Workflows

JSI Subgroup Discovery operators (1)

• Download

A simple example of how to use subgroup discovery operators for learning subgroup descriptions and how to test their classification accuracy using cross-validation.

Created: 2011-01-10 | Last updated: 2011-01-10

Text preprocessing (1)

• Download

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

RBioconductor Tutorial Process (1)

• Download

This Process illustrates how to create complex Data Analysis processes using R Scripts. In this case the Bioconductor Basic Tutorial is splitted into reusable components.

Created: 2011-01-03

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

• Download

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

Lemmatization (3)

• Download

The workflow lemmatizes the text in the input port. Takes text as input and returns (language dependent) lemmatized text as output. All the words in the resulting text are in the same order as in the original text, but they are transformed to their dictionary form. The workflow asks for the language of lemmatization. Currently, 12 languages are supported: en,sl,ge,bg,cs,et,fr,hu,ro,sr,it,sp.

Created: 2010-12-17 | Last updated: 2010-12-23

Credits: Petra Kralj Novak

Attributions: Select from a list of possible web service parameter values

Get Molecular Weight Distribution From QSA... (2)

• Download

This workflow calculates a molecular weight distribution from given QSAR vector. The QSAR data containing the molecular weight values is read from a CSV file and converted into a QSAR vector. Finally, the Get_molecular_Weight_Distribution_From_QSAR_vector extracts the weight data and saves it as CSV files.

Created: 2010-12-15 | Last updated: 2011-07-21

Compound Library Screen For Reaction Enume... (2)

• Download

This workflow performs a compound library screen for molecules which match the given template reaction. The reaction is loaded from a RXN file and the Reaction_Reactant_Splitter splits the reaction into its reactants. The compound library is loaded iteratively from a SD file. Afterwards a substructure search is performed for each reactant and the results are saved as SD files.

Created: 2010-12-14 | Last updated: 2011-07-21

Biomart and 2x BLAST (1)

• Download

Perform Roden and Invertebrates BLAST sequence alignments (using DDBJ Blast) on the gene sequences for a (semi-random) selection of genes from Human sapiens chromosome 22. (Using Biomart). blast_ddbj_invertebrates and blast_ddbj_rodents should execute in parallel as they don't depend on each other.

Created: 2010-12-13 | Last updated: 2010-12-13

Biomart and Blast with concatinated gene id (1)

• Download

Perform Rodent BLAST sequence alignments (using DDBJ Blast) on the gene sequences for a (semi-random) selection of genes from Human sapiens chromosome 22. (Using Biomart). Finally (to showcase Taverna pipelining) - the Ensembl gene ID is added as a prefix on the BLAST report. Referenced in the Taverna knowledge blog.

Created: 2010-12-13 | Last updated: 2010-12-13

Attributions: BLAST using DDBJ service Biomart and Blast

Biomart and Blast (1)

• Download

Perform Rodent BLAST sequence alignments (using DDBJ Blast) on the gene sequences for a (semi-random) selection of genes from Human sapiens chromosome 22. (Using Biomart) Referenced in the Taverna knowledge blog.

Created: 2010-12-13 | Last updated: 2010-12-13

Attributions: BLAST using DDBJ service