Workflows

digital-preservation-migration-office-jodc... (1)

• Download

Converts Excel to OpenDocument Spreadsheet

Created: 2014-08-13

digital-preservation-migration-office-jodc... (1)

• Download

Converts Powerpoint (.pptx) to Flash

Created: 2014-08-13

digital-preservation-migration-office-jodc... (1)

• Download

Converts Powerpoint (.pptx) to PDF

Created: 2014-08-13

digital-preservation-migration-office-jodc... (1)

• Download

Converts Powerpoint (.pptx) to OpenDocument Presentation

Created: 2014-08-13

digital-preservation-migration-office-jodc... (1)

• Download

Converts Powerpoint to Flash

Created: 2014-08-13

digital-preservation-migration-office-jodc... (1)

• Download

Converts Powerpoint to PDF

Created: 2014-08-13

digital-preservation-migration-office-jodc... (1)

• Download

Converts Powerpoint to OpenDocument Presentation

Created: 2014-08-13

digital-preservation-migration-office-jodc... (1)

• Download

Converts OpenDocument Text to PDF

Created: 2014-08-13

digital-preservation-migration-office-jodc... (1)

• Download

Converts OpenDocument Text to Word

Created: 2014-08-13

digital-preservation-migration-office-jodc... (1)

• Download

Converts OpenDocument Spreadsheet to Excel

Created: 2014-08-13

digital-preservation-migration-office-jodc... (1)

• Download

Converts OpenDocument Spreadsheet to PDF

Created: 2014-08-13

digital-preservation-migration-office-jodc... (1)

• Download

Converts OpenDocument Presentation to Flash

Created: 2014-08-13

digital-preservation-migration-office-jodc... (1)

• Download

Converts OpenDocument Presentation to Powerpoint

Created: 2014-08-13

digital-preservation-migration-office-jodc... (1)

• Download

Converts OpenDocument Presentation to PDF

Created: 2014-08-13

digital-preservation-migration-office-jodc... (1)

• Download

Converts Word to PDF

Created: 2014-08-13

digital-preservation-migration-office-jodc... (1)

• Download

Converts Word to OpenDocument Text

Created: 2014-08-13

digital-preservation-migration-office-ffmp... (1)

• Download

Converts Text to TIFF

Created: 2014-08-13

digital-preservation-migration-office-abiw... (1)

• Download

Converts Word (.docx) to Text

Created: 2014-08-13

digital-preservation-migration-office-abiw... (1)

• Download

Converts Word (.docx) to PDF

Created: 2014-08-13

digital-preservation-migration-office-abiw... (1)

• Download

Converts Word (.docx) to OpenDocument Text

Created: 2014-08-13

digital-preservation-migration-office-abiw... (1)

• Download

Converts Word (.docx) to HTML

Created: 2014-08-13

digital-preservation-migration-office-abiw... (1)

• Download

Converts Word (.docx) to Word

Created: 2014-08-13

digital-preservation-migration-office-abiw... (1)

• Download

Converts Word to Text

Created: 2014-08-13

digital-preservation-migration-office-abiw... (1)

• Download

Converts Word to PDF

Created: 2014-08-13

digital-preservation-migration-office-abiw... (1)

• Download

Converts Word to OpenDocument Text

Created: 2014-08-13

digital-preservation-migration-office-abiw... (1)

• Download

Converts Word to HTML

Created: 2014-08-13

digital-preservation-migration-image-tesse... (1)

• Download

Converts TIF image to Text

Created: 2014-08-13

digital-preservation-migration-image-sanse... (1)

• Download

Converts any Apache Sanselan supported image format to PNG

Created: 2014-08-13

digital-preservation-migration-image-sanse... (1)

• Download

Converts any Apache Sanselan supported image format to BMP

Created: 2014-08-13

digital-preservation-migration-image-openj... (1)

• Download

Converts any OpenJPEG supported image format to JPEG2000

Created: 2014-08-13

digital-preservation-migration-image-netpb... (1)

• Download

Converts TIFF to PNG

Created: 2014-08-13

digital-preservation-migration-image-netpb... (1)

• Download

Converts TIFF to JPEG

Created: 2014-08-13

digital-preservation-migration-image-jaspe... (1)

• Download

Converts JP2 to JPG

Created: 2014-08-13

digital-preservation-migration-image-inksc... (1)

• Download

Converts SVG to PNG

Created: 2014-08-13

digital-preservation-migration-image-inksc... (1)

• Download

Converts SVG to PDF

Created: 2014-08-13

digital-preservation-migration-image-image... (1)

• Download

Converts Text to TIFF

Created: 2014-08-13

digital-preservation-migration-image-image... (1)

• Download

Converts Text to JPEG2000

Created: 2014-08-13

digital-preservation-migration-image-image... (1)

• Download

Converts any ImageMagick supported image format to Text

Created: 2014-08-13

digital-preservation-migration-image-image... (1)

• Download

Converts any ImageMagick supported image format to JPEG2000

Created: 2014-08-13

digital-preservation-migration-image-image... (1)

• Download

Converts HTML to Text

Created: 2014-08-13

digital-preservation-migration-image-image... (1)

• Download

Converts HTML to TIFF

Created: 2014-08-13

digital-preservation-migration-image-image... (1)

• Download

Converts HTML to JPEG2000

Created: 2014-08-13

digital-preservation-migration-image-image... (1)

