Workflows

Pathways and Gene annotations forQTL region (1)

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This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the mouse, Mus musculus. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG path...

Created: 2012-01-20 | Last updated: 2012-01-20

Credits: Bonilla

Item rating predictions collaborative-based (1)

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This workflow takes input 2 as as train set for several item recommendation predictions. We build four different recommendation model which are combined into one model with operator Model Combiner. Then we take input 1 as a test set and apply merged model. Train and test set must contain user_id, item_id and rating attributes which need to have special roles user identification, item identification and label. This workflow uses recommender system extension.

Created: 2012-01-19

Item recommendation hybrid-based workflow (1)

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This workflow takes input 2 as a train set for recommender systems. We build two item recommendation models: item k-NN (collaborative based) and item attribute k-NN (content based). Item attribute k-NN operator takes additional item attributes from input 3. We combine two models with operator model combiner and test performance on test set (input 1). Train and test set must contain user_id and item_id attributes which need to have special roles user identification and item identification. Th...

Created: 2012-01-19

RDKit-bioisosteres (1)

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Implementation of a simple bioisostere replacement workflow using the RDKit (2.0.0) nodes in KNIME (2.5.1). Includes short list of classical bioisostere replacements (not exhaustive), selectable by the functional group to be transformed. We added this control to the workflow as our own internal list of bioisostere replacements generated huge libraries for each structure fed into the workflow. The bioisostere replacement list is stored in a tab separated text file, so can be replaced...

Created: 2012-01-18 | Last updated: 2012-01-18

Credits: sauberns

Attributions: RDKit-pains

FFmpeg convert audio2aac (SOAP) (1)

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Converts supported audio files to AAC using FFmpeg through a SOAP webservice.

Created: 2012-01-16 | Last updated: 2012-01-16

Credits: Rui Castro

ImageMagick convert image2jp2 (SOAP) (1)

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Converts supported image files to JPEG2000 using ImageMagick through a SOAP webservice.

Created: 2012-01-16 | Last updated: 2012-01-16

Credits: Rui Castro

ImageMagick convert image2jp2 (REST) (1)

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Converts supported image files to JPEG2000 using ImageMagick through a REST webservice.

Created: 2012-01-16 | Last updated: 2012-01-16

Credits: Rui Castro

FFmpeg convert audio2aac (REST) (1)

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Converts supported audio files to AAC using FFmpeg through a REST webservice.

Created: 2012-01-16 | Last updated: 2012-01-16

Credits: Rui Castro

Reactome pathways (1)

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This workflow returns a list of pathways gene products are involved in, along with their descriptions and Gene Ontology annotations

Created: 2012-01-16

Credits: Katy Wolstencroft

VM distributional morpheme analysis (1)

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Distributional analysis of the Morphemes from the Voynich Manuskript.

Created: 2012-01-16

Credits: jhermes

PIII distributional morpheme analysis (1)

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Distributional analysis of the Morphemes from the Polygraphia III codebook.

Created: 2012-01-16 | Last updated: 2012-01-16

Credits: jhermes

VM grapheme clustering (1)

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Clustering of Graphemes from the Voynich Manuskript,determined by minimal pair analysis.

Created: 2012-01-16

Credits: jhermes

PIII grapheme clustering (1)

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Clustering of Graphemes from Polygraphia III, determined by minimal pair analysis.

Created: 2012-01-16 | Last updated: 2012-01-16

Credits: jhermes

Import and convert gene list (1)

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This workflow extracts a column of RefSeq gene IDs from a CSV file and then converts them to Unigene identifiers

Created: 2012-01-15 | Last updated: 2012-03-12

Credits: Katy Wolstencroft

getFirstElementDFS (2)

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Returns the first element of a nested list using depth first search. The maximum depth of the input is set to 2. You can savely increase this by increasing the depth of the workflow input port and the beanshell input port. Taverna will wrap the input into a list with correct depth. However this will create a little overhead.

Created: 2012-01-13 | Last updated: 2012-02-13

workflow in systems (1)

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Created: 2012-01-12

Credits: Ahmed hosny

VM text parameters (1)

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Calculation of some basic parameters of the text from the Voynich Manuskript (VMS). Parameters: type count, token count, type token ratio, wordlength, entropy, conditional entropy, coincidence values, random walk values, repeated words and minimal pairs. The VMS text (EVA Interlinear Archive File) is referenced in http://www.myexperiment.org/files/660.html)

Created: 2012-01-11

Credits: jhermes

Polygraphia III encription text parameters (1)

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Calculation of some basic parameters of a text, enciphered with the method that the german ape Johannes Trithemius described in his book Polygraphia III Parameters: type count, token count, type token ratio, wordlength, entropy, conditional entropy, coincidence values, random walk values, repeated words and minimal pairs. Enciphed text (from project Guttenberg, referenced in http://www.myexperiment.org/files/660.html): Melanchton: Confessions (ger)

Created: 2012-01-11 | Last updated: 2012-01-11

Credits: jhermes

Renaissance texts parameters (1)

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Calculation of some basic parameters of renaissance texts written in different languages. Parameters: type count, token count, type token ratio, wordlength, entropy, conditional entropy, coincidence values, random walk values, repeated words and minimal pairs. Texts (from project Guttenberg, referenced in http://www.myexperiment.org/files/660.html): Dee (en), dante (it), descartes (lat), ceasar (anc lat), paracelsus (ger), melanchton (ger)

Created: 2012-01-11 | Last updated: 2012-01-11

Credits: jhermes

Calculation of distances, magnitutes and l... (2)

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Calculation of distances, corrected apparent B magnitude mB-corr and luminosities with values gathered from the HyperLEDA database. This workflow receives a list of galaxy names (hyperLEDA names. ie: KIG0001) and a file with the morphological types of those galaxies Using the name of a galaxy, the workflow querys Hyperleda to extract some properties of this galaxy (J2000 Coordinates, velocity, galactic extinction,log of axis ratio, and the Total B-magnitude ). With this properties it calcula...

Created: 2012-01-10 | Last updated: 2012-01-16

Credits: Stian Soiland-Reyes

Attributions: Calculation of distances, magnitutes and luminosities using HyperLEDA Data involved in RO Propagation of quantities Scripts in RO Propagation of quantites

Item recommendation collaborative-based wo... (1)

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This workflow takes input 2 as a train set for item-k-NN recommender system. The model peformance is evaluated on test set (input 1). This workflow uses recommender system extension. Train and test set must contain user_id and item_id atrributes which need to have special roles user identification and item identification.

Created: 2012-01-09 | Last updated: 2012-01-09

Map a Entrez Gene ID to a Gene Ontology ID (1)

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Created: 2012-01-07

Credits: Egon Willighagen

Hello Anyone (1)

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An extension to helloworld.t2flow - this workflow takes a workflow input "name" which is combined with the string constant "Hello, " using the local worker "Concatenate two strings", and outputs the produced string to the workflow output "greeting".

Created: 2012-01-03 | Last updated: 2014-03-03

Credits: Stian Soiland-Reyes

Attributions: Hello World

Hello World (1)

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One of the simplest workflows possible. No workflow input ports, a single workflow output port "greeting", outputting "Hello, world!" as produced by the String Constant "hello".

Created: 2012-01-03 | Last updated: 2014-03-03

Credits: Stian Soiland-Reyes

[untitled] (1)

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 A KUP domain image segmentation workflow that identifies ans annotates important regions on microscopic Kidney biopsy images (vessels and glomerulus)

Created: 2012-01-03 | Last updated: 2012-01-03

Credits: Charalampos