myExperiment - Workflows

Taverna 2

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Paul Fisher

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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

Created: 2010-03-10 | Last updated: 2010-03-10

Credits: Paul Fisher

Taverna 2

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Wicker

OpenTox Get Algorithms on TUM server (6)

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Get URIs of all available algorithms on TUM server

Created: 2010-05-11 | Last updated: 2011-05-11

Taverna 2

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Wicker

OpenTox Apply Algorithm (7)

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Apply an OpenTox algorithm

Created: 2010-05-11 | Last updated: 2011-05-11

Taverna 2

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Wicker

OpenTox Apply Model On Dataset (3)

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Apply a model to predict a dataset

Created: 2010-05-11 | Last updated: 2010-05-11

Taverna 2

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Wicker

OpenTox Handle Task (8)

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Waits for a task to be finished and returns resulting URI

Created: 2010-05-18

Taverna 2

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Wicker

OpenTox Get Datasets (3)

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Gets a list of available data set URIs

Created: 2010-05-11

Taverna 2

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Jannetta

Kegg pathway diagrams (1)

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Find pathways in which all the genes in the list are involved. For each pathway draw the pathway diagram.for each protein draw a diagram of the Kegg pathway that its protein is involved in and where available visualise the structures

Created: 2010-03-13

Credits: Jannetta

Taverna 2

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Jannetta

Kegg pathway diagrams (3)

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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 - ...

Created: 2010-03-19 | Last updated: 2010-03-19

Taverna 2

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Gregg Iceton

Compare two genomes for similarity (4)

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This workflow takes the file path to two genome nucleotide files in fasta format and requests a minimum similarity required from the user. The genomes are aligned according to the M-GCAT algorithm (http://alggen.lsi.upc.es/recerca/align/mgcat/intro-mgcat.html) and the genome similarity parsed out of the resultant log file. Output is either 0 (genome similarity less than required similarity) or 1 (genome similarity equal to or greater than the required similarity). NB - The file p...

Created: 2010-03-17 | Last updated: 2010-03-17

Credits: Gregg Iceton

Taverna 2

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Peter Li

Calculating frequencies of gene expression... (1)

This workflow retrieves data from the MaxD microarray database and calculates the frequencies of gene expression levels using an R script

Created: 2010-03-15

Credits: Peter Li

Taverna 2

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abretaud

Cross-references search, duplicated genes ... (1)

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This workflow is composed of 3 steps: -First, it search for Ensembl gene Ids matching a list of identifier, using the GenOuest Xref webservice. -Then it uses the Duplicated Genes Database webservice to search for duplication information about each found gene. -Finally, it uses the GenOuest Xref webservice to fetch external identifier for each found gene (GO term in this example).

Created: 2010-03-16 | Last updated: 2010-03-16

Credits: abretaud

Taverna 2

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Paul Fisher

[untitled] (1)

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No description

Created: 2010-03-16

Credits: Paul Fisher

Taverna 2

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White duncan100

Split multi-sequence FASTA file into list (1)

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Splits a flat file containing multiple fasta sequences into a list of fasta sequences.

Created: 2010-03-16

Taverna 2

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Paul Fisher

microRNA to KEGG Pathways and Abstracts (1)

Workflow takes in a text file of microRNAs from microCOSM (at the EBI) and outputs a list of KEGG pathway information, including genes in pathways and pathway abstracts from PubMed. The results can then be used in various text mining applications/workflows to rank the results against a given disease.Workflow takes in a file of microRNAs