Workflows

Spreadsheet Import Example (1)

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Example using the SpreadsheetImport service to import data from an Excel spreadsheet. The workflow imports the file spreadsheet file WaterUse.xlsx and generates a graph from the date. The source data is from http://data.gov.uk/

Created: 2012-04-05

Credits: Alan Williams

Unix tool service using string replacement (1)

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The tool service outputs a message that greets using the names specified on Greet's input ports.

Created: 2012-04-05

Credits: Alan Williams

Create and execute a simulation on the RIS... (1)

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Create and execute a simulation on the RISE server. This workflow take 3 inputs: the XML to configure the RISE framework, the URL of the ZIP file model (a zipped directory containing the model files), and the new framework name. This workflow produce on the output the simulation LOG file.

Created: 2012-04-09

Pathways and Gene annotations forQTL region (1)

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This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the mouse, Mus musculus. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG path...

Created: 2012-01-20 | Last updated: 2012-01-20

Credits: Bonilla

A heuristic measure for detecting undesire... (2)

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The workflow takes TIFF image instances as input, applies a list of JP2 compression parameter values, executes OCR using an open source OCR engine, evaluates the results, and creates a diagram visualising the results. Dependencies on external tools for the tool service components: Tesseract ImageMagick Kakadu Gnuplot Dependencies on external Java libraries of beanshells: Apache commons lang

Created: 2012-02-06 | Last updated: 2012-03-09

Credits: Sven

Explain concept scores (7)

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Purpose of workflow: This workflow takes two concept ids as input and returns the top ranking "B" concepts according to Swanson's ABC model of discovery, where the relationships AB and BC are known and reported in the literature, and the implicit relationship AC is a putative new discovery. It might also be the case that AC is already known. In that case AC does not represent a new discovery but will still be returned (see workflow example values). The B concepts are returned sorted on the pe...

Created: 2012-02-07 | Last updated: 2014-07-14

Credits: Reinout van Schouwen

Define Associated Regions and Genes (2)

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Defines regions and genes from associated SNPs A JAVA MySQL connector is required to run the workflow and must be placed in the $TAVERNA_HOME/lib directory.

Created: 2012-02-08 | Last updated: 2012-05-09

Credits: Paul martin

Migration Imagemagick convert no compression (2)

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Converts an image using imagemagick convert -compress None

Created: 2013-02-25 | Last updated: 2013-02-26

Credits: Kraxner Markus Plangg

Attributions:

Test RShell (1)

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workflow hacked to include empty username and password elements

Created: 2013-02-27

Credits: Reinout van Schouwen Eleni

Attributions: workflow to test Rshell (for internal purposes)

Calculate_Isotopic_Distribution (1)

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This small workflow takes as input a peptide sequence and calculates the elemental composition of the peptide (Calculate_Elemental_Composition). This is then transferred as a numerical vector to the Rshell Calculate_Isotopic_Distribution, that calculates the (integer mass) isotopic distribution using the FFT method. To shift to approximate real masses (or m/z values), transpose the distribution with the difference between the integer and real monoisotopic masses (both easily calculated using ...

Created: 2013-03-05

Credits: Magnus Palmblad

Visualize PAV provenance as SVG (2)

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VoID descriptions are fetched as Turtle, cleaned up to be valid OWL ontology and include useful labels, processed through the OWL reasoner Pellet; this adds inferred PROV statements to the RDF, which is then fed to the PROV Toolbox, generating an SVG visualization of the provenance. Note that this workflow downloads CWM, Pellet and ProvToolbox on demand, and uses UNIX command line tools like wget and md5 which are unlikely to work in Windows. This workflow has been tested on Ubuntu 12.10 wit...

Created: 2013-03-05 | Last updated: 2013-04-05

Credits: Stian Soiland-Reyes

First Taverna workflow (1)

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No description

Created: 2013-03-06

Credits: Prasundutta87

imagemagick-convert-tiff2tiff-compression (1)

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Migration of tiff2tiff with compression action

Created: 2013-03-06 | Last updated: 2013-03-06

Three Microbase responders used for the Id... (1)

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Three microbase responders are used to take .sff data from IonTorrent and report on the organisms present within the data. It also takes three JSON input messages. The first calls sff_extract python script, the next calls MIRA or Ray and the final responder calls BLAST. For more information including a user manual visit www.bioinformatix.co.uk

Created: 2013-03-07

Credits: Team A

Metabolic profiling from NCBI GIs (1)

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This workflow will take NCBI GIs and produce the following output: KEGG identifier corresponding to the NCBI GI Information about the gene corresponding to the NCBI GI Pathway IDs corresponding to the the KEGG identifier Images of the pathways that the proteins defined by the NCBI GIs are involved in.

