Gb User: Paul Fisher Admin_badge

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Name: Paul Fisher

Joined: Thursday 26 July 2007 @ 16:46:52 (BST)

Last seen: Thursday 11 March 2010 @ 11:29:33 (GMT)

Email (public): fisherp [at] cs.manchester.ac.uk

Website: http://www.cs.man.ac.uk/~fisherp/

Location: Manchester, United Kingdom

Paul Fisher has been credited 222 times

Paul Fisher has an average rating of:

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I am a fourth year PhD student. My research focuses on using QTL and microarray data, looking at the level of biological pathway, to identify novel links between Genotype and Phenotype. I am conducting these correlations thorugh the use of web services and workflows.

These have been tested on African Trypanosomiasis in both Cattle and mice, Lung Cancer, infection of a mouse with Trichuris muris, and Colitis / Inflammatory bowel disease.


Other contact details:

Not specified

Interests:

Workflows
QTL analysis
Microarrays
Biological pathway analysis
In silico automation
Protein 3D structure prediction
Disease gene identification

Field/Industry: Bioinformatics

Occupation/Role(s): 4th Year PhD Student

Organisation(s):

University of Manchester

 

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Taverna 2

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Workflow Get Kegg Pathway information (v1)

Created: 10/03/10 @ 17:15:47 | Last updated: 10/03/10 @ 17:18:47

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_kegg_pathway_information
This workflow gets a series of information relating to a list of KEGG pathways supplied to it. It also removes any null values from a list of strings. Example input: path:mmu04010 path:mmu05014

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Taverna 2

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Workflow Get Gene Ids for Human (v1)

Created: 04/02/10 @ 12:47:17 | Last updated: 04/02/10 @ 12:48:12

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_gene_ids_for_human
This workflow gets a list of gene ids (number depending on Ret_Max_value variable) for Homo sapiens. The species may be changed according to that desired, by altering the term_value string constant

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Taverna 1

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Workflow Pathways and Gene annotations for QTL region (v2)

Created: 19/10/09 @ 12:39:05 | Last updated: 20/11/09 @ 14:04:41

Credits: User Paul Fisher

Attributions: Workflow Pathways and Gene annotations for QTL region

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Pathways_and_gene_annotations_for_qtl_region
This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the Pig, Sus scrofa. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway ...

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Taverna 2

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Workflow Spreadsheet Importer (v1)

Created: 24/08/09 @ 14:11:52 | Last updated: 24/08/09 @ 14:11:53

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Spreadsheet_importer
This workflow is designed to import a spreadhseet from a local computer. The imported spreadsheet is parsed to extract the first two columns, A and B, for all rows in the spreadsheet. These are returned as two separate outputs.

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Taverna 1

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Workflow Unconnected Filter (v1)

Created: 19/08/09 @ 16:35:09 | Last updated: 19/08/09 @ 16:35:11

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Unconnected_filter
This workflow removes any unconnected nodes from a given Ondex graph through filtering, and returns a new Ondex Graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. RemoveContextDependencies - Set true to remove context dependencies, otherwise unconnected concepts will still remain in the ...

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Taverna 1

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Workflow Tranitive Filter (v1)

Created: 19/08/09 @ 16:34:17 | Last updated: 19/08/09 @ 16:34:18

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Tranitive_filter
This workflow filters an Ondex graph to extract a sub-graph. The result is a new Ondex graph containing only the transitive sub-graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. CV - Seed cv that will be used to extract the subgraph (Optional). AttributeName - Seed attribute name that will be us...

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Taverna 1

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Workflow SubGraph Filter (v2)

Created: 19/08/09 @ 16:32:41 | Last updated: 19/08/09 @ 16:38:18

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Subgraph_filter
This workflow filters a given Ondex graph to return a new ondex sub-graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. ConceptID - The root concept to start at. Valid value range is 1 to 2147483647. FirstRelationType - RelationType limitation for depth 1 (Optional). FirstConceptClass - C...

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Taverna 1

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Workflow Significance Filter (v1)

Created: 19/08/09 @ 16:31:25 | Last updated: 19/08/09 @ 16:31:26

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Significance_filter
This workflow filters a given Ondex graph according to a level of significance set by the user. The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. TargetAttributeName - Target AttributeName to filter for significance. Significance - A significance value to filter relatio...

