Workflows

Ajusting galaxy paramenters using sextractor (5)

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This workflow creates configuration files for sextractor, it runs sextractor using this configuration files, it adds sextractor results to the input votable and adds new calculated columns. This task requires a votable as input, a template, a vocabulary and the specification of the column names that contain some required files (configuration files, image files, ...). These files must be accesible from taverna. Sextractor is called by an bash script as 'sex'. Every row in the votable cotains ...

Created: 2012-07-26 | Last updated: 2012-09-07

Credits: Julian Garrido

Attributions: Create configuration files from a template and a votable Run sextractor using a votable Create votable from sextractor results Add columns to a votable resulting from executing sextractor.

Run galfit using a votable (2)

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It runs galfit and adjust the paramenters specified. This workflow has a dependency on the stil library (http://www.star.bris.ac.uk/~mbt/stil/). Galfit is called by a bash script as 'galfit'. Galfit is called for every row in the votable. Columns where the result file name and the configuration file name are defined must be especified. These files should be accesibles from taverna. ExperimentFolder provides the root folder for the experiment. If the configuration files contain references to o...

Created: 2012-07-26 | Last updated: 2012-09-07

Credits: Julian Garrido

Create votable from galfit results (4)

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The workflow creates a votable from the results provided by galfit. It returns this table and an aditional table that is joined to the input table. It requires a votable that contains a column with the file name resulting from running galfit and such files must be accesible from taverna. It uses astrotaverna plugin (http://wf4ever.github.com/astrotaverna/) and it has a dependency on stil library (http://www.star.bris.ac.uk/~mbt/stil/).

Created: 2012-07-26 | Last updated: 2012-09-07

Credits: Julian Garrido

Create galfit configuration files with par... (1)

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This workflow creates galfit configuration files using a partition criteria. The resulting configuration files are different depending on whether the galaxy has o doesn't have a bar. They are created (one for every row in the votable) using a template whose keys are replaced by data from a votable. Keys must appear also in the vocabulary file and match column names in the votable. A column in the votable must contain the name of the result configuration file. This workflow uses astrotaverna ...

Created: 2012-07-26 | Last updated: 2012-07-26

Credits: Julian Garrido

Adjusting galaxy parameters using galfit (4)

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This workflow creates galfit configuration files using data from a votable, it runs galfit, its results is added to the votable, it creates new config files for galfit using the previous results, it runs galfit a second time considering galaxies that have and do not have bars in order to adjust the objective parameters and it finally includes the results into the votable. It requires the specification of the columns that contain file names (these files should be accesibles from taverna). If t...

Created: 2012-07-26 | Last updated: 2012-09-07

Credits: Julian Garrido

Attributions: Create configuration files from a template and a votable Run galfit using a votable Create votable from galfit results Create votable from different galfit paramenter adjustments Create galfit configuration files with partition criteria using votable

Check the content of the Registry for mism... (1)

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This workflow check for tables which are registered in the HELIO registry but not available in the HFC and for tables which are in the UOC but which are not registred.

Created: 2012-07-26

Credits: Anja Le Blanc

Extract SDSS field information and PSF (5)

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This workflow gathers information needed by the execution of Sextractor, Galfit and Ellipse, from the SDSS VO service. It receives two inputs: 1) An ascii table with information about the image such as data of the field, name of the fits file or if it is barred or not. 2) A configuration file with the paths where the files needed by the workflow can be found and other paths where to store the files generated by the workflow This workflow extracts the band from the image header, and the info...

Created: 2012-07-26 | Last updated: 2012-09-07

Credits: Susana

Genome variant to Protein change (1)

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Reports protein change, given a genomic variant, using mutalyzer

Created: 2012-07-27 | Last updated: 2012-10-29

Credits: Helen Hulme

Find Duplicates using Matchbox command lin... (1)

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The workflow takes a list of digital documents as input, extracts SIFT features using image processing algorithms, creates dictionary of visual words, generates BoW (Bag of Words) histogramms and finds duplicates. The count of parallel threads can be passed as a parameter. Finally search results are stored in a text file that contains a list of possible duplicates with associated similarity score. This score values are spread between 0 (low similarity) and 1 (high similarity). Image compariso...