Created: 2013-03-08

Credits: Team A

Identification of Virulence Factors from a... (1)

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 This workflow takes a user specified genomic sequence and, via BLAST, queries a database containing genomic sequences of virulence factors. The database and genome sequence must be held locally. A python script is associated with this workflow and should be downloaded from www.bioinformatix.co.uk. A user and maintenance manual relating to this workflow can be found at www.bioinformatix.co.uk and should be consulted before this workflow is utilised.

Created: 2013-03-08

Credits: Team A

Antibiotic resistance profiling (1)

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 A workflow that takes a user defined genomic sequence and queries a third party database of genes encoding antibiotic resistance through a BLAST search for matching sequences. The accession IDs from the matches are extracted and the Entrez webservice is used to retrieve genbank records for the antibiotic resistance genes found. A python script is essential in the functioning of this workflow and this can be found at www.bioinformatix.co.uk along with a user and maintenance manual whic...

Created: 2013-03-08

Credits: Team A

Microbase S3CMD and AWS Workflow to Analys... (1)

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 This workflow is designed to interact with the aws and a specific VM, to carry out commands and analsye next gen sequence data (SFF FASTQ)

Created: 2013-03-08

Credits: ROBSeq Tech. Ltd.

Extract a column from a VOTable into a List (3)

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Snippet showing how to use AstroTaverna tool for extracting a column from a VOTable into a single List.

Created: 2013-03-08 | Last updated: 2013-04-22

Credits: Julian Garrido Susana

Simulate_Mass_Spectrum (1)

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This workflow takes as input a peptide sequence and calculates the elemental composition of the peptide (Calculate_Elemental_Composition). This is then transferred as a numerical vector to the Rshell Simulate_Mass_Spectrum, that calculates the isotopic distribution using the FFT method and convolutes the theoretical (infinite resolution) distribution with a Gaussian peak shape. The building blocks can be used in any other workflows using the isotopic distribution of peptides or other molecul...

Created: 2013-03-12

Credits: Magnus Palmblad

Untitled (1)

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Initial version

Created: 2013-03-15

Untitled (1)

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Initial version

Created: 2013-03-15

Untitled (1)

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2

Created: 2013-03-15

Untitled (1)

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v2

Created: 2013-03-15

retrive dpas data for all ics instruments ... (2)

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No description

Created: 2013-03-20 | Last updated: 2013-03-21

Credits: Nadia Cerezo

Attributions: retrive dpas data for all ics instruments for HEC event data

Find data from a list of instruments and a... (1)

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For a certain time range, it looks for flares between a energy range (GOES x-ray flare class), and it provides the observations for such time range for the list of instruments asked. It also provides the table of flares with its properties. Note: This workflow does not look whether the instrument was not looking to the right field of view (eg., CDS)

Created: 2013-03-20

Credits: David PS Anja Le Blanc Nadia Cerezo Gab

Attributions: find events in xray and radio

Monthly counts for event occurences betwee... (1)

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This workflow provides monthly counts of events in HEC between the beginning of year_start and the end of year_end. Returns the result as comma separated file (csv) and as list of lists.

Created: 2013-03-21

Credits: Nadia Cerezo Anja Le Blanc David PS

Attributions: Monthly counts for event occurences between beginning of year_start and end of year_end

When do the Fastest type II CME should be ... (1)

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The fastest CME is found from an interval of time, and propagated to Earth, in two steps, first to obtain the Solar wind speed at Earth and then propagated again with a more reasonable CME speed. The output produces Min-Max ETAs for each object in the heliosphere and the plots of the final propagation model. This Workflow was produced as one of the challenges in the HELIO CDAW-IV hosted at TCD

Created: 2013-03-21

Credits: Gab Anja Le Blanc David PS

Attributions: When did the fastest type II CME happened?

