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Kegg pathway diagrams

Created: 2010-03-19 12:41:27 Last updated: 2010-03-19 12:41:28

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Find pathways in which all the genes in the list are involved. For each pathway draw the pathway diagram.

Find pathways in which all the genes in the list are involved. For each pathway draw the pathway diagram. Colour all enzyme boxes with colours specified. This workflow still has one problem. The list of colours have to be specified. I would like ideally to only except one background and one foreground colour and expand that to a list with length equivalent to the number of enzymes found - just duplicating the specified colours. However with almost no Taverna documentation to speak of, none of my efforts wanted to work so far.

for each protein draw a diagram of the Kegg pathway that its protein is involved in and where available visualise the structures

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Workflow Components

Authors (1)

Titles (2)

Descriptions (3)

Dependencies (0)

Inputs (4)

Name	Description
gene_ids	A list of KEGG gene ids
Species	The three letter species code used by KEGG KEGG The three letter species code
bg_color	The background colour for the boxes containing enzymes. Values can be given as strings or hexadecimal RGB colour codes. The background colour for the boxes containing enzymes.
fg_color	The text colour for the boxes containing enzymes. Values can be given as strings or hexadecimal RGB colour codes.

Processors (16)

Name	Type	Description
Workflow89	workflow
Get_Image_From_URL_2	localworker	Script URL inputURL = null; if (base != void) { inputURL = new URL(new URL(base), url); } else { inputURL = new URL(url); } byte[] contents; if (inputURL.openConnection().getContentLength() == -1) { // Content size unknown, must read first... byte[] buffer = new byte[1024]; int bytesRead = 0; int totalBytesRead = 0; InputStream is = inputURL.openStream(); while (bytesRead != -1) { totalBytesRead += bytesRead; bytesRead = is.read(buffer, 0, 1024); } contents = new byte[totalBytesRead]; } else { contents = new byte[inputURL.openConnection().getContentLength()]; } int bytesRead = 0; int totalBytesRead = 0; InputStream is = inputURL.openStream(); while (bytesRead != -1) { bytesRead = is.read(contents, totalBytesRead, contents.length - totalBytesRead); totalBytesRead += bytesRead; if (contents.length==totalBytesRead) break; } image = contents;
color_pathway_by_objects	wsdl	Wsdl http://soap.genome.jp/KEGG.wsdl Wsdl Operation color_pathway_by_objects
get_enzymes_by_gene	wsdl	Wsdl http://soap.genome.jp/KEGG.wsdl Wsdl Operation get_enzymes_by_gene
get_genes_by_enzyme	wsdl	Wsdl http://soap.genome.jp/KEGG.wsdl Wsdl Operation get_genes_by_enzyme
get_pathways_by_genes	wsdl	Wsdl http://soap.genome.jp/KEGG.wsdl Wsdl Operation get_pathways_by_genes
Flatten_List	localworker	Script flatten(inputs, outputs, depth) { for (i = inputs.iterator(); i.hasNext();) { element = i.next(); if (element instanceof Collection && depth > 0) { flatten(element, outputs, depth - 1); } else { outputs.add(element); } } } outputlist = new ArrayList(); flatten(inputlist, outputlist, 1);
Flatten_List_2	localworker	Script flatten(inputs, outputs, depth) { for (i = inputs.iterator(); i.hasNext();) { element = i.next(); if (element instanceof Collection && depth > 0) { flatten(element, outputs, depth - 1); } else { outputs.add(element); } } } outputlist = new ArrayList(); flatten(inputlist, outputlist, 1);
Remove_String_Duplicates	localworker	Script List strippedlist = new ArrayList(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); if (strippedlist.contains(item) == false) { strippedlist.add(item); } }
Beanshell	beanshell	Script List bg_colors = new ArrayList(); List fg_colors = new ArrayList(); for (int i = 0; i < genes_list.size(); i++) { fg_colors.add(fg_color); bg_colors.add(bg_color); }
Flatten_List_3	localworker	Script flatten(inputs, outputs, depth) { for (i = inputs.iterator(); i.hasNext();) { element = i.next(); if (element instanceof Collection && depth > 0) { flatten(element, outputs, depth - 1); } else { outputs.add(element); } } } outputlist = new ArrayList(); flatten(inputlist, outputlist, 1);
Flatten_List_4	localworker	Script flatten(inputs, outputs, depth) { for (i = inputs.iterator(); i.hasNext();) { element = i.next(); if (element instanceof Collection && depth > 0) { flatten(element, outputs, depth - 1); } else { outputs.add(element); } } } outputlist = new ArrayList(); flatten(inputlist, outputlist, 1);
Flatten_List_5	localworker	Script flatten(inputs, outputs, depth) { for (i = inputs.iterator(); i.hasNext();) { element = i.next(); if (element instanceof Collection && depth > 0) { flatten(element, outputs, depth - 1); } else { outputs.add(element); } } } outputlist = new ArrayList(); flatten(inputlist, outputlist, 1);
Flatten_List_6	localworker	Script flatten(inputs, outputs, depth) { for (i = inputs.iterator(); i.hasNext();) { element = i.next(); if (element instanceof Collection && depth > 0) { flatten(element, outputs, depth - 1); } else { outputs.add(element); } } } outputlist = new ArrayList(); flatten(inputlist, outputlist, 1);
Flatten_List_7	localworker	Script flatten(inputs, outputs, depth) { for (i = inputs.iterator(); i.hasNext();) { element = i.next(); if (element instanceof Collection && depth > 0) { flatten(element, outputs, depth - 1); } else { outputs.add(element); } } } outputlist = new ArrayList(); flatten(inputlist, outputlist, 1);
Flatten_List_8	localworker	Script flatten(inputs, outputs, depth) { for (i = inputs.iterator(); i.hasNext();) { element = i.next(); if (element instanceof Collection && depth > 0) { flatten(element, outputs, depth - 1); } else { outputs.add(element); } } } outputlist = new ArrayList(); flatten(inputlist, outputlist, 1);