Created: 2012-07-31 | Last updated: 2012-07-31

Credits: Roman

Plasma Precipitation Analysis (1)

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ABOUT THE WORKFLOW This workflow was used to analyze the data in a manuscript by Mostovenko et al. (2012, submitted), comparing proteins in the precipitate with those left in solution after organic solvent precipitation. However, the workflow is generally applicable in comparisons of any binary fractionation method in proteomics, where the fractions are analyzed by liquid chromatography-tandem mass spectrometry. The workflow identifies proteins by SpectraST spectral library search and X!Ta...

Created: 2012-07-31 | Last updated: 2012-07-31

Credits: Magnus Palmblad Kate Mostovenko Yassene

de Bruin et al. Workflow 1 (1)

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This is "Workflow 1" from de Bruin et al., Mol. Cell. Proteomics 2012.

Created: 2012-08-01 | Last updated: 2012-08-01

Credits: Magnus Palmblad

de Bruin et al. Workflow 2 (1)

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This is "Workflow 2" from de Bruin et al., Mol. Cell. Proteomics 2012.

Created: 2012-08-01 | Last updated: 2012-08-01

Credits: Magnus Palmblad

de Bruin et al. Workflow 3 (1)

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This is "Workflow 3" from de Bruin et al., Mol. Cell. Proteomics 2012.

Created: 2012-08-01 | Last updated: 2012-08-01

Credits: Magnus Palmblad

de Bruin et al. Workflow 4 (1)

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This is "Workflow 4" from de Bruin et al., Mol. Cell. Proteomics 2012.

Created: 2012-08-01 | Last updated: 2012-08-01

Credits: Magnus Palmblad

Gene_To_Pathways (1)

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 This workflow identifier the pathways that are associated with given Kegg gene identifiers. Example inputs that can be used to run the workflow are eco:b0002, eco:b0078

Created: 2012-08-06 | Last updated: 2012-09-07

Credits: Khalid Belhajjame Stian Soiland-Reyes

Attributions: Hello Anyone

Run scripts from a column in a votable (2)

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It runs scripts whose pathname are values of a column in a votable

Created: 2012-08-07 | Last updated: 2012-09-07

Credits: Julian Garrido

Create votable from ellipse results (2)

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The workflow takes from a votable the names of files where the ellipse result is stored. These files contain data for several ellipses and the workflow takes the center from the inner ellipse and the ellipticitiy from one of the outter ones. It uses astrotaverna plugin (http://wf4ever.github.com/astrotaverna/).

Created: 2012-08-07 | Last updated: 2012-09-07

Credits: Julian Garrido

Calculate ellipses that describe a galaxy ... (2)

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This workflow calculates the ellipses that better match a galaxy by doing two iterations. In the first one the center and the outer ellipse are aproximated because there might be bars that affect to the inner ellipses. In the second one, files with the ellipse data are built. It creates ellipse scripts using data from a votable, it runs ellipse, its results are added to the votable, it creates new scripts for ellipse using the previous results, it runs ellipse a second time and it finally in...

Created: 2012-08-07 | Last updated: 2012-09-11

Credits: Julian Garrido

Attributions: Create configuration files from a template and a votable Run scripts from a column in a votable Create votable from ellipse results Detect ellipse failures and get votable without ellipse failures

Hadoop hOCR parser (1)

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Big data processing: chaining Hadoop jobs using Taverna. This workflow demonstrates a simple way of linking different hadoop job components using the standard output of the hadoop jobs. It is not for thought for productive use, but for demonstration using small data sets. The code for the hadoop jobs is available on Github: tb-lsdr-hocrparser and tb-lsdr-seqfilecreator.

Created: 2012-08-07 | Last updated: 2012-08-07

Credits: Sven

Delete this (1)

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No description

Created: 2012-08-08

Credits: Wotan

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