Workflows

Extract DEC and RA from whitespace separat... (2)

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This workflow extracts DEC and RA coordinates from a whitespace seperated file and this is a silly description.

Created: 2012-05-10 | Last updated: 2012-09-24

Credits: Stian Soiland-Reyes

Mp3ToWav Mig+QA (2)

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Migrates Mp3 files from input List to Wav files and performs QA. The QA steps include File Format Validation, Significant Property Comparison and migrationQA file content comparison (all CLI). This workflow matches solution SO4 on the SCAPE opf wiki, see http://wiki.opf-labs.org/display/SP/SO4+Audio+mp3+to+wav+Migration+and+QA+Workflow

Created: 2012-05-21 | Last updated: 2013-04-24

Credits: Bolette Jurik

Watershed (2)

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Local machine example

Created: 2012-05-21 | Last updated: 2012-05-21

Credits: Jorgejesus

Sesame service to get the RA and DEC of a ... (1)

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No description

Created: 2012-05-23

Getting information from LEDA service (1)

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No description

Created: 2012-05-23

Extract logr25 from LEDA service (1)

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No description

Created: 2012-05-23 | Last updated: 2012-05-24

Calculating the internal extinction with d... (3)

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No description

Created: 2012-05-23 | Last updated: 2015-03-25

Example of jdbc (1)

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No description

Created: 2012-05-24 | Last updated: 2012-05-24

Get data and images for a date +/- 12 hour... (1)

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From the date as input date +/- 12 hours of data from the MLSO web page is collated. Images for up to three images (closest to date; -1; +1) are created via autoplot

Created: 2012-05-24 | Last updated: 2012-05-24

Credits: Anja Le Blanc

Convert table to CDS format (1)

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It converts a csv file (comma separated values) to the CDS format. It also provides relevant information to create the ReadMe file. The first row in the input file must be the column names. If you want to run this workflow, you have to install astrotaverna plugin. You can easyly cusomize the workflow to provide a votable or fits table as input.

Created: 2012-05-28 | Last updated: 2012-05-28

Credits: Julian Garrido

Anatomical Atlas Generation (1)

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Computes an anatomical atlas based on a set of patient images using registration methods. This workflow is automatic and does not require user interaction. The anatomical atlas is composed of a mean image and the set of transformations for each patient's between the mean image and the patient image. The atlas can be used to segment the mean image once and propagate the segmentation results to each patient image automatically. This workflow has been tested using GIMIAS-1.5 (open source) with ...

Created: 2012-05-29 | Last updated: 2012-05-29

Credits: Gimias

[untitled] (1)

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No description

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

Credits: Neroptit

Image Characterisation - Fits (Extended) (1)

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Extracts metadata from images.

Created: 2012-06-06 | Last updated: 2012-06-06

Credits: Markus Plangg

Gaussian Blur (1)

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Convolves the image with a Gaussian kernel wherein the Gaussian has a standard deviation specified by the user ("sigma") and the kernel width in each dimension is 6 times the standard deviation of the Gaussian. You can find more details here

Created: 2012-06-13 | Last updated: 2012-06-13

ASA_IM__0P (1)

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No description

Created: 2012-06-13 | Last updated: 2012-06-13

Credits: Joel Wright

[untitled] (1)

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No description

Created: 2012-06-13 | Last updated: 2012-06-13

Credits: Joel Wright

DatabaseID to ConceptID (7)

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Purpose: This workflow maps input Identifiers, common database identifiers, to the Concept Identifiers from the EMC ontology. Result: Concept Identifiers from the EMC ontology. Comments: Database: one of CAS, DRUG, etc. The supported databases are listed below (database, description, example). CAS, Chemical Abstracts Service registry number, 64-17-5. DRUG, Drug Bank, DB00316. AF, Affymetrix, 200007_at. CHEB, ChEBI, 16236. CHID, ChemIDplus, 0000050000. EG, Entrez-Gene, 3064. GO, Gene Ontol...

Created: 2012-06-25 | Last updated: 2014-07-14

Credits: Marco Roos Martijn Schuemie Reinout van Schouwen BioSemantics

SNP_ID2EntrezGene_ID (4)

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Purpose: The workflow maps a SNP (dbSNP id) to a gene (EntrezGene id). Author comments: The window for gene inclusion can be set using the set_width parameter. This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery.

Created: 2012-06-26 | Last updated: 2013-03-11

Credits: Kristina Hettne Harish Dharuri

Find Supporting Documents (6)

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This workflow finds documents that serve as evidence for the association between two concepts. Results: Document titles Document identifiers There seems to be a bug at the moment, since it returns empty values.

Created: 2012-06-26 | Last updated: 2014-07-14

Credits: Kristina Hettne Marco Roos Reinout van Schouwen Martijn Schuemie BioSemantics

Find periods of time where two ILS objects... (2)

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Inputs: name of target_obj of ILS of two objects and a number of degrees which these obejcts are allowed to be appart in hci longitude coordinates. Output VOTable of time periods where these two objects are closer than +/- input angle together.