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Taverna 1

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Workflow Shortest Path (v1)

Created: 19/08/09 @ 16:30:36 | Last updated: 19/08/09 @ 16:30:38

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Shortest_path
This workflow filters a given Ondex graph according to the shortest path (graph) algorithm. The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. StartConceptID - The Concept ID that starts the path. Valid value range is 1 to 2147483647. UseWeights - Use gds values as edge ...

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Taverna 1

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Workflow Relation Type Filter (v1)

Created: 19/08/09 @ 16:29:12 | Last updated: 19/08/09 @ 16:29:13

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Relation_type_filter
This workflow filters a pre-existing ONdex graph based on a some paramters provided by the user. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional) parameter. If no output graph is specified filtered items will be removed from the input graph. TargetRelationType - Target RelationType to filter out. ConceptClassRestriction - Concept Class Restriction as ordered pair representing from/to C...

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Taverna 1

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Workflow Relation Neighbours Filter (v1)

Created: 19/08/09 @ 16:28:10 | Last updated: 19/08/09 @ 16:28:12

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Relation_neighbours_filter
This workflow filters a given Ondex graph based on some neighbour parameters supplied by the user. The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. Depth - The Depth (distance from seed in relations) to apply the filter to ConceptID - The Concept ID to seed th...

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Taverna 1

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Workflow Pfam Based Ortholog Filter (v1)

Created: 19/08/09 @ 16:26:56 | Last updated: 19/08/09 @ 16:26:58

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Pfam_based_ortholog_filter
This workflow filters an Ondex graph based on the occurrence of Pfam orthologs within the graph. The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. ConfidenceThreshold - Threshold value for inparanoid confidence. Default value is 100. AnnotationScoreThreshold - Threshold...

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Taverna 1

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Workflow Optimal Paths Filter (v1)

Created: 19/08/09 @ 16:25:51 | Last updated: 19/08/09 @ 16:25:53

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Optimal_paths_filter
This workflow filters a given Ondex graph based on the optimal path between one or more concepts. The result is a new Ondex graph. The parameters that can be used with service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. PathwayDefinition - pathway definition file. StatisticsOutputDir - The directory to output statistics (Optional). Incl...

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Taverna 1

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Workflow One Pair Shortest Path Filter (v1)

Created: 19/08/09 @ 16:24:42 | Last updated: 19/08/09 @ 16:24:44

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

One_pair_shortest_path_filter
This workflow filters a pre-existing Ondex graph using the shortest path algorithm on the graph. The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. StartConceptID - The Concept ID that starts the path EndConceptID - The Concept ID that ends the path UseWeights -...

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Taverna 1

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Workflow Isolate Clusters Filter (v1)

Created: 19/08/09 @ 16:23:46 | Last updated: 19/08/09 @ 16:23:48

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Isolate_clusters_filter
This workflow filters a given Ondex graph, isolating clusters within the graph and returning only those clusters as a new graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. TargetConceptClass - Target Concept Class to be contained in clusters.

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Taverna 1

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Workflow Graph Cloner (v1)

Created: 19/08/09 @ 16:22:14 | Last updated: 19/08/09 @ 16:22:16

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Graph_cloner
This workflow clones a given Ondex Graph, based on an Ondex Graph identifier.

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Taverna 1

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Workflow Genomic Filter (v1)

Created: 19/08/09 @ 16:19:02 | Last updated: 19/08/09 @ 16:19:05

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Genomic_filter
This workflow filters a given Ondex graph according to a chromosomal region, or QTL region. The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. ContextID - The Concept ID of the Context (Chromosome). From - The start position on the chromosome, e.g. 100. To - The stop pos...

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Taverna 1

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Workflow GDS Value Filter (v1)

Created: 19/08/09 @ 16:17:28 | Last updated: 19/08/09 @ 16:17:30

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Gds_value_filter
This workflow filters a given Ondex graph based on a given GDS value supplied by the user. The result is a new Ondex graph with filtered content. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. AttributeName - AttributeName to filter out. GDSValue - A value which will be matched against the ...

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Taverna 1

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Workflow Evidence Type Filter (v1)

Created: 19/08/09 @ 16:16:16 | Last updated: 19/08/09 @ 16:16:18

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Evidence_type_filter
This workflow filters a given Ondex graph according to some user defined evidence values. The result is a new Ondex graph. The parameters that can be used with this web service are given below: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. EvidenceType - EvidenceType to be taken into consideration. RefactorTrinaries - Where the qualifier of a trinary rel...

