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Example of a conditional execution workflow (1)

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If the input is true then the string 'foo' is emited, if false then 'bar'. Just a simple example to show how the monster works, so to speak.

Created: 2011-08-04

Credits: Taverna 1.7.1 workflow workbench examples

sampleDistribution Web service operation (1)

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Probabilistic distribution sampling operation which uses Mathematica software (http://www.wolfram.com/mathematica/).

Created: 2011-08-03 | Last updated: 2011-08-04

Credits: trybik

Find common events in HEC tables which use... (5)

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Use only tables which provide lat_hg and long_hg. Inputs: table names of two HEC tables; time interval in which the search is being conducted; delta for time and location to enlarge the search space. Output: VOTable which combines the resultset of the HEC by the common event.

Created: 2011-08-03 | Last updated: 2012-02-03

Credits: Anja Le Blanc

EUADR - Literature Analysis (1)

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The aim of the "Literature Analysis" workflow is to automate the search of publications related to ADRs corresponding to a given drug/adverse event association. To do so, we defined an approach based on the MeSH thesaurus, using the subheadings «chemically induced» and «adverse effects» with the “Pharmacological Action” knowledge.

Created: 2011-07-27 | Last updated: 2011-07-27

Credits: Avillach

EUADR Relationship Extraction Workflow (1)

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The workflow offers the ability to automatically determine if an ADR and a Drug are co-mentioned in any of the indexed resources. However the actual relationship between a Drug and an ADR can only be determined by referring to the actual resource The co-occurance relationship workflow seeks to automate the search for resources (publications, drug labels) related to ADRs corresponding to a given drug/ adverse event association. To enable this concept profiles for drugs and adverse effects wer...

Created: 2011-07-27 | Last updated: 2012-09-07

Credits: Bharat Singh

Get a PSICQUIC REST URL from a PSICQUIC SO... (1)

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Get a PSICQUIC REST URL from a PSICQUIC SOAP URL

Created: 2011-07-22 | Last updated: 2011-07-22

Credits: Rafael C. Jimenez

Genetic Algorithm for Input Component Anal... (1)

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This workflow uses a genetic algorithm to optimize the given molecular descriptor set. Afterwards the workflow splits the data into a training set and test set and evaluates the results which are stored as PDF files.

Created: 2011-07-22

Get Molecular Interactions from a PSICQUIC... (3)

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Check the different iput parameter you could use for this workflow in ... http://code.google.com/p/psicquic/wiki/RestAccess Check available PSICQUIC Services in ... http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS More about PSICQUIC ... http://code.google.com/p/psicquic/

Created: 2011-07-22 | Last updated: 2013-07-10

Credits: Rafael C. Jimenez

QSAR CSV to Weka Regression Dataset (1)

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This workflow converts the molecular descriptor data from a CSV file to a Weka XRFF file. The workflow merges the retention time values from IN IDRT CSV with the molecular descriptor values from IN QSAR CSV to create a valid Weka regression set.

Created: 2011-07-21

Weka Regression from XRFF file. (1)

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The here shown workflow splits the given data into a training set and a test set. Afterwards a machine learning model is created by the Weka Regression worker which is evaluated by the Evaluate Regression Results as PDF worker. The resulting sets are stored as XRFF files in the folder determined by the OUT TRAIN XRFF and OUT TEST XRFF input ports. The calcualted machine learning models and the evaluation results are saved in the folder of OUT MODEL input port

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

ELM Database Retrieval Workflow (1)

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This workflow retrieves all the current entries stored in the Eukaryotic Linear Motif (ELM) Database and returns all entries in a collated readable format. This requires the ELM Database retrieval WSDL file: http://elm.eu.org/webservice/ELMdb.wsdl

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

Credits: Kieren Lythgow

Probabilistic Model Checking (PMC): plot r... (1)

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Exemplary experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) Mathematica plotting Web service operation. This is a second-part for the computationaly exhaustive PMC: compute results workflow (http://www.myexperiment.org/workflows/2266).

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

Credits: trybik

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

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

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

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

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

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

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

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kidney factomics nominalised triples in RDF

Created: 2011-07-14 22:04:54

Credits: James Eales

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: RDF data

Comments: 0 | Viewed: 41 times | Downloaded: 24 times

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kidney factomics triples in RDF

Created: 2011-07-14 21:58:57

Credits: James Eales

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: RDF data

Comments: 0 | Viewed: 35 times | Downloaded: 23 times

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flower

Created: 2011-07-14 16:30:12

Credits: Pradeepa thomas

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: JPEG image

Comments: 0 | Viewed: 23 times | Downloaded: 15 times

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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

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

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RapidMiner Workspace with Processes and Results from...

Created: 2011-07-14 13:21:27 | Last updated: 2011-07-14 13:21:28

Credits: http://viswanathgs.myopenid.com/

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: ZIP archive

Comments: 0 | Viewed: 102 times | Downloaded: 64 times

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Fast Correlation Based Filter (FCBF) (1)

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Runs FCBF feature selector and accuracy is estimated using Naive Bayes. Grid Search Optimization is used for parameter optimization.

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

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

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

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

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

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 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

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addthem.sh

Created: 2011-07-13 10:15:22

Credits: Alan Williams Steffen Möller

Attributions: External Tool: Numerically adding two values with 'bc'.

License: Creative Commons Attribution 3.0 Unported License

File type: UNIX script

Comments: 0 | Viewed: 45 times | Downloaded: 19 times

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Presentation - Web Services in the Scientific Wilds

Created: 2011-07-12 22:35:26 | Last updated: 2011-07-12 23:18:41

3 items in this pack

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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

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

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

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

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

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

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

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

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

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

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

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

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

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

Iterate over Attribute Subsets and Store A... (1)

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This process iterates over all possible feature subsets and stores a) the names of all attribute subsets, b) the number of used features, and c) the achieved performance in a log table which can then be further analyzed.

Created: 2011-07-07

Trim and Replace White Space (1)

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This process removed leading and trailing white spaces from an attribute and replaces inner white spaces of any type by a single space. Might be useful for text processing (if you are not using tokenization anyway...)

Created: 2011-07-07