Workflows

usability test workflow (1)

Created: 2014-06-30 | Last updated: 2014-06-30

Credits: Yuliya Fetyukova

split_by_newline (1)

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Splits a string into a list of strings. The initial string must use newline as a separator

Created: 2014-06-24 | Last updated: 2014-10-02

RetrivingJob1 (1)

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Get Retrieve result of a job for which you possess the ID

Created: 2014-06-17 | Last updated: 2014-06-24

Imagemagick identify - image size (1)

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Extracts the image size using imagemagick identify

Created: 2014-06-16

Credits: Markus Plangg

usability test workflow (1)

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This is a test workflow for usability study of myExperiment from May to August 2014

Created: 2014-06-10 | Last updated: 2014-06-23

Credits: Gab

Attributions: SimpleTest

CPGP Summary table (2)

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Requirements: Have MySQL installed with a database called mydb or please create one. Have a mysql connector file. This can be downloaded from mysql.com. Rename the downloaded file to mysql-connector-java.jar and place it in the the local lib file of Taverna as written on the dependencies tab. Choose this dependency by rightclicking a beanshell script and selecting it for the whole workflow as system classloader. Download the Peregrine SKOS CLI from: https://trac.nbic.nl/biosemantics/downlo...

Created: 2014-05-27 | Last updated: 2014-06-30

Credits: Amrish Mahes

CPGP Concept matching calculation with inn... (2)

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Requirements: Have MySQL installed with a database called mydb or please create one. Have a mysql connector file. This can be downloaded from mysql.com. Rename the downloaded file to mysql-connector-java.jar and place it in the the local lib file of Taverna as written on the dependencies tab. Choose this dependency by rightclicking a beanshell script and selecting it for the whole workflow as system classloader. Download the Peregrine SKOS CLI from: https://trac.nbic.nl/biosemantics/downlo...

Created: 2014-05-27 | Last updated: 2014-06-30

Credits: Amrish Mahes

Concept profile calculation CPGP (2)

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Requirements: Have MySQL installed with a database called mydb or please create one. Have a mysql connector file. This can be downloaded from mysql.com. Rename the downloaded file to mysql-connector-java.jar and place it in the the local lib file of Taverna as written on the dependencies tab. Choose this dependency by rightclicking a beanshell script and selecting it for the whole workflow as system classloader. Download the Peregrine SKOS CLI from: https://trac.nbic.nl/biosemantics/downlo...

Created: 2014-05-27 | Last updated: 2014-06-30

Credits: Amrish Mahes

CPGP 2x2 Contingency table (3)

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Requirements: Have MySQL installed with a database called mydb or please create one. Have a mysql connector file. This can be downloaded from mysql.com. Rename the downloaded file to mysql-connector-java.jar and place it in the the local lib file of Taverna as written on the dependencies tab. Choose this dependency by rightclicking a beanshell script and selecting it for the whole workflow as system classloader. Download the Peregrine SKOS CLI from: https://trac.nbic.nl/biosemantics/downlo...

Created: 2014-05-27 | Last updated: 2014-06-30

Credits: Amrish Mahes

CPGP Peregrine Get Abstracts Create tables (3)

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Requirements: Have MySQL installed with a database called mydb or please create one. Have a mysql connector file. This can be downloaded from mysql.com. Rename the downloaded file to mysql-connector-java.jar and place it in the the local lib file of Taverna as written on the dependencies tab. Choose this dependency by rightclicking a beanshell script and selecting it for the whole workflow as system classloader. Download the Peregrine SKOS CLI from: https://trac.nbic.nl/biosemantics/downlo...

Created: 2014-05-27 | Last updated: 2014-06-30

Credits: Amrish Mahes

Use Case C, Worflow 4 (1)

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Workflow used to obtain data for the research paper ‘The application of the Open Pharmacological Concepts Triple Store (Open PHACTS) to support Drug Discovery Research’, currently submitted to PLOS ONE.  Requirements:- Knime v2.9- Open PHACTS Knime nodes 1.0.0 (DON'T use any later version!): https://github.com/openphacts/OPS-KnimeInstallation:- Download "org.openphacts.utils.json_1.0.0.zip" and unzip it in the plugins folder of your KNIME installation- Download ...