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Taverna 1

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Workflow CV Filter (v1)

Created: 19/08/09 @ 16:15:21 | Last updated: 19/08/09 @ 16:15:23

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Cv_filter
This workflow filters a given Ondex graph according to a controlled vocabulary specified by the user. The result is a new Ondex graph with only those concepts that passed the filter. The parameters that can be used with this service graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. CV - A CV to include/exclude Concepts and Relations of (see Exclude param). R...

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Taverna 1

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Workflow Context Filter (v1)

Created: 19/08/09 @ 16:14:14 | Last updated: 19/08/09 @ 16:14:16

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Context_filter
This workflow filters an Ondex graph according to a given context. The result is a new Ondex graph with only selected contexts. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. ContextID - The Concept ID of the Context that starts the path. ContextBoolean - Defines two ContextIDs and a boolean operati...

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Taverna 1

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Workflow Context Consensus Filter (v1)

Created: 19/08/09 @ 16:13:12 | Last updated: 19/08/09 @ 16:13:14

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Context_consensus_filter
This workflow filters a given Ondex graph according to a consensus with regards to a specific context (concept list). The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. Threshold - Double value representing the share of contexts that qualify a graph element for ...

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Taverna 1

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Workflow Concept Class Neighbours Filter (v1)

Created: 19/08/09 @ 16:11:57 | Last updated: 19/08/09 @ 16:11:59

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Concept_class_neighbours_filter
This workflow filters a given Ondex graph based on a user defined concept class. The neighbours of the concept class are returned as a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. Depth - The Depth (distance from seed in relations) to apply the filter to. ConceptClass - The Conce...

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Taverna 1

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Workflow Concept Class Filter (v1)

Created: 19/08/09 @ 16:10:38 | Last updated: 19/08/09 @ 16:10:39

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Concept_class_filter
This workflow filters a Ondex graph based on a specific concept class. The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. TargetConceptClass - Target Concept Class to filter out. RefactorTrinaries - Where the qualifier of a trinary relation is out of scope create a bina...

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Taverna 1

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Workflow Clean UniProt Filter (v1)

Created: 19/08/09 @ 16:08:49 | Last updated: 19/08/09 @ 16:08:50

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Clean_uniprot_filter
This workflow filters a given Ondex graph, removing any erroneous UniProt data. The result is a new Ondex graph that conatains only connected UniProt data. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph.

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Taverna 1

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Workflow Clean GO Filter (v1)

Created: 19/08/09 @ 16:07:28 | Last updated: 19/08/09 @ 16:07:29

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Clean_go_filter
This workflow filters an Ondex graph, by cleaning up any GO terms within the Graph (?). The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph.

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Taverna 1

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Workflow All Pairs Filter (v1)

Created: 19/08/09 @ 16:06:31 | Last updated: 19/08/09 @ 16:06:32

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

All_pairs_filter
This workflow filters a given Ondex graph based on the occurrence of directed edges within the graph. Only those concepts that have directional edges are returned to the user, in the form of a new graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph. Optional parameter. If no output graph is specified filtered items will be removed from the input graph. GdsWeight - The name of the GDS type to ...

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Taverna 1

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Workflow Tab Parser (v1)

Created: 19/08/09 @ 16:05:21 | Last updated: 19/08/09 @ 16:05:22

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Tab_parser
This workflow takes in a tab separated file, and then parses specific rows and columns from the file into an Ondex Graph. Additional prarameters are provided, though these are optional: graphId Long the ID of the Graph (REQUIRED) input String the plugin input (REQUIRED) skip Integer How many rows to skip at begin of document (Optional). Default value is 22. fromCol Integer Index of concept parser id for from concept. Default value is 0. (REQUIRED) toCol Integer Index of concept par...

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Taverna 1

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Workflow Table Parser (v1)

Created: 19/08/09 @ 16:04:14 | Last updated: 19/08/09 @ 16:04:15

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Table_parser
This workflow parsers a table (specified by the user), into an Ondex Graph on the web server.

