Workflows

nested_echo (2)

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Just calls the echoer

Created: 2013-10-30 | Last updated: 2013-10-30

Download data from array express + create ... (1)

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This workflow uses the array express library to download data from the array express repository and creates two separate files. The gene expression and the phenotype files. The files are saved in the directory that the user has to specify in the input. NOTE: The library(ArrayExpress) is a prerequisite for this workflow

Created: 2013-11-04

Credits: Eleni

Get differentially expressed genes for Arr... (1)

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****IMPORTANT****:if libraries: library(ArrayExpress), library(hgu133a.db), library(limma) are not installed in the local R installation, then they need to be installed before running this workflow. Original data come from Hodges et. al 2006 "Regional and cellular gene expression changes in human Huntington’s disease brain" This workflow loads the two necessary files (gene expression data & phenotype data), and creates the expression set object to be used by the R package limma, to test for ...

Created: 2013-11-04

Credits: Eleni

Get differentially expressed genes for Arr... (1)

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****IMPORTANT****:if libraries: library(ArrayExpress), library(hgu133b.db), library(limma) are not installed in the local R installation, then they need to be installed before running this workflow. Original data come from Hodges et. al 2006 "Regional and cellular gene expression changes in human Huntington’s disease brain" This workflow loads the two necessary files (gene expression data & phenotype data), and creates the expression set object to be used by the R package limma, to test for ...

Created: 2013-11-04

Credits: Eleni

Map genes to chromosomal location (1)

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This workflow maps a gene list to the genome using the biomart service, and afterwards computes a promoter region for each gene. The user needs to define the promoter region to be computed. The direction that a gene is transcribed is being taken into account in the "compute_promoter_region_with_strand" component. The variable "strand" is responsible for that. NOTE: The library(biomaRt) is a prerequisite for this workflow

Created: 2013-11-04

Credits: Eleni

get promoter region + operate on genomic i... (1)

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Finds the overlap between two datasets which contain genomic information (e.g. [gene id], chromosome name, gene start, gene end), plus some statistics. Returns rows of file_1 which overlap with the second file. A kolmogorov smirnov test is applied between the list that overlaps and the one that does not. NOTE: The library(GenomicRanges) is a prerequisite for this workflow

Created: 2013-11-04

Credits: Eleni

Map genes to chromosomal location for T2WEB (1)

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This workflow maps a gene list on the genome using the biomart service. IMPORTANT NOTE: Keep in mind that for uploading files on t2web, you need to wait few minutes before executing the workflow. That's essential because the file needs first to be uploaded on the server.

Created: 2013-11-04

Credits: Eleni

MatchboxHadoopAPI (1)

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The workflow MatchboxHadoopApi.t2flow enables using of matchbox tool on Hadoop with Taverna. This workflow is based on Python scripts and Hadoop Streaming API included in"pythonwf" folder of pc-qa-matchbox project on github (https://github.com/openplanets/scape/tree/master/pc-qa-matchbox/hadoop/pythonwf).For this workflow we assume that digital collection is located on HDFS and we have a list of input files in format "hdfs:///user/training/collection/00000032.jp2" - one ro...

Created: 2013-11-05

Credits: Roman SCAPE

Imagemagick convert - tiff2tiff - compression (1)

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Converts tiff to tiff using imagemagick convert with the provided compression

Created: 2013-11-08

Credits: Markus Plangg

pubmed abstracts from pathways (1)

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Extraction of the abstracts from pubmed pubblications related to the pathways involving the input genes

Created: 2014-02-28

Credits: Massimo La Rosa Antonino Fiannaca

Attributions: NCBI Gi to Kegg Pathway Descriptions Pathway to Pubmed

ToMaR HDFS Input Directory Processing (2)

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This workflow allows processing an HDFS input directory using ToMaR. The "hdfs_working_dir" input port is the HDFS input directory which containes the data to be processed by ToMaR. The "toolspec" input port contains the toolspec XML describing operations that can be used (see "operation" input port). The "operation" input port defines the operation to be used in the current ToMaR job execution (see "toolspec" input port, an operation port used here must be defined in the tool specificatio...

Created: 2014-03-04 | Last updated: 2014-03-11

Credits: Sven

ARC2WARC Hadoop Job (1)

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Just a wrapper workflow for a Hadoop job converting ARC to WARC files.

Created: 2014-03-06

Credits: Sven

Hello World (1)

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One of the simplest workflows possible. No workflow input ports, a single workflow output port "greeting", outputting "Hello, world!" as produced by the String Constant "hello".

Created: 2014-03-06

test_workflow (2)

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test_upload

Created: 2014-03-10 | Last updated: 2014-03-10

XPath From VOTable (1)

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A XPath From text version for VOTables. This is useful to extract certain information from the header of the VOTables but it could work for any XPath.

Created: 2014-03-12

Credits: David PS Anja Le Blanc

Attributions: Extracting data from VOTable format by using XPath query

calculateCube by SINP (3)

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Workflow for Taverna based on the IMPEx-FP7 method calculateCube. This calculates a 3DCube based on the paraboloid model of SINP around Earth (see http://smdc.sinp.msu.ru/index.py?nav=paraboloid/index).

Created: 2014-03-28 | Last updated: 2014-05-19

calculateDataPointValue by SINP (3)

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Workflow for Taverna based on the IMPEx-FP7 method calculateDataPointValue. This method can be used to return the magnetic field (calculated by SINP PMM) in given points inside the planetary magnetosphere and in different time moments for each point.

Created: 2014-03-28 | Last updated: 2014-05-20

calculateDataPointValueMercury by SINP (6)

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Workflow for Taverna based on the IMPEx-FP7 method calculateDataPointValueMercury. This method can be used to return the magnetic field (calculated by SINP PMM) in given points inside the Hermean magnetosphere.

Created: 2014-03-28 | Last updated: 2014-05-19

Credits: Manuel Scherf

An iframe test (1)

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But this works

Created: 2014-03-28

Credits: Alan Williams

calculateCubeMercury by SINP (3)

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Workflow for Taverna based on the IMPEx-FP7 method calculateCubeMercury. This method returns the magnetic field, calculated by SINP PMM, in grid points of a cube with chosen boundaries inside the Hermean magnetosphere with chosen sampling.

Created: 2014-03-31 | Last updated: 2014-05-19

getDataPointValue by FMI (3)

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Workflow for Taverna based on the IMPEx-FP7 method getDataPointValue. This method is used to compute values of various physical quantitites (e.g. density, magnetic field strengths etc.) for a given simulation run at a user given set of 3D points.

Created: 2014-03-31 | Last updated: 2014-05-19

getDataPointValue by LATMOS (5)

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Workflow for Taverna based on the IMPEx-FP7 method getDataPointValue. This is a generic method which can be used to return parameters for 0D, 1D, 2D, or 3D.

Created: 2014-03-31 | Last updated: 2014-05-19