Workflows

PRM With External Data (1)

• Download

IN PROGRESS! Runs the PRM using data from an external on-line source.

Created: 2011-01-19 | Last updated: 2011-01-19

Credits: Nick Malleson

QSPR Model Discovery -- workflow structure... (2)

• Download

replicates the structure of the QSPR model discovery workflow. Ref.: replicates the structure of the QSPR model discovery workflow. Ref.: http://www.openqsar.com/

Created: 2011-01-18 | Last updated: 2011-01-18

EBI_InterproScan_NewServices (2)

• Download

This workflow performs an interproscan on provided sequencesThis 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: 2011-01-17 | Last updated: 2011-01-17

Credits: Katy Wolstencroft Hamish McWilliam Stian Soiland-Reyes

Attributions: EBI_InterProScan for Taverna 2 EBI_InterProScan for Taverna 2 EBI_InterProScan

Split Molecules Into Clusters (1)

• Download

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

2. Getting Started: Retrieve and Apply a M... (1)

• Download

This getting started process demonstrates how to load (retrieve) a model from the repository and apply it to a data set. The result is a data set (at the lab output for "labeled data" ) with has a new "prediction" attribute which indicated the prediction for each example (ie. row/record). You will need to adjust the path of the retrieve data operator to the actual location where the model is stored by a previews execution of the "1. Getting Started: Learn and Store a...

Created: 2011-01-17 | Last updated: 2011-01-19

1. Getting Started: Learn and Store a Model (1)

• Download

This getting started process shows the first step of learning and storing a model. After a model is learned, you can load (Retrieve operator) the model and apply it to a test data set (see 2. Getting Started: Retrieve and Apply Model). The process is NOT concerned with evaluation of the model. This process will not immediately run in RapidMiner because you have to adjust the repository path in the Retrieve operator. Tags: Rapidminer, model, learn, learning, training, train, store, first step

Created: 2011-01-17 | Last updated: 2011-01-17

Count co-occurences in matrix with Aggrega... (1)

• Download

The process counts and shows all combinations of values of two attributes and shows them in a count matrix. The process uses the operators Aggregate and Pivot for this purpose.

Created: 2011-01-15

Weka Clustering Considering Different Orig... (2)

• Download

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

Population reconstruction and dynamic popu... (2)

• Download

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

Text stemming with Porter Stemmer (1)

• Download

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

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