Workflows

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)

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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