Created: 2011-11-04 | Last updated: 2011-11-18

Credits: Anja Le Blanc

Basic Call of HELIO Coordinate Transformat... (1)

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Transforms an input VOTable Coordinate set to a specified output VOTable Coordinate set. This workflow performs some remote computation and may take some time to complete.

Created: 2011-11-08 | Last updated: 2011-11-08

Credits: Anja Le Blanc

Basic Call of HELIO Coordinate Transformat... (2)

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Transforms an input VOTable Coordinate set to a specified output VOTable Coordinate set. This workflow performs some remote computation and may take some time to complete.

Created: 2011-11-09 | Last updated: 2012-07-09

Credits: Anja Le Blanc

Attributions: Basic Call of HELIO Coordinate Transformation Service

Sample IMPACT hackathon workflow (1)

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Workflow that implements the Use Case for Group 2 at the IMPACT/Taverna hackathon. What it does is to take the URL of a TIFF image and compute the Levenshtein difference between the OCR output of the uncompressed version with various ones compressed at various bit rates.

Created: 2011-11-14 | Last updated: 2012-06-19

Credits: Donal Fellows

Calculation of distances, magnitutes and l... (4)

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Calculation of distances, corrected apparent B magnitude mB-corr and luminosities with values gathered from the HyperLEDA database. This workflow receives a list of galaxy names (hyperLEDA names. ie: KIG0001) and a file with the morphological types of those galaxies Using the name of a galaxy, the workflow querys Hyperleda to extract some properties of this galaxy (J2000 Coordinates, velocity, galactic extinction,log of axis ratio, and the Total B-magnitude ). With this properties it calcula...

Created: 2011-11-14 | Last updated: 2012-01-11

Example of conditional invocation (1)

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This workflow demonstrates how nested workflows can be conditionally invoked

Created: 2011-11-15 | Last updated: 2011-11-15

Credits: Alan Williams

Example of explicit looping (1)

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This workflow demonstrates how a nested workflow can be called an explicit number of times. Note that the loop iterator does not need to be used in the logic of the loop contents. It can be used as a sentinel (see the conditional workflow)

Created: 2011-11-15 | Last updated: 2011-11-15

Credits: Alan Williams

Arc/Warc mounter (2)

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No description

Created: 2011-11-15 | Last updated: 2011-11-15

Credits: Asger Askov Blekinge

Find source at Sun of SW events on Earth (5)

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Try to detect the solar wind source on the Sun. Use backpropagation, ILS, HEC and HFC.

Created: 2011-11-15 | Last updated: 2012-05-24

Credits: Anja Le Blanc David PS

Connect flare events with proton events on... (4)

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This workflow uses flares listed in the goes_sxf_flare list, checks wether this flare is connected to Earth via the Parker spiral, and looks for proton events at earth listed in the goes_proton_event list. The flare listing and the proton listing is combinded into a VOTable output.

Created: 2011-11-15 | Last updated: 2012-05-15

Credits: Anja Le Blanc

Associate a Shock at Earth with Flare and ... (2)

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Using start date and end date all shock events at Earth are backpropagated to the Sun. Arround the time all flares (above certain levels) and cmes are assoicated. The possition of the flare and speed of the CME are used to forward propagate the event to Mars.

Created: 2011-11-15 | Last updated: 2012-07-20

Credits: Anja Le Blanc David PS

Pathways and Gene annotations forQTL region (2)

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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: 2011-11-21 | Last updated: 2011-11-21

Credits: Prashanth

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: 2011-11-21 | Last updated: 2011-11-21

Credits: Prashanth

Image files comparison using histograms an... (2)

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This workflow extracts histogram and profile features from image file applying image processing command line tool. Necessary configuration files are stored on Github (https://github.com/openplanets/scape/tree/master/pc-qa-toolwrapper). As a template for creation of image workflows was used xa-toolwrapper project from Sven Schlarb (https://github.com/openplanets/scape/tree/master/xa-toolwrapper). This workflow provides WSDL web service that wraps command line tool with tho options ‘extra...

Created: 2011-11-22 | Last updated: 2011-11-23

Credits: Roman

NSF Funds dataset US dollar to Euro curren... (1)

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This workflow uses a 2012 Fiscal Year dataset from the National Science Foundation (NSF), a currency conversion web service from WebservicesX.NET and processes data using the workflow tool Taverna.  It converts US dollars from a spreadsheet to Euros.

Created: 2011-11-25 | Last updated: 2011-11-25

Credits: Trisha Adamus

FetchandDisplaySpecies (3)

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This workflow uses GBIF to search and report species occurrence data and then displays them on Google Earth. An interactive step then allows you to alter the co-ordinates of data displayed.

Created: 2011-11-27 | Last updated: 2011-11-29

Credits: Alan Williams

Comparison of Birth and Death Rates for a ... (1)

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This workflow extracts the relevant data from two spreadsheets, formats the data strings, and puts that data through a REST to Google Charts. Data collected for this project comes from data.un.org. Currently, the workflow supports data from only one country at a time (data from data.un.org can be filtered and exported directly from the website). Data from the Live births by month and Deaths by month works best with this workflow.

