showDatasetsGenomic

Created: 2013-10-07 15:37:03

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Shows all the datasets available in the Nencki Genomics Database (www.nencki-genomics.org). Click 'Use examples' to see all the datasets, separated into datasets of TFBS motifs, and all the remaining datasets (areas), the latter including data from Ensembl funcgen and (thus) Encode.

Publication doi: 10.1093/database/bat069

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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (4)

Name	Description
password	Password. Click 'Set value' to use the default null value (xsi:nil) for the user 'public'.
species_short	One of: hsap, mmus, rnor.
user	NGD user name. Click 'Set value' to use the default user 'public'.
version	A valid version of the Nencki Genomic Database.

Processors (4)

Name	Type	Description
ShowDataset_2	xmlsplitter
2_authenticate	xmlsplitter
ShowDataset_3	wsdl	Wsdl http://webservices.nencki-genomics.org/genomic?wsdl Wsdl Operation ShowDataset
ShowDataset_3_ShowDatasetResponse	xmlsplitter

Beanshells (0)

Outputs (2)

Name	Description
area_datasets
motif_datasets

Datalinks (9)

Source	Sink
2_authenticate:output	ShowDataset_2:authenticate
password	2_authenticate:password
species_short	2_authenticate:species
user	2_authenticate:username
version	2_authenticate:version
ShowDataset_2:output	ShowDataset_3:ShowDataset
ShowDataset_3:ShowDatasetResponse	ShowDataset_3_ShowDatasetResponse:input
ShowDataset_3_ShowDatasetResponse:ShowDatasetResult0	area_datasets
ShowDataset_3_ShowDatasetResponse:ShowDatasetResult1	motif_datasets

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Information Workflow Type

Taverna 2

Information Uploader

mdabr

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Information Version 1 (of 1)

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mdabr

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Information Statistics

801 viewings

702 downloads

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Citations (1)

1. Izabella Krystkowiak; Jakub Lenart; Konrad Debski; Piotr Kuterba; Michal Petas; Bozena Kaminska; Michal Dabrowski, Nencki Genomics Database--Ensembl funcgen enhanced with intersections, user data and genome-wide TFBS motifs, Database 2013; doi: 10.1093/database/bat069, 02 October 2013, http://database.oxfordjournals.org/cgi/content/full/bat069? ijkey=ml5GxAmJmA0S7wS&keytype=ref

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showDatasetsGenomic

Created by mdabr on Monday 07 October 2013 15:37:03 (UTC)

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Other workflows that use similar services (1)

Taverna 2

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mdabr

plotGenomic (1)

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This workflow returns a graphical representation of selected Nencki Genomics Database (www.nencki-genomics.org) content in the ± 10 kb flank of the transcription start site of a chosen gene. More precisely, it returns instances of selected area types, and instances of selected motif types that intersect any of the returned area instances. The results are returned as three files: a pdf file with the plot, and two tab-separated files with the details of areas and motifs shown in the plot. P...

Created: 2013-10-07

Credits: mdabr

showDatasetsGenomic

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Workflow Components

Wsdl

Wsdl Operation

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