• Download

Converts any Java Image IO supported image format to JPEG

Created: 2014-08-13

digital-preservation-migration-image-image... (1)

• Download

Converts any Java Image IO supported image format to GIF

Created: 2014-08-13

digital-preservation-migration-image-image... (1)

• Download

Converts any Java Image IO supported image format to BMP

Created: 2014-08-13

digital-preservation-migration-image-graph... (1)

• Download

Converts TIFF to PNG

Created: 2014-08-13

digital-preservation-migration-image-graph... (1)

• Download

Converts TIFF to JP2000

Created: 2014-08-13

digital-preservation-migration-image-gimp-... (1)

• Download

Converts TIFF to PNG

Created: 2014-08-13

digital-preservation-migration-image-gimp-... (1)

• Download

Converts TIFF to JPG

Created: 2014-08-13

digital-preservation-migration-audio-sox-m... (1)

• Download

Converts MP3 to WAV

Created: 2014-08-13

digital-preservation-migration-audio-sox-a... (1)

• Download

Converts any SoX supported audio format to WAV

Created: 2014-08-13

digital-preservation-migration-audio-mpg32... (1)

• Download

Converts mp3 to wav

Created: 2014-08-13

digital-preservation-migration-audio-gstre... (1)

• Download

Converts an audio file in MP3 to WAV using GStreamer

Created: 2014-08-13

digital-preservation-migration-audio-gstre... (1)

• Download

Converts an audio file in MP3 to Ogg using GStreamer

Created: 2014-08-13

digital-preservation-migration-audio-gstre... (1)

• Download

Converts an audio file in MP3 to Flac using GStreamer

Created: 2014-08-13

digital-preservation-migration-audio-ffmpe... (1)

• Download

Converts MP3 to WAV

Created: 2014-08-13

digital-preservation-migration-audio-ffmpe... (1)

• Download

Converts any FFmpeg supported audio format to MP3

Created: 2014-08-13

digital-preservation-migration-audio-ffmpe... (1)

• Download

Converts any FFmpeg supported audio format to AAC

Created: 2014-08-13

sort_stereo_transient_list_into_cirs_and_c... (1)

• Download

The workflow concept is below. Current workflow is proof of concept and works for default event.1. The initial query is to the stereo_hi_sw_transient list in a particular time range. From this catalogue we extract the longitude of the source of the transient, the longitude error, the start time (launch time of the transient) and the estimated time of arrival. The time of the event is then passed to the HELIO Instrument Location Service (ILS) to extract the Heliocentric Earth Equatorial longit...

Created: 2014-08-11

Credits: Eoincar

EBI_InterproScan (1)

• Download

Perform EBI Interproscan

Created: 2014-07-16 | Last updated: 2014-07-16

Experiments for gene (2)

• Download

This workflow uses the Allen Brain REST API to fetch the experiements corresponding to a named gene

Created: 2014-07-15 | Last updated: 2014-07-15

Credits: Alan Williams

Download images for gene (3)

• Download

This workflow downloads the first few images corresponding to experiments for the specified gene

Created: 2014-07-13 | Last updated: 2014-07-15

Credits: Alan Williams

Demonstration of configurable iteration (1)

• Download

This workflow shows the use of the iteration strategy editor to ensure that only relevant combinations of inputs are used during an implicit iteration.

Created: 2014-07-09

Credits: Alan Williams

Attributions: Demonstration of configurable iteration

EBI_InterproScan_broken (1)

• Download

This workflow performs an interproscan at the EBI on sequences provided as input. The output is provided as text and xml. This workflow uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now work in this way, so you can use this workflow as an example of the invocation pattern and looping configuration. Note that this workflow is deliberately broken

Created: 2014-07-09

Credits: Alan Williams Katy Wolstencroft Hamish McWilliam

Attributions: EBI_InterproScan_NewServices

Jpylyzer - JP2 Image characteristics (1)

• Download

Extracts image width, image height, file size, and validity of a jpeg2000 image.

Created: 2014-07-08 | Last updated: 2014-07-08

Openjpeg tools - tiff2jp2 (1)

• Download

Converts tiff to jp2 images using Openjpeg tools.

Created: 2014-07-08 | Last updated: 2014-07-08

The Demo Process in RapidAnalytics Video (1)

• Download

The first demo process used in the new version of RapidAnalytics video on exposing RapidAnalytics Processes as Web Services.

Created: 2014-07-08 | Last updated: 2014-07-08

Graphicsmagick tiff/jp2/png/jpeg (1)

• Download

Converts tiff/jp2/png/jpeg images using graphicsmagick convert. The target format can be seleced with the format parameter.

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

Imagemagick tiff/jp2/png/jpeg (2)

• Download

Converts tiff/jp2/png/jpeg images using imagemagick convert. The target format can be seleced with the format parameter.

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

usability test workflow (1)

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

Credits: Yuliya Fetyukova

split_by_newline (1)

• Download

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)

• Download

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)

• Download

Extracts the image size using imagemagick identify

Created: 2014-06-16

Credits: Markus Plangg

usability test workflow (1)

• Download

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)

• Download

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)

• Download

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)

• Download

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)

• Download

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)

• Download

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)

• Download

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)

• Download

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)

• Download

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)

• Download

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)

• Download

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)

• Download

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)

• Download

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)

• Download

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)

• Download

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)

• Download

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)

• Download

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)

• Download

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)

• Download

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

Created: 2014-05-06

Credits: Markus Plangg