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Taverna 1

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Workflow KEGG Pasrer (v1)

Created: 19/08/09 @ 16:03:09 | Last updated: 19/08/09 @ 16:03:10

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Kegg_pasrer
This workflow parses a KEGG species database into an Ondex Graph graphId - the ID of the Graph. inputDir - the plugin input directory Species - Use this parameter to specify the species to be loaded from the kegg database. Default value is all. ParseSequences - KEGG species code. Default value is false (boolean) ImportOrthologFillers - Import Ortholog Pathway Fillers. Default value is false (boolean)

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Taverna 1

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Workflow Rank Phenotype Terms (v1)

Created: 10/08/09 @ 15:43:50 | Last updated: 10/08/09 @ 15:43:54

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Rank_phenotype_terms
This workflow counts the number of articles in the pubmed database in which each term occurs, and identifies the total number of articles in the entire PubMed database. It also identified the total number of articles within pubmed so that a term enrichment score may be calculated. The workflow also takes in a document containing abstracts that are related to a particular phenotype. Scientiifc terms are then extracted from this text and given a weighting according to the number of terms that ...

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Taverna 1

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Workflow Phenotype to pubmed (v1)

Created: 10/08/09 @ 15:40:18 | Last updated: 10/08/09 @ 15:40:21

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Phenotype_to_pubmed
This workflow takes in a phenotype search term, and searches for abstracts in the PubMed database. These are passed to the eSearch function and searched for in PubMed. Those abstracts found are returned to the user

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Taverna 1

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Workflow Gene to Pubmed (v2)

Created: 10/08/09 @ 15:31:15 | Last updated: 10/08/09 @ 15:38:32

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Gene_to_pubmed
This workflow takes in a list of gene names and searches the PubMed database for corresponding articles. Any matches to the genes are then retrieved (abstracts only). These abstracts are then returned to the user.

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Taverna 1

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Workflow Extract Scientific Terms (v1)

Created: 10/08/09 @ 13:31:07 | Last updated: 10/08/09 @ 13:32:22

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Extract_scientific_terms
This workflow takes in a document containg text and removes any non-ascii characters. The cleaned text is then sent to a service in Dresden, to extract all scientific terms. These terms represent a concept profile for the input concpet. Any null values are also removed.

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Workflow Cosine vector space (v1)

Created: 10/08/09 @ 13:19:36 | Last updated: 10/08/09 @ 13:24:29

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Cosine_vector_space
This workflow calculates the cosine vector space between two sets of corpora. The workflow then removes any null values from the output. The result is a cosine vector score between 0 and 1, showing the significance of any links between one concept (e.g. pathway) to another (e.g. phenotype). A score of 0 means there is no or an undetermined correlation between the two concepts. A score approaching 1 represents positive correlation.

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Workflow Arabidopsis thaliana Microarray Analysis (v1)

Created: 08/07/09 @ 16:28:35 | Last updated: 08/07/09 @ 16:28:38

Credits: User Paul Fisher

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

Arabidopsis_thaliana_microarray_analysis
This workflow searches for genes which are found to be differentially expressed in a microarray study using Arabidopsis thaliana. The workflow requires an input of a list of differentially expressed AffyMetrix Probeset identifiers. Data is then extracted from BioMart to annotate each of the genes. The UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway database.

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Workflow Arabidopsis thaliana QTL Analysis (v1)

Created: 08/07/09 @ 16:26:13 | Last updated: 14/12/09 @ 11:59:16

Credits: User Paul Fisher

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

Arabidopsis_thaliana_qtl_analysis
This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in Arabidopsis thaliana. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway database. ...

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Workflow NCBI Gi to Kegg Pathways (v1)

Created: 08/06/09 @ 18:39:38 | Last updated: 14/12/09 @ 11:51:22

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Ncbi_gi_to_kegg_pathways
This workflow converts a list of NCBI gi numbers and  converts them to a list of KEGG genes. Those KEGG gene ids are subsequently turned into KEGG pathway identifiers and descriptions. It also removes any null values from a list of strings. Example input for this workflow is as follows (new line separated): gi:215422388 gi:120407068

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Workflow inchi to Chebi (v1)

Created: 22/05/09 @ 16:07:51 | Last updated: 22/05/09 @ 16:07:52

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Inchi_to_chebi
This workflow converts an inchi string to a chebi id.

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Workflow Pathways and Gene annotations for Arabidopsis affy data (v2)

Created: 05/03/09 @ 15:15:59 | Last updated: 03/12/09 @ 16:59:13

Credits: User Paul Fisher User Peter Li

Attributions: Workflow Pathways and Gene annotations for QTL region

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

Pathways_and_gene_annotations_for_arabidopsis_affy_data
This workflow searches for genes obtained from affy_ath1 affymetrix probeset identifiers. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway database.

