Workflow27:overallSimilarity	overallSimilarity
Workflow36:gi_numbers	gi_numbers
NCBIGitoKeggPathways:KEGGID	KEGGID
NCBIGitoKeggPathways:kegg_descriptions	kegg_description
NCBIGitoKeggPathways:pathway_descriptions	pathway_description
NCBIGitoKeggPathways:pathway_by_genes	pathway_by_genes
NCBIGitoKeggPathways:image	image
NCBIGitoKeggPathways:URL	url

Coordinations (1)

Controller	Target
Write_Text_File	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 3 (of 6)

Information Credits (2)

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None

Information Tags (7)

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Information Shared with Groups (1)

A Team

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Information Attributed By (0)

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None

Information Favourited By (0)

No one

Information Statistics

4455 viewings

1820 downloads

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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)

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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...