Workflows

Extract histogram features from image file... (1)

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The main element of this workflow is a RESTful service designed in the SCAPE QA command line tools RESTful package https://github.com/openplanets/scape/tree/master/pc-qa-toolwrapper-rest. The Github project https://github.com/openplanets/scape/tree/master/xa-rester from Andy Jackson is a basis implementation for pc-qa-toolwrapper-rest package. The QA REST package enables creation of RESTful web service that wraps QA command line tool like ‘extractfeatures’ or ‘create’...

Created: 2011-07-01 | Last updated: 2012-04-04

Credits: Roman

Common SCAPE QA command line tool RESTful ... (1)

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The QA REST package enables creation of RESTful web service that wraps any QA command line tools. The main element of this workflow is a RESTful service designed in the SCAPE QA command line tools RESTful package https://github.com/openplanets/scape/tree/master/pc-qa-toolwrapper-rest. The Github project https://github.com/openplanets/scape/tree/master/xa-rester from Andy Jackson is a basis implementation for pc-qa-toolwrapper-rest package. The workflow comprises path to the RESTful servi...

Created: 2011-07-01 | Last updated: 2012-04-04

Credits: Roman

BiomartAndEMBOSSDisease (2)

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This workflow retrieves all genes on human chromosome 22 that are associated with a disease and aligns the upstream regions with mouse and rat homologues. The alignments are plotted and corresponding sequence ids are also returned.

Created: 2011-07-12 | Last updated: 2012-03-19

Credits: Katy Wolstencroft

Attributions: BiomartAndEMBOSSDisease

EBI_InterproScan_NewServices (1)

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This workflow performs an interproscan at the EBI on sequences provided as input. The output is provided as text, xml or png. 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.

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: Alan Williams Katy Wolstencroft

Attributions: EBI_InterproScan_NewServices

Example workflow for REST and XPath activi... (1)

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This workflow fetches weather forecast for the user-specified location. First of all it uses the provided location name to obtain a WOEID ("Where On Earth ID") of that location, then uses that unique identifier to fetch the weather forecast from Yahoo server. Multiple results may be obtained in case there is no unique translation of the location to a WOEID. REST activity is used to perform HTTP requests and fetch data from remote servers; XPath activity is then used to parse the XML data a...

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: Alan Williams

Multiple choice quiz (1)

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A fun example workflow showing user-interaction and service looping

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: Alan Williams George

Attributions: Multiple choice quiz

Fetch Dragon images from BioMoby (1)

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Fetch images and annotations of snapdragons

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: Tomoinn

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: 2011-07-12 | Last updated: 2011-07-12

Credits: David Withers

Attributions: Spreadsheed Data Import Example

Retrieve sequence in EMBL format (1)

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This workflow retrieves a sequence associated with its features in embl format

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: Franck Tanoh

Attributions: Retrieve sequence in EMBL format

Pipelined list iteration (1)

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Perform multiple iterations of services in order to show pipelining

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: Ian Dunlop Stian Soiland-Reyes

Attributions: Pipelined list iteration

GBSeq test (1)

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This workflow retrieves nucleotide and protein sequences with the literature and references associated to them given a protein and a nucleotide id.

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: Franck Tanoh

Attributions: GBSeq test

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: 2011-07-12 | Last updated: 2011-07-12

Credits: Tomoinn Stian Soiland-Reyes

Attributions: Fetch today's xkcd comic

Fetch PDB flatfile from RCSB server (1)

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Given an identifier such as '1crn' fetches the PDB format flatfile from the RCSB

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: Alan Williams Tomoinn

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: 2011-07-12 | Last updated: 2011-07-12

Credits: Alan Williams Tomoinn

BioMoby tutorial workflow (1)

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A workflow from part of the BioMoby tutorial

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: EdwardKawas

A workflow version of the EMBOSS tutorial (1)

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Designed to show the use of EMBOSS based Soaplab services from Taverna, this workflow has no inputs as all initial values are specified as string constants. A sequence set is fetched using the seqret tool, then simultaneously scanned for predicted transmembrane regions and subjected to a multiple alignment using emma. This alignment is then plotted to a set of PNG images and also used to build a profile using the prophecy and prophet tools.

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: Tomoinn

Attributions: A workflow version of the EMBOSS tutorial

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: 2011-07-13 | Last updated: 2011-07-13

Credits: Alan Williams

Unix tools with zip, unzip and diff (1)

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This workflow only works on a Unix machine. This workflow takes a fixed URL from which a text file is downloaded (output as Original_file). That file is zipped (output as Zipped_File) and then unzipped again (output as Unzipped_File). The orginal file and the unzipped version are then diff'd/

Created: 2011-07-13 | Last updated: 2011-07-13

Credits: Alan Williams Steffen Möller

Attributions: Example for external tools with gzip and gunzip

Unix tool for numerically adding two values. (1)

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This workflow relies on a Unix system. It wraps the "bc" command line calculator. It downloads the calculation script from a URL.

