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

Parts 4-6

Created: 2010-03-18 12:39:55 Last updated: 2010-03-18 12:40:43

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/1152/download?version=1
[ More Info Expand ]

Workflow Components

Authors (0)

Titles (1)

Descriptions (0)

Dependencies (0)

Inputs (3)

Name	Description
known_drug_targets_list
input_sequences
drug_target_minimum_similarity

Processors (8)

Name	Type	Description
6_Kegg_pathway_diagrams_with_enzymes_coloured_on_path_diagram	workflow
4_5_Find_potential_drug_targets	workflow
pass_protein_id_if_similar_to_a_drug_target	beanshell	Script if (((ArrayList)targets).size() > 0) { protein_id_out = protein_desc.split("\n")[0]; }
fg_color_value	stringconstant	Value black
bg_color_value	stringconstant	Value green
Concatenate_two_strings	localworker	Script output = string1 + string2;
Namespace	stringconstant	Value UniProt
convert_to_kegg_id	workflow

Beanshells (6)

Name	Inputs	Outputs
pass_protein_id_if_similar_to_a_drug_target	protein_desc targets	protein_id_out
insert_query_seq	fasta MergeString	result
extract_number_sequences	insertSeq	result
Extract_Seq_Description	Sequences	result
Alignment_thresholder	stringlist regex group minscore	filteredlist
addIDtotarget	identifiers targets regex group	filteredlist

Outputs (5)

Name	Description
kegg_image_url
potential_drug_targets
alignments
image_alignments
kegg_image

Datalinks (17)

Source	Sink
fg_color_value:value	6_Kegg_pathway_diagrams_with_enzymes_coloured_on_path_diagram:fg_color
bg_color_value:value	6_Kegg_pathway_diagrams_with_enzymes_coloured_on_path_diagram:bg_color
convert_to_kegg_id:kegg_id	6_Kegg_pathway_diagrams_with_enzymes_coloured_on_path_diagram:gene_ids
known_drug_targets_list	4_5_Find_potential_drug_targets:drug_list
input_sequences	4_5_Find_potential_drug_targets:Input_Sequences
drug_target_minimum_similarity	4_5_Find_potential_drug_targets:similarity_threshold
4_5_Find_potential_drug_targets:Protein_Desc	pass_protein_id_if_similar_to_a_drug_target:protein_desc
4_5_Find_potential_drug_targets:Targets	pass_protein_id_if_similar_to_a_drug_target:targets
4_5_Find_potential_drug_targets:Targets	Concatenate_two_strings:string2
4_5_Find_potential_drug_targets:Protein_Desc	Concatenate_two_strings:string1
Namespace:value	convert_to_kegg_id:namespace
pass_protein_id_if_similar_to_a_drug_target:protein_id_out	convert_to_kegg_id:id
6_Kegg_pathway_diagrams_with_enzymes_coloured_on_path_diagram:keggimageurl	kegg_image_url
Concatenate_two_strings:output	potential_drug_targets
4_5_Find_potential_drug_targets:Alignment	alignments
4_5_Find_potential_drug_targets:Image_Alignment	image_alignments
6_Kegg_pathway_diagrams_with_enzymes_coloured_on_path_diagram:coloured_images	kegg_image

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

White duncan100

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

Information Credits (1)

(People/Groups)

White duncan100

Information Attributions (0)

(Workflows/Files)

None

Information Tags (0)

None

Log in to add Tags

Information Shared with Groups (1)

Steyn Pharmaceuticals Ltd Unplanned Genetic Experiments (SPLUGE)

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

1256 viewings

1137 downloads

[ see breakdown ]

Citations (0)Version History

None

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 (93)

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

Taverna 2

Uploader

Alibukhari

NCBI Gi to Kegg Pathways (1)

Download

"This workflow gets a series of information relating to a list of KEGG genes supplied to it. It also removes any null values from a list of strings."This workflow gets a series of information relating to a list of KEGG genes supplied to it. It also removes any null values from a list of strings.

Created: 2011-03-28 | Last updated: 2011-03-28

Credits: Alibukhari

Taverna 1

Uploader

Paul Fisher

Entrez Gene to KEGG Pathway (5)

Download

This workflow takes in Entrez gene ids then adds the string "ncbi-geneid:" to the start of each gene id. These gene ids are then cross-referenced to KEGG gene ids. Each KEGG gene id is then sent to the KEGG pathway database and its relevant pathways returned.

Created: 2009-12-04 | Last updated: 2010-11-30

Credits: Paul Fisher

Parts 4-6

Preview

Run

Run this Workflow in the Taverna Workbench...

Workflow Components

Script

Value

Value

Script

Value

Reviews (0)

Comments (0)

Other workflows that use similar services (93)