Workflows

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