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Workflow Get relations (v1)

Created: 27/02/09 @ 16:45:40 | Last updated: 27/02/09 @ 16:45:41

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_relations
This workflow gets all the realtions from a given Ondex graph

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Workflow Get Graphs of Name (v1)

Created: 27/02/09 @ 16:42:36 | Last updated: 27/02/09 @ 16:42:37

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_graphs_of_name
This workflow gets the Ondex graphs relating to a specified name

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Workflow Get graphs (v2)

Created: 27/02/09 @ 16:41:49 | Last updated: 05/11/09 @ 12:38:23

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_graphs
Thiw workflow simply returns all the Ondex graphs that are present on a given server (where the web service is)

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Workflow Get Evidence Types (v1)

Created: 27/02/09 @ 16:40:23 | Last updated: 27/02/09 @ 16:40:24

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_evidence_types
This workflow gets all the evidence types within a specified Ondex graph

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Workflow Get CVs (v1)

Created: 27/02/09 @ 16:38:40

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_cvs
This workflow lets users retrive all controlled vocabularies for a given Ondex graph

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Workflow Get Concepts (v1)

Created: 27/02/09 @ 16:33:40

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_concepts
This workflow gets all the concepts in an Ondex graph, using a given graph id

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Workflow Get Kegg Gene information (v2)

Created: 05/01/09 @ 13:20:34 | Last updated: 14/12/09 @ 12:05:23

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Get_kegg_gene_information
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.   Example input for this workflow is given below (new line separated): mmu:13163 hsa:1616

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Workflow Retrieve Protein Sequence (v1)

Created: 30/07/08 @ 16:36:56 | Last updated: 03/12/09 @ 16:54:03

Credits: User Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Retrieve_protein_sequence_31678_1
Retrieves a protein sequence in Fasta format from GenBank, given a GenBank identifier. Example input for this workflow is: EDL10223.1

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Workflow KEGG Pathway to Pubmed (v2)

Created: 09/03/08 @ 15:03:12 | Last updated: 03/12/09 @ 16:52:10

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Pathway_to_pubmed_25676_2
This workflow takes in a list of KEGG pathway descriptions and searches the PubMed database for corresponding articles. Any matches to the pathways are then retrieved (abstracts only). These abstracts are then returned to the user.   Example input for this workflow is as follows (new line separated): path:mmu04530    Tight junction - Mus musculus (mouse) path:mmu04540    Gap junction - Mus musculus (mouse) path:mmu04730    Long-term depre...

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Workflow Human Microarray Analysis (v1)

Created: 08/02/08 @ 14:30:18 | Last updated: 03/12/09 @ 16:50:30

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Human_pathways_from_diff_expressed_genes_4391_1
This workflow takes in probesets from and AffyMetrix  Affy HG U133A micorarray experiment and returns: genes ; gene start and end positions; chromosome where genes reside; ensembl trasncripts; SwissProt ids. The final output of the workflow is a list of candidate pathways which are linked to the genes expressed in the microarray data.   Example input for this workflow is: 212283_at 221634_at 220399_at  

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Workflow Microarray CEL file to candidate pathways (v2)

Created: 08/02/08 @ 14:17:23 | Last updated: 13/02/09 @ 11:29:54

Credits: User Paul Fisher User Saeedeh

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Microarray_cel_file_to_candidate_pathways_1844_2
This workflow takes in a CEL file and a normalisation method then returns a series of images/graphs which represent the same output obtained using the MADAT software package (MicroArray Data Analysis Tool) http://www.bioinf.manchester.ac.uk/MADAT/index.html. Also retruned by this workflow are a list of the top differentialy expressed genes (size dependant on the number specified as input - geneNumber), which are then used to find the candidate pathways which may be influencing the observed ch...

