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Bonn Taverna Shims

Created: 2012-08-30 14:18:06

Credits: Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

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Bonn Taverna WF Engine

Created: 2012-08-30 14:15:51

Credits: Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

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Bonn Taverna Intro Tutorial

Created: 2012-08-30 14:11:55

Credits: Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

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Cocatenates several VOTables into one (3)

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Snippet showing how to use AstroTaverna tool for concatenating several VOTables. The input is four VOTables with the same number of columns. The result if using sample values provided will be a four times vertically duplicated VOTable.

Created: 2012-08-30 | Last updated: 2013-04-22

Credits: Julian Garrido

Build plots from galfit and ellipse results (2)

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Build plots from galfit and ellipse results (http://www.myexperiment.org/workflows/3068.html, http://www.myexperiment.org/workflows/3052.html).

Created: 2012-08-30 | Last updated: 2012-09-07

Credits: Julian Garrido

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HELIO Service List for Taverna 2.4

Created: 2012-08-30 09:45:06

Credits: Anja Le Blanc

License: BSD License

File type: XML

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Add columns to a votable resulting from ex... (1)

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Addcolumns that are needed to run galfit and ellipse. it requires columns coming from sextractor and the astrotaverna plugin.

Created: 2012-08-30

Credits: Julian Garrido

Sort 1000 fastest CMEs from a given list a... (1)

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The fastest 1000 CME of the input list are bined in categories by factor of 10 according to their pa_width value. List must contain fields v and pa_width. Output VOTable with the counts in the categories.

Created: 2012-08-30 | Last updated: 2012-08-30

Credits: Anja Le Blanc

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Presentation - Creating Research Objects that contai...

Created: 2012-08-24 16:48:46 | Last updated: 2012-08-24 16:54:54

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Write file to S3 bucket (1)

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This workflow simply writes a text file to an AWS S3 bucket. It is provided as an example of how to do this, rather than be a complete, reusable solution. You need to have s3fs installed and configured with your AWS credentials to use this workflow (see http://code.google.com/p/s3fs/).

Created: 2012-08-23

Credits: Robert Haines

Attributions: Read file from S3 bucket

Read file from S3 bucket (1)

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This workflow simply loads a text file that is stored in an AWS S3 bucket. It is provided as an example of how to do this, rather than be a complete, reusable solution. You need to have s3fs installed and configured with your AWS credentials to use this workflow (see http://code.google.com/p/s3fs/).

Created: 2012-08-23

Credits: Robert Haines

Monthly counts for event occurences betwee... (1)

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This workflow provides monthly counts of events in HEC between the beginning of year_start and the end of year_end. Returns the result as comma separated file (csv) and as list of lists.

Created: 2012-08-23

Credits: Anja Le Blanc

Attributions: Counts number of events per month in HEC table Split VOTable into its values

Counts number of events per month in HEC t... (1)

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This workflow counts the monthly number of events in a HEC table from the begining of year year_start to the end of year year_end. Returns a VOTable with the count

Created: 2012-08-22

Credits: Anja Le Blanc

Monthly counts for feature occurences betw... (1)

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This workflow provides monthly counts of features in HFC between the beginning of year_start and the end of year_end. Returns the result as comma separated file (csv) and as list of lists.

Created: 2012-08-22

Credits: Anja Le Blanc

Attributions: Number of recorded features in catalogue per month Split VOTable into its values

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Bozeman Tutorial

Created: 2012-08-22 09:59:37

Credits: Katy Wolstencroft

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

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Number of recorded features in catalogue p... (1)

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The number of features of the specified catalogue are counted per month between beginning of the year_start und the end of the year_end. Return format is VOTable

Created: 2012-08-22

Credits: Anja Le Blanc

Get a list of proteins annotated with an O... (3)

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A service to look for models in BioModels using an Ontology Id as input. First the workflow will look in QuickGO for UniProt accessions annotated with the provided Ontology Id. Then it will look for models using the list of proteins. If one of the input protein is found in one model the workflow will provide the BioModels Id, the SBML and a link to the BioModels database. Please use taverna 2.4 or above.

Created: 2012-08-22 | Last updated: 2013-07-10

Credits: Rafael C. Jimenez

Get models from BioModels including the in... (3)

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A service to look for models in BioModels using a UniProt accession as input. If the input protein is found in one model the workflow will provide the BioModels Id, the SBML and a link to the BioModels database. Please use taverna 2.4 or above.

Created: 2012-08-22 | Last updated: 2012-08-24

Credits: Rafael C. Jimenez

Number of features in a month in a year (1)

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Returns the number of features in a HFC catalogue which occured in a month in a year given as inputs.

Created: 2012-08-21

Credits: Anja Le Blanc

Create votable from different galfit param... (2)

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The workflow creates a votable from the results provided by galfit. It returns this table and an aditional table that is joined to the input table. It requires a votable that contains a column with the file name resulting from running galfit and such files must be accesible from taverna. It uses astrotaverna plugin (http://wf4ever.github.com/astrotaverna/) and it has a dependency on stil library (http://www.star.bris.ac.uk/~mbt/stil/). The galfit files may come from adjusting 'disk, bulb, ba...

Created: 2012-08-21 | Last updated: 2012-09-07

Credits: Julian Garrido

Create_SNP_Set (1)

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The purpose of the workflow is to determine SNPs in the vicinity of the genes and create a SNP set for a given set of genes. The user has the freedom to choose the flanking width around the gene for determining the SNPs. The input is in the form of entrez gene ids. Biomart services are used to determine the chromosome and position of the gene as well as determining Affy gene chip 6k ids. The final report is stored as a tab-delimited text file with Affy 6 gene chip ids for the SNP and Kegg inf...

Created: 2012-08-21

Credits: Harish Dharuri

Kegg:Reactions Scheme (2)

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The purpose of this workflow is to determine all the enzymes/genes that participate in a radius of 2 reaction steps around a given metabolite. Broadly, the scheme involves the following steps: 1. determine all the reactions that the given metabolite participates in 2. determine all the compounds that participate in these reactions 3. filter certain compounds like H2O, ATP etc to avoid non-specific connections 4. determine all the reactions that the compounds passing through step 3 participate...

Created: 2012-08-20 | Last updated: 2013-08-27

Credits: Harish Dharuri

Check HEC instances for diverging content (2)

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This workflow check all tables in HEC on festung1 and festung3 for diverging content by comparing the last 1000 entries in each table. Output is a list of tabel names with different content.

Created: 2012-08-20 | Last updated: 2012-08-20

Credits: Anja Le Blanc

Hadoop Large Document Collection Data Prep... (1)

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Workflow for preparing large document collections for data analysis. Different types of hadoop jobs (Hadoop-Streaming-API, Hadoop Map/Reduce, and Hive) are used for specific purposes. The *PathCreator components create text files with absolute file paths using the unix command 'find'. The workflow then uses 1) a Hadoop Streaming API component (HadoopStreamingExiftoolRead) based on a bash script for reading image metadata using Exiftool, 2) the Map/Reduce component (HadoopHocrAvBlockWidthMapR...

Created: 2012-08-17 | Last updated: 2012-08-18

Credits: Sven

KEGG:Pathway Scheme (2)

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The purpose of the workflow is to determine all the genes operating in the pathways that the input metabolite participates in. The overall idea is to generate a set of genes that potentially influence the levels of a metabolite due to the common pathways that they share.

Created: 2012-08-14 | Last updated: 2013-08-27

Credits: Harish Dharuri