Comparison of Peptide and Protein Fraction... (1)

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This workflow was used to analyze the data in a manuscript by Mostovenko et al. (2013, submitted), comparing peptide and protein fractionation methods. The workflow identifies proteins by X!Tandem database search and validates the results using PeptideProphet. Additional information such as pI and fraction number is extracted and plotted for IEF and SCX data. For each protein identified in SDS-PAGE derived data sequences are downloaded from UniProt and plotted against the fraction number. Rs...

Created: 2013-03-27

Credits: Kate Mostovenko Yassene Magnus Palmblad

Attributions: Plasma Precipitation Analysis

EB-eye getAllResultIds and WSDbfetch fetch... (1)

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Get database entries for a query using EB-eye to perform the initial query against the database to get entry identifiers and using the identifiers with WSDbfetch to retrieve the entry data in the desired format. Note: this particular implementation is not suitable for queries which return large numbers of results.

Created: 2013-03-28

Credits: Hamish McWilliam

ImageMagick: Convert JPG to TIFF (3)

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Converts a JPG image to a TIFF image

Created: 2013-04-04 | Last updated: 2013-04-04

jpylyzer: Extract width and height (1)

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No description

Created: 2013-04-04

Venus: Compare VEX data with HYB model (1)

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It compares data from VEX from a certain date range with what HYB has modeled in the coordinates where VEX spacecraft is at that moment.

Created: 2013-04-07

Credits: David PS Natasha

Discovery of Brown Dwarfs mining the 2MASS... (1)

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Brown dwarfs are objects occupying the gap between the least massive stars and the most massive planets. They are intrinsically faint objects so their detection is not straighforward and, in fact, was almost impossible until the advent of global surveys at deep optical and near-infrared bands like SDSS, 2MASS or DENIS among others. Here we propose to mine the SDSS and 2MASS databases to identify T-type brown dwarfs through an appropriate combination of colours in the optical and the infra-red...

Created: 2013-04-12

Credits: Jose Enrique Ruiz

Crossmatching VOTables (2)

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Snippet showing how to use AstroTaverna tool for crossmatching two VOTables VOTable samples may be downloaded from MyExperiment http://www.myexperiment.org/files/911/versions/1/download/SDSS7.vot http://www.myexperiment.org/files/910/versions/1/download/2MASS.vot

Created: 2013-04-12 | Last updated: 2013-04-22

Credits: Jose Enrique Ruiz

Retrieving information from HST ConeSearch... (1)

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This workflow retieves information from Hubble Space Telescope VO Services in the form of VOTables. The input of the workflow is an ASCII file with a list of source names. This file is converted to a VOTable, and coordinates added with an extra-column needed to query SIAP Image service. The final result are two different VOTables issued as the response of both VO Services, Images VOTable has been previously filtered.

Created: 2013-04-12

Table format coversion: ASCII to VOTable (2)

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Snippet showing how to use AstroTaverna tool for table format conversion

Created: 2013-04-12 | Last updated: 2013-04-12

Find pathways in which two genes co-occur ... (1)

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This workflow finds all pathways in which two gene symbols co-occur. This workflow was created as an exercise for the "Managing and Integrating Information in the Life Sciences course 2013" at the LUMC, which is organized by the Netherlands Bioinformatics Center (NBIC).

Created: 2013-06-28 | Last updated: 2013-06-28

OPS REST services (1)

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Library of REST services developed for the Open Pharmacological Space (OPS) by the OpenPHACTS project. Usage: 1. Copy-paste a service into your workflow 2. Add an output to responseBody 3. Run the workflow (this will produce output in XML) 4. Copy the XML output 5. Go back to the design window and add the XPath widget to the canvas 6. Link the responseBody output to the XPath widget input 7. Paste the XML output to the example window in the XPath configure window 8. Select the desired eleme...

Created: 2013-07-06

Credits: Marco Roos Open PHACTS

Imagemagick convert - tiff2tiff - compression (2)

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Converts tiff to tiff using imagemagick convert with the provided compression

Created: 2013-07-08 | Last updated: 2013-07-08

Credits: Markus Plangg