Workflows

Oryza Sativa QTLs and genes retrieval from... (2)

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For a given trait and QTL maximum size, retrieve accession numbers of the QTLs along with their mapping positions in Oryza sativa and retrieve genes present in the mapping genomic interval of a given QTL. Data integration from TropGene, Gramene and Ensembl relational databases. Semi-automatic creation of 7 Semantic Web Services for TropGene and Gramene with BioSemantic Use of BioMart Web Services for Ensembl interrogation

Created: 2012-08-08 | Last updated: 2012-09-28

Credits: Julien wollbrett

Convert a list into a VO Column (2)

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This workflow converts a list of values into a VO table with only one column. It receives two inputs: the list of values and the header name of the column to be built.

Created: 2012-08-13 | Last updated: 2013-03-08

Credits: Susana

Joining VOtables with information to execu... (3)

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This workflow join 13 votables, obtained from the workflow "Extract SDSS field information and PSF" in order to get a only one votable with all the information. Also it adds the columns "zp", "magzeropoint", xconvsize, yconvsize that are calculated from values provided in the inputs. The zp is -( aa + kk * airmass ), the magzeropoint is zp + 2.5 * log10(53.907456), the xconvsize is roundUp(nx/10) and the yconvsize is roundUp(ny/10)

Created: 2012-08-13 | Last updated: 2013-03-08

Credits: Susana

Gathering info from SDSS into a VOTable to... (4)

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This workflow joins two main nested workflows: - "Extract SDSS field information and PSF" workflow, which gathers information from SDSS VO service and from the header image in several VOtable. It also generates the psf files. - "Joining VOtables with information to execute Sextractor, Galfit and Ellipse" workflow, which joins the VOtables generated by the previous workflow to get only one VOtable with all the information

Created: 2012-08-13 | Last updated: 2013-03-08

Credits: Susana

KEGG:Pathway Scheme (2)

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The purpose of the workflow is to determine all the genes operating in the pathways that the input metabolite participates in. The overall idea is to generate a set of genes that potentially influence the levels of a metabolite due to the common pathways that they share.

Created: 2012-08-14 | Last updated: 2013-08-27

Credits: Harish Dharuri

Hadoop Large Document Collection Data Prep... (1)

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Workflow for preparing large document collections for data analysis. Different types of hadoop jobs (Hadoop-Streaming-API, Hadoop Map/Reduce, and Hive) are used for specific purposes. The *PathCreator components create text files with absolute file paths using the unix command 'find'. The workflow then uses 1) a Hadoop Streaming API component (HadoopStreamingExiftoolRead) based on a bash script for reading image metadata using Exiftool, 2) the Map/Reduce component (HadoopHocrAvBlockWidthMapR...

Created: 2012-08-17 | Last updated: 2012-08-18

Credits: Sven

Blast_Align_and_Tree (2)

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This workflow accepts a protein sequence as input. This sequence is compared to others in the Uniprot database, using the NCBI BLAST Web Service from the EBI (WSDL), and the top 10 hits are returned (Nested workflow:EBI_NCBI_BLast). For each extracted hit, the Uniprot REST service returns the protein sequence in FASTA format. The workflow concatenates the 10 protein sequences and submits them as input to the EBI CLustalw service (Nested workflow EMBL_EBI_clustalw2_SOAP). These sequences are ...

Created: 2013-01-28 | Last updated: 2013-01-30

Credits: Katy Wolstencroft Hamish McWilliam

Attributions: Protein_search_fetch_align_tree

clustal_phylogeny (3)

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This workflow accepts a ClustalW protein sequence alignment and produces a phylogenetic tree, using the EBI clustalw_phylogeny web service, which implements phylip.

Created: 2013-01-28 | Last updated: 2013-03-11

Credits: Katy Wolstencroft

Blast_and_Interproscan (5)

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This workflow performs an NCBI blast at the EBI. It accepts a protein sequence as input. Default values have been set for the search database (Uniprot), the number of hits to return (10), and all scoring and matrix options. These can be changed in the workflow by altering the string constant values if required. The sequences for the top 10 hits are retrieved from the UniProt database and analysed using InterproScan (also from the EBI) to determine functional domains and motifs in each sequenc...

Created: 2013-01-28 | Last updated: 2013-01-30

Credits: Katy Wolstencroft

InterproScan_Example (3)

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This workflow performs an interproscan at the EBI on sequences provided as input. The output is provided as text, xml or png. This workflow uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished.

Created: 2013-01-28 | Last updated: 2013-01-30

Credits: Katy Wolstencroft