Created: 2011-07-13 | Last updated: 2011-07-13

Credits: Alan Williams Steffen Möller

Multi-parameter sensitivity analysis (MPSA) (2)

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Exemplary multi-parameter sensitivity analysis (MPSA) experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) WS operations. In this version of MPSA, ODEs simulations are basis of analysis of SBML model parameters space.

Created: 2011-07-14 | Last updated: 2011-07-21

Credits: trybik

Select from a list of possible web service... (1)

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The workflow for selecting from a list of possible web service parameter values has two input ports: the wsdl address of the web service and the variable name. It parses the web service wsdl description (the web service http://ropot.ijs.si/webservices/janez/getvalues.php?wsdl does that) and then it asks the user to select one value from a drop-down menu. This workflow is very useful when web services have inputs which expect as a parameter one value from a list of possible values.

Created: 2010-12-23 | Last updated: 2010-12-23

Credits: Petra Kralj Novak Janez Kranjc

Text preprocessing (1)

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The input to this workflow is plain text. The text is preprocessed so that non- alfanumeric symbols are removed, the text is transformed to to lower case and stop words are removed. The workflow first removes the charachters from this set: `~!@#$%^&*()_+=-{}|\][":;'?><,./. Then it transforms the text to lower case. The user will be prompted to select a dictionary for stop words from a list. The workflow will, based on the selected list, remove the stop words. Stop words are...

Created: 2011-01-07 | Last updated: 2011-01-07

Credits: Petra Kralj Novak

Text stemming with Porter Stemmer (1)

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This workflow does text stemming. Stemming removes the inflicted endings of words. It is often used as text preprocessing for text mining, since stemmed words can be easily matched and counted. The input to the workflow is the text to be stemmed, the output is the stemmed text.  

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

Credits: Petra Kralj Novak

Population reconstruction and dynamic popu... (2)

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Runs the population reconstruction model (PRM) to create a synthetic individual-level population and then projects the population through a number of years. This is still in progress, results cannot be made public yet.

Created: 2011-01-12 | Last updated: 2011-01-19

Credits: Nick Malleson

Weka Clustering With Silhouette Analysis A... (2)

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This workflow clusters given QSAR CSV file and performs a silhouette analysis which is visualised in a PDF file. The QSAR data is loaded from a CSV file and converted into a Weka dataset. After that the data is clustered and the results are visualised in a PDF file.

Created: 2011-01-13 | Last updated: 2011-07-21

Weka Clustering Considering Different Orig... (2)

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This workflow clusters the given CSV files with the chosen Weka algorithm. The results are visualized in a PDF file. The CSV files are loaded from hard disk and merged together. Afterwards they are converted into a Weka dataset which is the suitable data type for the Weka clustering activity. The results are visualized as a PDF file showing the cluster membership of each input CSV file.

Created: 2011-01-13 | Last updated: 2011-07-21

Split Molecules Into Clusters (1)

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This workflow splits given molecules into their cluster memberships. The molecules are loaded from a SD file and the relationship data from a CSV file. The results are saved into N different SD files, where N is the number of clusters.

Created: 2011-01-17 | Last updated: 2011-07-21

EBI_NCBI_BLAST (4)

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This workflow performs an NCBI blast at the EBI. It accepts a protein sequence as input. Default values have been set for the search database (Uniprot), the number of hits to return (10), and all scoring and matrix options. These can be changed in the workflow by altering the string constant values if required. This workflow uses the new EBI services. They are asynchronous and so require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now wo...

Created: 2011-01-17 | Last updated: 2013-05-30

Credits: Katy Wolstencroft Hamish McWilliam

Attributions: EBI_NCBI_BLAST

Multi-parameter sensitivity analysis (MPSA... (2)

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Exemplary multi-parameter sensitivity analysis (MPSA) experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) WS operations. In this version of MPSA PRISM probabilistic model checking is basis of analysis of SBML model parameters space.

Created: 2011-07-14 | Last updated: 2011-07-21

Credits: trybik

Plot error surface (1)

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Exemplary workflow for plotting error surface using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) mahtPlot WS operation. Data input format is compatibile with Tav4SB MPSA workflows.

Created: 2011-07-14 | Last updated: 2011-07-14

Credits: trybik

Secure REST service call example (1)

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This is an example of a workflow that contains a call to a secure REST service that requires user to authenticate with HTTP Basic Authentication. You can use testuser/testpasswd as username and password for authentication when running the workflow.