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Workflow Add Mesh String to Biological Process (v2)

Created: 03/10/07 @ 18:36:28 | Last updated: 03/12/09 @ 16:42:49

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

Add_mesh_string_to_biological_process_12549
This workflow is designed to add the following MeSH term to the end of a KEGG pathway name: AND "Metabolic Networks and Pathways" [MeSH Terms]   Example input for this service is as follows:   VEGF signaling pathway Hematopoietic cell lineage GnRH signaling pathway Type II diabetes mellitus  

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Workflow Perform a text based search through PubMed (v3)

Created: 03/10/07 @ 18:36:08 | Last updated: 03/12/09 @ 16:39:20

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

Perfrom_a_text_based_search_through_pubmed_2447_3
This workflow takes in a number of search terms in which to perform a search over the PubMed literature database. These search terms may be input as if entered in the web based version of PubMed. The output from this workflow is a list of PubMed identifiers in xml based format. Example input for this workflow is given as: 9215629

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Workflow Parse UniProt text file (v2)

Created: 03/10/07 @ 18:36:08 | Last updated: 03/12/09 @ 16:36:55

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

Parse_uniprot_text_file_9226
This workflow performs a search through the SRS linking system to find the text files for a particular UniProt identifier. This UniProt text file is then parsed to extract a small list to summarise the file, primarily consisting of external identifiers. Example input for this workflow is: O35613

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Workflow Perform a search through NCBI eUtils eSearch (v3)

Created: 03/10/07 @ 18:36:07 | Last updated: 03/12/09 @ 16:32:27

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

Perform_a_search_through_ncbi_eutils_esearch
This workflow takes in a search term and a database (e.g. snp, gene, protein) in which to perfom the search over. The result is an xml file containing summary information about the search term. Example input for this workflow are given below: database: pubmed terms: cancer AND diabetes

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Workflow BLAST using DDBJ service (v2)

Created: 03/10/07 @ 18:36:06 | Last updated: 03/12/09 @ 16:31:21

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

Blast_using_ddbj_service_29247
Perform a sequence similarity search using the BLAST algorithm through the DDBJ web service.   Example input for this service are given below. query: >MySequence MATDDSIIVLDDDDEDEAAAQPGPSNLPPNPASTGPGPGLSQQATGLSEPRVDGGSS NSGSRKCYKLDNEKLFEEFLELCKTETSDHPEVVPFLHKLQQRAQSVFLASAEFCNIL SRVLARSRKRPAKIYVYINELCTVLKAHSIKKKLNLAPAASTTSEASGPNPPTEPPSDLT NTENTASEASRTRGSRRQIQRLEQLLALYVAEIRRLQEKELDLSELDDPDSSYLQEAR LKRKLIRLFGRLCELKDCSSLTGRVIEQRIPYRGTRYPEVNRRIERLINKPGLDTFPDY GDVLRAVEKAATRHSLGLP...

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Workflow Simplify a BLAST text file (v2)

Created: 03/10/07 @ 18:36:06 | Last updated: 28/07/09 @ 13:01:46

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

Simpliy_a_blast_text_file_23463
This workflow simplifies a BLAST text file into identifiers, descriptions and values (P, E-values). In order to extract the relevant ids etc. you need to pass the relevant string into the corresponding port, e.g. the default port being used is gi. This has been passed "gi". For any other ports simply pass in the string the SAME as the port name, e.g. seq_id, p, per etc.

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Workflow BLASTP with simplified results returned (v2)

Created: 03/10/07 @ 18:36:06 | Last updated: 03/12/09 @ 16:28:51

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

Blastp_with_simplified_results_returned_28648
Perform a blastp search on protein sequence and extract information based on the user input, e.g. a list of GI numbers. N.B. this workflow does not function correctly as it is designed for use with NCBI blast scripts. Some errors may occur. Please use two blast text file inputs for a secure result output.   Example input for this service are given below. query: >MySequence MATDDSIIVLDDDDEDEAAAQPGPSNLPPNPASTGPGPGLSQQATGLSEPRVDGGSS NSGSRKCYKLDNEKLFEEFLELCKTETSDHPEVVPFLHKLQQRAQSV...

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Workflow Mouse Microarray Analysis (v3)

Created: 03/10/07 @ 18:36:05 | Last updated: 03/12/09 @ 16:20:34

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Pathways_from_diff_expressed_genes_22895_3
This workflow takes in probesets from and AffyMetrix micorarray experiment and returns: the genes ; gene start and end positions; chromosome where genes reside; ensembl trasncripts; SwissProt ids; affy probeset identifiers for chips Mouse430_2 and Mouse430a_2. Example ids from the Mouse430_2 affymetrix array are as follows (newline separated): 1447227_at 1440624_at 1436240_at 1454904_at 1435665_at 1418148_at 1429831_at

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Workflow Remove null values (v2)

