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

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

ROC_AUC_Workflow (1)

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This small workflow extracts the area under the curve (AUC) from the receiver operating characteristic (ROC) curve for all charge states analyzed by PeptideProphet. This measure can be used to compare the sensitivity and specificity of different search engines for matching tandem mass spectra to peptides.

Created: 2013-01-28

Credits: Magnus Palmblad

Mining the Kegg pathway database with the ... (1)

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Genome-Wide Association studies (GWAS) with metabolomic phenotypes yield several statistically significant SNP-metabolite associations. To understand the biological basis of the association, scientists typically dwell on identifying genes in the vicinity of the SNP and the possible pathways that the gene participates in. The information needed to arrive at an understanding of the mechanistic basis of the association requires integration of disparate data sources. The purpose of this workflow ...

Created: 2013-01-30

Credits: Marco Roos

Match concept profiles with predefined set (2)

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Purpose of workflow: The workflow can be used to match a set of concept profiles with predefined set of concept profiles. Result: A list of concepts ordered by their match to the query concept profiles.

Created: 2013-02-05 | Last updated: 2014-07-14

Credits: Kristina Hettne Marco Roos Reinout van Schouwen BioSemantics

Annotate a gene list with disease concepts (1)

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Purpose: Currently, this workflow takes a list of genes and a concept set as input, calculates the matching score between these and finds the concept that contributes the most to the match. Author comments: The workflow is in Beta stage. It runs, but needs more testing with different parameter settings. This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/368 for functional gene annotation and knowledge discovery.

Created: 2013-02-06

Credits: Kristina Hettne Reinout van Schouwen Marco Roos BioSemantics

Attributions: SNPs to Concept Set through Concept Profile Matching v2

JP2 to TIFF file format migration with qua... (1)

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This workflow reads a textfile containing absolute paths to JP2 image files and converts them to TIFF image files using Kakadu's j2k_to_image command line application (http://www.kakadusoftware.com). Based on the input text file, the workflow creates a Taverna list to be processed file by file. A temporary directory is created (createtmpdir) where the migrated image files and some temporary tool outputs are stored. Before converting the files, the JP2 input files are validated using the SC...

Created: 2013-02-07

Credits: Sven

workflow to test Rshell (for internal purp... (1)

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 This is a workflow to test if Rserve is working properly, for internal purposes.  Takes as input two integers. output is the sum of integer 1 and integer 2  

Created: 2013-01-21 | Last updated: 2013-03-11

Credits: Eleni

GET statuses/home_timeline | Twitter (1)

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Returns a collection of the most recent tweets and retweets posted by the authenticating user and the users they follow. Uses the OAuth plugin for Taverna Workbench.

Created: 2013-01-22

Credits: Mark Borkum

Migration ffmpeg audio to wav pcm_s32le (1)

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Converts audio to wav using ffmpeg with codec pcm_s32le

Created: 2013-01-24

Credits: Markus Plangg

Author Publications and Citations by Year ... (1)

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This workflow demonstrates how to connect to and use Europe PMC (http://europepmc.org/RestfulWebService) to count the number of publications and citations per year for one author. Two Web service calls are made. First, we searchPublications to retrieve the bibliographic records for all published work of a single author. Then, we getCitations to extract the year of all articles citing the work of this author. The pubYear fields is extracted from the raw Web service results and fed to an Rshel...

Created: 2015-12-04

Credits: Magnus Palmblad

Trans-proteomic-pipeline like ('TTPish') w... (2)

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No description

Created: 2015-12-10 | Last updated: 2016-09-29

Credits: Robert Winkler

TTPish workflow for MASSyPup64 with text s... (1)

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This proteomics workflow performs a comet search and subsequently a validation of the results with PeptideProphet/Protein Prophet. Results are exported in various formats, to facilitate the downstream evaluation in other programs and the sharing of data (EXCEL, csv, mzIdentML).Contrary to a standard Trans-Proteomic-Pipeline (TPP) installation, the workflow can be to mass spectrometry data in whatever localization (i.e. the files do not have to be uploaded/ copied to a special directory).The w...

Created: 2015-12-10

Credits: Robert Winkler

Get similar phenotypes for a disease and a... (1)

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This workflow retrieves the similar phenotypes between a disease and a gene based on the Monarch services at http://monarchinitiative.org/page/services. Phenotype similarity is calculated based on OwlSim, see http://owlsim.org.

Created: 2016-02-22

Credits: Kristina Hettne

Get targets for compound (1)

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This workflow retrieves single protein targets for a compound from open PHACTS.

Created: 2016-02-22

Credits: Kristina Hettne Eelke van der Horst Aylin Metzner

Hello abcd (1)

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Example of using the same inserted nested workflow twice, iterating over it twice, which should mean 4 distinct calls to the inner "concatenate" process. This workflow is mainly useful for provenance testing purposes.

Created: 2016-03-15

Credits: Stian Soiland-Reyes

Extract taverna server run id and pass to ... (1)

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No description

Created: 2016-04-21

Credits: Stian Soiland-Reyes Alan Williams

ASTM D0427-04 - Preliminary Workflow (1)

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ASTM D0427-04: Standard Test Method for Shrinkage Factors of Soils by the Mercury MethodThis a preliminary version of a ASTM D0427 Workflow. This seems like a complex workflow but it does not. A lot of services is because I'm using a basic calculator web service to do simple a math calculations (http://www.dneonline.com/calculator.asmx) This simple web service calc use only two operands to do calc in four basic operations (add, divide, multiply and substract). So it's needed intermedi...

Created: 2016-04-25

Credits: Juan Felipe Muñoz Fernández