Created: 2011-07-14 | Last updated: 2011-07-14

Credits: Alex Nenadic

Secure Web service call example (1)

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This is an example of a workflow that contains a call to a secure Web service that runs behind HTTPS and requires user to authenticate. The first thing you can expect to see is a pop up dialog asking if you trust the Web service to be invoked over HTTPS. You can use testuser/testpasswd as username and password for authentication when running the workflow. To see where the security is being configured, right-click the service in the diagram and select "Configure security" from the menu.

Created: 2011-07-14 | Last updated: 2011-07-14

Credits: Alex Nenadic

Executes Python script (4)

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Snippet showing how to use Taverna Tool in Service template folder for executing a Python script. This workflow needs Python to be installed on the local system, and declared in the PATH enviromental variable, so any python script could be executed from a terminal.

Created: 2011-07-14 | Last updated: 2013-04-22

Credits: Jose Enrique Ruiz

NOR Service (2)

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Workflow for an automatic orthorectification of raw images service, using the NOR service developed by JRC under the GENESI-DEC and GENESI-DR projects. It takes as input a URL of a zipped SPOT4|SPOT5 raw image, and generates a new URL of a zipped file of the orthorectified image.

Created: 2011-07-15 | Last updated: 2011-07-15

Credits: Panos Thomas

EBI NCBI BLAST Multi FASTA (2)

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This workflow performs multiple sequence similarity searches using the NCBI blast at the EBI. It 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. If you want to make a blast search for more than 10 sequences I would recommend you to run the workflow using the comm...

Created: 2011-07-16 | Last updated: 2011-07-16

Credits: Rafael C. Jimenez

Isoelectric Point (1)

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Calculates the Isoelectric Point for a protein sequence using a protein accession as input

Created: 2011-07-19 | Last updated: 2011-07-20

Credits: Rafael C. Jimenez

getFFEntry WorkFlow (1)

No description

Created: 2011-07-19

PSICQUIC Registry (Molecular Interactions ... (1)

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Query the PSICQUIC registry to retrieve information about services providing molecular interactions

Created: 2011-07-20 | Last updated: 2011-07-20

Credits: Rafael C. Jimenez

Simulate SBML-derived ODEs (2)

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Exemplary experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) ODEs simulation and plotting Web service operations.

Created: 2011-07-20 | Last updated: 2011-07-20

Credits: trybik

List of PSICQUIC services (names and URLs)... (1)

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PSICQUIC provides access to molecular interaction databases. This workflow queries the registry and gets a list of available PSICQUIC services (names and URLs).

Created: 2011-07-20 | Last updated: 2011-07-20

Credits: Rafael C. Jimenez

Probabilistic Model Checking (PMC): comput... (1)

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Exemplary experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) PRISM model translation and model checking Web service operations.

Created: 2011-07-20 | Last updated: 2011-07-20

Credits: trybik

Tutorial 1 Workflow (2)

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Fetch and combine transcriptomics and proteomics data from NSC11 cells in GEO and PRIDE respectively. Apply spectral counting on the proteomics data. The workflow demonstrates how to combine data from different domains (here microarray- based transcriptomics and mass spectrometry-based proteomics) and do something useful with the data. The workflow also demonstrates spreadsheet import and XPath parsing of XML data. This workflow is for tutorial/educational use only. The cells were not grown...

Created: 2014-04-16 | Last updated: 2014-04-16

Credits: Magnus Palmblad

Make Groups for Tutorial (2)

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The workflow pairs people from two groups of equal size into the same number of pairs with one member from each group. This is done randomly, using the random.org randomization engine, which in turn is based on atmospheric radio noise.

Created: 2014-04-16 | Last updated: 2015-10-12

Credits: Magnus Palmblad

ARC to WARC Migration and CDX Index Compar... (1)

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Workflow for migrating ARC to WARC and comparing the CDX index files (Linux). The workflow has an input port “input_directory” which is a local path to the directory containing the ARC files, and an input port “output_directory” which is the directory where the workflow outputs are created. The files in the input directory are migrated using the “arc2warc_migration_cli” tool service component to perform the migration. The “cdx_creator_arc” and “cdx_creator_warc” tool service components creat...

Created: 2014-04-23

Credits: Sven

BUT_UVT_preservationWorkflow_template (1)

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No description

Created: 2014-04-24

Credits: Ondrej Klima

Concept Profile Generation Pipeline (9)

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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: 2014-04-30 | Last updated: 2014-06-15

Credits: Amrish Mahes

Get properties from a properties string (1)

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This workflow shows how to get specific properties from a properties string. The properties string has the format: some.key=Some value another.key=Another value

Created: 2014-05-01

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

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

3D reconstruction (1)

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No description

Created: 2014-05-07

Credits: Ondrej Klima