Created: 2014-05-27 | Last updated: 2014-11-25

Credits: Emiliano Cuadrado Joseline Ratnam Daniela Digles Open PHACTS

Use Case C, Worflow 3 (1)

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Workflow used to obtain data for the research paper ‘The application of the Open Pharmacological Concepts Triple Store (Open PHACTS) to support Drug Discovery Research’, currently submitted to PLOS ONE.  Requirements:- Knime v2.9- Open PHACTS Knime nodes 1.0.0 (DON'T use any later version!): https://github.com/openphacts/OPS-KnimeInstallation:- Download "org.openphacts.utils.json_1.0.0.zip" and unzip it in the plugins folder of your KNIME installation- Download ...

Created: 2014-05-27 | Last updated: 2014-11-25

Credits: Emiliano Cuadrado Joseline Ratnam Daniela Digles Open PHACTS

Use Case C, Worflow 2 (1)

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Workflow used to obtain data for the research paper ‘The application of the Open Pharmacological Concepts Triple Store (Open PHACTS) to support Drug Discovery Research’, currently submitted to PLOS ONE.  Requirements:- Knime v2.9- Open PHACTS Knime nodes version 1.0.0 (DON'T use any later version!): https://github.com/openphacts/OPS-KnimeInstallation:- Download "org.openphacts.utils.json_1.0.0.zip" and unzip it in the plugins folder of your KNIME installation- D...

Created: 2014-05-26 | Last updated: 2014-11-25

Credits: Emiliano Cuadrado Joseline Ratnam Daniela Digles Open PHACTS

Use Case C, Worflow 1 (1)

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Workflow used to obtain data for the research paper ‘The application of the Open Pharmacological Concepts Triple Store (Open PHACTS) to support Drug Discovery Research’, currently submitted to PLOS ONE.  This workflow can be used to get approved drugs from a pathway of interest using the Open PHACTS APIRequirements:- Knime v2.9- Open PHACTS Knime nodes 1.0.0 (DON'T use any later version!): https://github.com/openphacts/OPS-KnimeInstallation:- Download "org.openphacts...

Created: 2014-05-26 | Last updated: 2014-11-25

Credits: Emiliano Cuadrado Joseline Ratnam Daniela Digles Open PHACTS

Visualize PAV provenance as SVG (1)

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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: 2014-05-20

Credits: Peter Li

Hybrid Recommender System Using Linked Op... (1)

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This process is using the Rapid Miner Linked Open Data extension and the Recommender extension, to build a hybrid Linked Open Data enabled recommender system for books.The input data for the process can be found here.More information about the process can be found here.

Created: 2014-05-15 | Last updated: 2014-05-15

Predicting the fuel consumption of cars (1)

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This process is using features extracted from DBpedia to predict the fuel consumption of cars. It uses operators from the Linked Open Data and the Weka extensions.The process first reads a list of cars with the fuel consumption value. The DBpedia lookup linker is used to link the car names to DBpeida resources. The established links are used to generate additional features, i.e. direct types and categories of each car. Finally, a M5 Rules Operator is used to predict the fuel co...

Created: 2014-05-14 | Last updated: 2014-05-15

Fetch Abstracts (1)

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Example how to fetch abstracts using a component that performs SQL queries based on a database properties string.

Created: 2014-05-08

Visualize PAV provenance as SVG (1)

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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: 2014-05-08

Credits: Katy Wolstencroft Aleksandra Pawlik

getDataPointValueFixedTime by SINP (3)

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Workflow for Taverna based on the IMPEx-FP7 method getDataPointValueFixedTime. The method can be used to return the magnetic field (calculated by SINP paraboloid magnetic field model) in given points inside the planetary magnetosphere and at a fixed time for each point.

Created: 2014-05-07 | Last updated: 2014-05-19

Credits: Manuel Scherf

getDataPointValue by SINP (2)

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Workflow for Taverna based on the IMPEx-FP7 method getDataPointValue. This method is used to compute values of various physical quantitites (e.g. density, magnetic field strengths etc.) for a given simulation run at a user given set of 3D points.

Created: 2014-05-07 | Last updated: 2014-05-20

Credits: Manuel Scherf

TIF to JP2 file format migration with qual... (1)

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This workflow reads a textfile containing absolute paths to TIF image files and converts them to JP2 image files using OpenJPEG (https://code.google.com/p/openjpeg). 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 starting the actual migration, it is checked if the TIF input images are valid file format instances u...

Created: 2014-05-07 | Last updated: 2014-05-07

Credits: Sven

Imagemagic image size equals QA (1)

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QA component that extracts the image size of two images and checks if they match

Created: 2014-05-06

Credits: Markus Plangg