Beanshells (1)

Name	Description	Inputs	Outputs
Beanshell		bg_color fg_color genes_list	bg_colors fg_colors

Outputs (6)

Name	Description
KeggPathwayIDs	A list of the pathways found.
keggimageurl	The URLs of the images produced for the KeggImage output The URLs of the images produced for the KeggImage output.
keggGeneNames	A list of the gene ids, that was given as input with the species code concatenated.
coloured_images	List of pathway diagram with enzyme boxes coloured in specified colours
enzyme_list	List of enzyme id retrieve from Kegg using get_enzymes_by_gene
genes_list	List of ids that are enzymes

Datalinks (29)

Source	Sink
Species	Workflow89:part1
gene_ids	Workflow89:part2
color_pathway_by_objects:return	Get_Image_From_URL_2:url
get_pathways_by_genes:return	color_pathway_by_objects:pathway_id
Remove_String_Duplicates:strippedlist	color_pathway_by_objects:object_id_list
Flatten_List_6:outputlist	color_pathway_by_objects:bg_color_list
Flatten_List_8:outputlist	color_pathway_by_objects:fg_color_list
Workflow89:string	get_enzymes_by_gene:genes_id
Species	get_genes_by_enzyme:org
Flatten_List:outputlist	get_genes_by_enzyme:enzyme_id
Workflow89:string	get_pathways_by_genes:genes_id_list
get_enzymes_by_gene:return	Flatten_List:inputlist
get_genes_by_enzyme:return	Flatten_List_2:inputlist
Flatten_List_2:outputlist	Remove_String_Duplicates:stringlist
Remove_String_Duplicates:strippedlist	Beanshell:genes_list
bg_color	Beanshell:bg_color
fg_color	Beanshell:fg_color
Beanshell:bg_colors	Flatten_List_3:inputlist
Beanshell:fg_colors	Flatten_List_4:inputlist
Flatten_List_3:outputlist	Flatten_List_5:inputlist
Flatten_List_5:outputlist	Flatten_List_6:inputlist
Flatten_List_4:outputlist	Flatten_List_7:inputlist
Flatten_List_7:outputlist	Flatten_List_8:inputlist
get_pathways_by_genes:return	KeggPathwayIDs
color_pathway_by_objects:return	keggimageurl
Workflow89:string	keggGeneNames
Get_Image_From_URL_2:image	coloured_images
Flatten_List:outputlist	enzyme_list
Remove_String_Duplicates:strippedlist	genes_list

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Information Workflow Type

Taverna 2

Information Uploader

Jannetta

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Information Statistics

3247 viewings

1829 downloads

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Version History

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Kegg pathway diagrams with enzymes coloured

Created by Jannetta on Sunday 14 March 2010 13:56:02 (UTC)
Kegg pathway diagrams

Created by Jannetta on Wednesday 17 March 2010 14:44:44 (UTC)

Revision comment:

Changed colour input to take single inputs and create a list of colours equivalent in length to the gene list. All genes identified will be coloured on the Kegg diagram in the same colour.
Kegg pathway diagrams

Created by Jannetta on Friday 19 March 2010 12:41:27 (UTC)

Revision comment:

Flatten output values

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Kegg pathway diagrams

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