Created: 2011-11-27 | Last updated: 2011-11-27

Credits: tpacurtis

[untitled] (2)

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This is a workflow for a Cyberinfrastructure class (Fall 2011) at Syracuse University. It takes information from GapMinder and runs it through a workflow to produce a graph. The original data sets can be found here: https://spreadsheets.google.com/pub?key=pyj6tScZqmEdrsBnj2ROXAg&gid=0 (Literacy rate, adult total) https://spreadsheets.google.com/pub?key=pyj6tScZqmEdIyrBS31XAaw&gid=0 (Income share of poorest 20%)

Created: 2011-11-27 | Last updated: 2011-11-27

Credits: Kayleigh Ayn Bohémier

Attributions: Spreadsheet Import Example Broccoli: A State Comparison

Literacy Rate and GDP/Capita Increase (Per... (1)

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This is a workflow for a Cyberinfrastructure class (Fall 2011) at Syracuse University. It takes information from GapMinder and runs it through a workflow to produce a graph. The original data sets can be found here: https://spreadsheets.google.com/pub?key=pyj6tScZqmEdrsBnj2ROXAg&gid=0 (Literacy rate, adult total) https://spreadsheets.google.com/pub?key=phAwcNAVuyj1jiMAkmq1iMg&gid=0 (Income per person)

Created: 2011-11-28 | Last updated: 2011-11-28

Credits: Kayleigh Ayn Bohémier

Attributions: Spreadsheet Import Example

Make XML Parameters (1)

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Reformats a SNP list with optional p-value into the required XML input for the 'Define Associated Regions and Genes' workflow. Additional parameters can be supplied to add to the XML document.

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

Credits: Paul martin

Associated Region to Gene List (1)

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Produces a gene list from the Associated Region XML file

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

Credits: Paul martin

Render gene via BioGPS (2)

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This workflow uses the REST API of BioGPS to list the plugins and then allow the user to select which plugin to use to display the input gene id

Created: 2012-02-10 | Last updated: 2012-02-15

Credits: Alan Williams

Radio lists search over time period (2)

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This workflow searches the wind stereo II IV radioburst list, wind tyhpe II soho cme list, hfc radioburst type III list, tsrs solar radio event list and combines the return of these lists chronologically. Only time_start, time_end, and comment sections are preserved in the result list.

Created: 2012-02-13 | Last updated: 2012-02-14

Credits: Anja Le Blanc

Simulation workflow for flooding emergency... (1)

Simulation workflow for flooding emergency simulation. This workflow cannot be executed as is due to authentification restriction, and local tools dependancies.

Created: 2012-02-15

Run a Workflow on Taverna Server (1)

Uses the URL to a t2flow file to submit and run this workflow on the taverna server. You need a user name and password to execute this workflow. Input to the workflow which runs remotely will be requested interactively.

Created: 2012-02-17 | Last updated: 2012-02-17

Credits: Anja Le Blanc

Run a Workflow on Taverna Server (local t2... (1)

Uses a local t2flow file to submit and run this workflow on the taverna server. You need a user name and password to execute this workflow. Input to the workflow which runs remotely will be requested interactively.

Created: 2012-02-20

Credits: Anja Le Blanc

Attributions: Run a Workflow on Taverna Server

Get a list of proteins from a Gene Ontolog... (1)

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Get a list of UniProt proteins that have been annotated with the same Gene Ontology (GO) term. This workflow uses the the QuickGO service

Created: 2012-02-20 | Last updated: 2012-02-22

Credits: Rafael C. Jimenez

WCP-04 Exclusive choice - if/else branching (1)

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The choice of executing choiceA or choiceB is determined by using String_List_Intersection and String_List_Difference. If in="true" then the intersection will yield a non-empty list, triggering execution of choiceA. This list will however not differ from the input, and so choiceB will iterate over an empty list (ie. not execute). Note how using 'difference' for the else-case here means that if you run the workflow with in="bob", choiceB would still run. Some early if/el...

Created: 2012-02-20 | Last updated: 2012-02-20

Credits: Stian Soiland-Reyes

Attributions: Example of a conditional execution workflow Example of conditional invocation

Parse QuickGO "proteinList" file format (2)

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Parse QuickGO "proteinList" file format. http://www.ebi.ac.uk/QuickGO/reference.html

Created: 2012-02-20 | Last updated: 2013-07-10

Credits: Rafael C. Jimenez

Get a list of Protein Identification exper... (3)

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Get a list of Protein Identification experiments from PRIDE by a Gene Ontology query

Created: 2012-02-21 | Last updated: 2013-07-10

Credits: Rafael C. Jimenez

Convert by target path (1)

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Converts a file to a target format depending on the target path extension.

Created: 2012-02-21 | Last updated: 2012-08-14

Credits: Markus Plangg