Workflows

Image annotation (2)

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No description

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

Credits: Ondrej Klima

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

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

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

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: 2014-05-20

Credits: Peter Li

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

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

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 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

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

template (1)

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No description

Created: 2014-05-28

Credits: Ondrej Klima

3Drec (1)

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No description

Created: 2014-05-28

Credits: Ondrej Klima

Anot (1)

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No description

Created: 2014-05-28

Credits: Ondrej Klima

Imagemagick identify - image size (1)

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Extracts the image size using imagemagick identify

Created: 2014-06-16

Credits: Markus Plangg

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

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

Imagemagick tiff/jp2/png/jpeg (2)

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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

Graphicsmagick tiff/jp2/png/jpeg (1)

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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

Openjpeg tools - tiff2jp2 (1)

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Converts tiff to jp2 images using Openjpeg tools.

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

Jpylyzer - JP2 Image characteristics (1)

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

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

EBI_InterproScan_broken (1)

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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

Demonstration of configurable iteration (1)

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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

String upload (1)

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The component uploads the string within the InputBody to the File_name within the fixed WebDAV

Created: 2013-09-16 | Last updated: 2014-02-03

In2Out (1)

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No description

Created: 2013-09-19

Use of rest services described with PDL (1)

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Workflow that exemplifies the use of PDL (parameter description language) descriptions for rest services. There are two cases. - the artifact provides as output the response from the service (rest config). - the web service provides a VOTable that is processed according to the PDL description. Some of the columns in the votable are provided as output in the artifacts (smartVOrest config).

Created: 2013-09-20

Credits: Julian Garrido

Example of interoperability validation on ... (2)

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Workflow that exemplifies the use of PDL (parameter description language) descriptions for rest services. The web service provides a VOTable that is processed according to the PDL description. Some of the columns in the votable are provided as output in the artifacts (smartVORest config). To check interoperability we have to validatate the connections between outputs and inputs of the artifacts. In this case, there is an error in the connections. dec output is connected to dec input but d...

Created: 2013-09-20 | Last updated: 2013-10-31

Credits: Julian Garrido

Building a knowledge base for data mining ... (7)

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Scientific workflow for creating the knowledge base. 

Created: 2013-10-03 | Last updated: 2018-09-20

Credits: respinosa

Attributions: Measuring data quality criteria in arff files Data Mining Algorithms

Measuring data quality criteria in arff files (4)

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No description

Created: 2013-10-03 | Last updated: 2014-11-17

Credits: respinosa

Data Mining Algorithms (7)

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No description

Created: 2013-10-03 | Last updated: 2014-11-17

Credits: respinosa

User friendly data mining (7)

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This scientific workflow was designed for the novice data miners to learn how mining algorithms behave when applied on their datasets. The workflow is the responsible for invoking the mining recommender, as well as using the datasets required by the user, thus returning the ranking of algorithms according to the design criteria of the recommender. 

Created: 2013-10-03 | Last updated: 2019-01-08

Credits: respinosa

get promoter region + operate on genomic i... (5)

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This workflow computes a promoter region for each gene that we provide as input carrying the genomic information. Then it computes the overlap between the two datasets that contain genomic information plus some statistics. Returns rows of file_1 which overlap with the second file. A kolmogorov smirnov test is applied between the list that overlaps and the one that does not. Uses the R package GenomicRanges.

Created: 2013-10-04 | Last updated: 2013-11-04

Credits: Eleni

plotGenomic (1)

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This workflow returns a graphical representation of selected Nencki Genomics Database (www.nencki-genomics.org) content in the ± 10 kb flank of the transcription start site of a chosen gene. More precisely, it returns instances of selected area types, and instances of selected motif types that intersect any of the returned area instances. The results are returned as three files: a pdf file with the plot, and two tab-separated files with the details of areas and motifs shown in the plot. P...

Created: 2013-10-07

Credits: mdabr

showDatasetsGenomic (1)

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Shows all the datasets available in the Nencki Genomics Database (www.nencki-genomics.org). Click 'Use examples' to see all the datasets, separated into datasets of TFBS motifs, and all the remaining datasets (areas), the latter including data from Ensembl funcgen and (thus) Encode. Publication doi: 10.1093/database/bat069

Created: 2013-10-07

Credits: mdabr

loadData (1)

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Permits loading data to Nencki Genomics Database.

Created: 2013-10-08

Credits: mdabr

concatTwoStrings (1)

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for tests of TavernaServer

Created: 2013-10-10 | Last updated: 2013-10-10

Credits: mdabr

Hello World (1)

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One of the simplest workflows possible. No workflow input ports, a single workflow output port "greeting", outputting "Hello, world!" as produced by the String Constant "hello".

Created: 2013-10-15

Credits: Stian Soiland-Reyes

Hello Anyone (1)

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An extension to helloworld.t2flow - this workflow takes a workflow input "name" which is combined with the string constant "Hello, " using the local worker "Concatenate two strings", and outputs the produced string to the workflow output "greeting".

Created: 2013-10-15

Credits: Stian Soiland-Reyes

Fetch today's xkcd comic (1)

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Use the local services and some filtering operations to fetch the comic strip image from http://xkcd.com/ Based on the FetchDailyDilbert workflow.

Created: 2013-10-15

Credits: Stian Soiland-Reyes

Find compounds pharmacology and align agai... (1)

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Look up concept URI from freetext, e.g. "aspirin", find compound pharmacology and their target info. For each target, blast+tree on its sequence - if any. Uses the Open PHACTs API https://dev.openphacts.org/docs/alpha and the myExperiment workflow 3369 "Blast_Align_and_Tree" http://www.myexperiment.org/workflows/3369. Notice that in tihs workflow, most concepts won't have compounds, and most compounds won't have targets, and most targets won't have a sequence - Open PHACT API wise this mean...

Created: 2013-10-16

Credits: Stian Soiland-Reyes Katy Wolstencroft

Attributions: Blast_Align_and_Tree

Find compounds pharmacology targets in Ope... (2)

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Look up concept URI from freetext, e.g. "aspirin", find compound pharmacology and their target info. For each target, blast+tree on its sequence - if any. Uses the Open PHACTS API https://dev.openphacts.org/docs/1.5. Notice that in tihs workflow, most concepts won't have compounds, and most compounds won't have targets, and most targets won't have a sequence - Open PHACT API wise this means this workflow would be propagating 404 Not Found errors. Until there is a Local worker to filter out...

Created: 2013-10-16 | Last updated: 2015-11-19

Credits: Stian Soiland-Reyes

Attributions: Find compounds pharmacology and align against target sequences

echoer (6)

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Renamed beanshell

Created: 2013-10-25 | Last updated: 2014-05-07