Created: 03/10/07 @ 18:36:05 | Last updated: 13/11/07 @ 16:20:42

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

Remove_null_values_27982
This workflow removes any null values from a list of strings

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Workflow Back translate a protein sequence into a dna sequence (v2)

Created: 03/10/07 @ 18:36:03 | Last updated: 03/12/09 @ 16:18:44

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

Back_translate_a_protein_sequence_into_a_dna_sequence_19857
This workflow back translates a protein sequence into a DNA sequence. Example input for this workflow is: MATDDSIIVLDDDDEDEAAAQPGPSNLPPNPASTGPGPGLSQQATGLSEPRVDGGSSNSG SRKCYKLDNEKLFEEFLELCKTETSDHPEVVPFLHKLQQRAQSVFLASAEFCNILSRVLA RSRKRPAKIYVYINELCTVLKAHSIKKKLNLAPAASTTSEASGPNPPTEPPSDLTNTENT ASEASRTRGSRRQIQRLEQLLALYVAEIRRLQEKELDLSELDDPDSSYLQEARLKRKLIR LFGRLCELKDCSSLTGRVIEQRIPYRGTRYPEVNRRIERLINKPGLDTFPDYGDVLRAVE KAATRHSLGLPRQQLQLLAQDAFRDVGVRLQERRHLDLIYNFGCHLTDDYRPGVDPALSD PTLARRLRENRTLAM...

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Workflow Remove duplicate strings (v2)

Created: 03/10/07 @ 18:36:03 | Last updated: 13/11/07 @ 16:25:42

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

Remove_duplicate_strings_10375
This workflow takes in two list of strings and then concatenates them together. Any duplicates that are present are then removed, and the resulting file is returned back to the user.

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Workflow Pathways and Gene annotations for QTL region (v5)

Created: 03/10/07 @ 18:36:02 | Last updated: 20/11/09 @ 10:33:28

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Pathways_and_gene_annotations_forqtl_region
This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the mouse, Mus musculus. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG path...

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Workflow Entrez Gene to KEGG Pathway (v4)

Created: 03/10/07 @ 18:36:00 | Last updated: 04/12/09 @ 16:04:39

Credits: User Paul Fisher

License: Creative Commons Attribution 3.0 Unported License

Entrez_gene_to_kegg_pathway
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.

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Workflow Cow-Human Ortholog Pathways and Gene annotations for QTL Phenotype (v2)

Created: 03/10/07 @ 18:36:00 | Last updated: 03/12/09 @ 16:16:33

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

Pathways_and_gene_annotations_for_qtl_phenotype_25510
This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the cow, Bos taurus. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. As the Cow genome is currently unfinished, the workflow subsequently maps the cow ensembl gene ids to human orthologues. Entrez and UniProt identifiers are then identified...

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Workflow KEGG pathways common to both QTL and microarray based investigations (v3)

Created: 03/10/07 @ 18:35:58 | Last updated: 03/12/09 @ 15:28:50

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

Kegg_pathways_common_to_both_qtl_and_microarray_based_investigations
This workflow takes in two lists of KEGG pathway ids. These are designed to come from pathways found from genes in a QTL (Quantitative Trait Loci) region, and from pathways found from genes differentially expressed in a microarray study. By identifying the intersecting pathways from both studies, a more informative picture is obtained of the candidate processes involved in the expression of a phenotype.   Example input for this workflow is given below (as newline separated values). qt...

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Workflow Transcribe a DNA sequence into an RNA sequence (v2)

Created: 03/10/07 @ 18:35:58 | Last updated: 13/11/07 @ 16:16:54

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

Transcribe_a_dna_sequence_into_an_rna_sequence_27205
This workflow transcribes a DNA sequence into an RNA sequence

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Workflow HUMAN Microarray CEL file to candidate pathways (v4)

Created: 03/10/07 @ 18:35:55 | Last updated: 26/11/09 @ 17:34:25

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

Microarray_cel_file_to_candidate_pathways_17032_4
This workflow takes in a CEL file and a normalisation method then returns a series of images/graphs which represent the same output obtained using the MADAT software package (MicroArray Data Analysis Tool) [http://www.bioinf.manchester.ac.uk/MADAT/index.html]. Also returned by this workflow are a list of the top differentialy expressed genes (size dependant on the number specified as input - geneNumber), which are then used to find the candidate pathways which may be influencing the observed ...

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