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

Propagation of the Solar Energetic Particl... (2)

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use of the processing service to calculate time delays to the planets Inputs: time when propagation should start longitude of starting point on the sun speed of the solar wind error value of solar wind speed traveling speed of energetic particals as percentage of the speed of light

Created: 2011-12-13 | Last updated: 2012-02-03

Credits: Anja Le Blanc HELIO

Propagation of the Co-roationg interaction... (2)

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use of the processing service to calculate time delays to the planets Inputs: time when propagation should start longitude of starting point on the sun speed of the solar wind error speed of the solar wind

Created: 2011-12-13 | Last updated: 2012-02-03

Credits: Anja Le Blanc

Connect flare events with proton events on... (2)

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This workflow uses flares listed in any HELIO HEC flare catalogue (using the semantic mapping service), checks whether these flares are connected to Earth via the Parker spiral, and looks for proton events at earth listed in the goes_proton_event list. The flare listing and the proton listing are combinded into a list of VOTable outputs (one VOTable per flare catalogue with results).

Created: 2011-12-09 | Last updated: 2011-12-13

Credits: Anja Le Blanc

Attributions: Connect flare events with proton events on Earth via propagation model

dcraw (sRGB, ColorInterpolated, FixedWhite... (2)

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Reads a RAW image with these parameters using dcraw and returns the image data as byte array.

Created: 2011-12-08 | Last updated: 2011-12-16

dcraw (sRGB, ColorInterpolated, FixedWhite... (2)

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Reads a RAW image with these parameters using dcraw and returns the image data as byte array.

Created: 2011-12-08 | Last updated: 2011-12-16

dcraw (NoConversion, NoInterpretation, Fix... (4)

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Reads a RAW image with these parameters using dcraw and returns the image data as byte array.

Created: 2011-12-08 | Last updated: 2011-12-16

Match concept profiles (6)

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Purpose of workflow: The workflow can be used to match a set of concept profiles with another set of concept profiles. Result: A list of concepts ordered by their match to the query concept profiles.

Created: 2011-12-02 | Last updated: 2014-07-14

Credits: Marco Roos Kristina Hettne Martijn Schuemie Reinout van Schouwen

Comparison and update values (1)

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This workflow receives two files, the name of a table and the name of a field as input. One of the file should be contain a list of old values (name galaxy and value), and the other one should be a list of new values (name galaxy,value) The workflow makes a comparison between the two files. This comparison will be a list of 7 columns: name of the galaxy, old value, old error, new value, new error, difference of value, difference of error. In other hand, this workflow makes a sql script with ...

Created: 2011-11-30 | Last updated: 2011-11-30

Gathering galaxy properties using HyperLEDA (2)

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The user provides an ASCII text file with a list of galaxy names, and the workflow queries the HyperLEDA database and parses the response with the help of regular expressions included in simple Python scripts. The result of the workflow is a series of ASCII text files with the values of the equatorial coordinates in J2000 epoch, the velocities in km/s, the dust extinction coefficient Ag, the axis ratio of the isophote 25 mag/arcsec2 logr25 and the apparent total B magnitude BT. The performanc...

Created: 2011-11-30 | Last updated: 2013-03-08

Propagation of physical quantities in the ... (3)

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This workflow takes as input a file for each of this properties: J2000 Coordinates, velocity, galactic extinction, log of axis ratio, and the Total B-magnitude. With this properties it calculates the distance of the galaxy and, in other hand, the total apparent corrected B-magnitude. It takes account if the velocity of the galaxy is lower than a threshold (1000km/s), it can not be possible to calculate the distance so, in those cases the distance will be "NaN". At the end, it calculates the ...

Created: 2011-11-30 | Last updated: 2013-04-22

Literacy Rate and GDP/Capita Increase (Per... (1)

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This is a workflow for a Cyberinfrastructure class (Fall 2011) at Syracuse University. It takes information from GapMinder and runs it through a workflow to produce a graph. The original data sets can be found here: https://spreadsheets.google.com/pub?key=pyj6tScZqmEdrsBnj2ROXAg&gid=0 (Literacy rate, adult total) https://spreadsheets.google.com/pub?key=phAwcNAVuyj1jiMAkmq1iMg&gid=0 (Income per person)

Created: 2011-11-28 | Last updated: 2011-11-28

Credits: Kayleigh Ayn Bohémier

Attributions: Spreadsheet Import Example

Handling data and time example (1)

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This process shows how date and time formats can be converted from arbitrary formats to other arbitrary formats with the operators "Nominal to Date" and "Date to Nominal".

Created: 2011-11-28

[untitled] (2)

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This is a workflow for a Cyberinfrastructure class (Fall 2011) at Syracuse University. It takes information from GapMinder and runs it through a workflow to produce a graph. The original data sets can be found here: https://spreadsheets.google.com/pub?key=pyj6tScZqmEdrsBnj2ROXAg&gid=0 (Literacy rate, adult total) https://spreadsheets.google.com/pub?key=pyj6tScZqmEdIyrBS31XAaw&gid=0 (Income share of poorest 20%)

Created: 2011-11-27 | Last updated: 2011-11-27

Credits: Kayleigh Ayn Bohémier

Attributions: Spreadsheet Import Example Broccoli: A State Comparison

Comparison of Birth and Death Rates for a ... (1)

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This workflow extracts the relevant data from two spreadsheets, formats the data strings, and puts that data through a REST to Google Charts. Data collected for this project comes from data.un.org. Currently, the workflow supports data from only one country at a time (data from data.un.org can be filtered and exported directly from the website). Data from the Live births by month and Deaths by month works best with this workflow.

Created: 2011-11-27 | Last updated: 2011-11-27

Credits: tpacurtis

FetchandDisplaySpecies (3)

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This workflow uses GBIF to search and report species occurrence data and then displays them on Google Earth. An interactive step then allows you to alter the co-ordinates of data displayed.

Created: 2011-11-27 | Last updated: 2011-11-29

Credits: Alan Williams

NSF Funds dataset US dollar to Euro curren... (1)

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This workflow uses a 2012 Fiscal Year dataset from the National Science Foundation (NSF), a currency conversion web service from WebservicesX.NET and processes data using the workflow tool Taverna.  It converts US dollars from a spreadsheet to Euros.

Created: 2011-11-25 | Last updated: 2011-11-25

Credits: Trisha Adamus

Image files comparison using histograms an... (2)

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This workflow extracts histogram and profile features from image file applying image processing command line tool. Necessary configuration files are stored on Github (https://github.com/openplanets/scape/tree/master/pc-qa-toolwrapper). As a template for creation of image workflows was used xa-toolwrapper project from Sven Schlarb (https://github.com/openplanets/scape/tree/master/xa-toolwrapper). This workflow provides WSDL web service that wraps command line tool with tho options ‘extra...

Created: 2011-11-22 | Last updated: 2011-11-23

Credits: Roman

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: 2011-11-21 | Last updated: 2011-11-21

Credits: Prashanth

Pathways and Gene annotations forQTL region (2)

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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: 2011-11-21 | Last updated: 2011-11-21

Credits: Prashanth

Tag Clustering (TaCl) (1)

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This is a sample process for a tag clustering. See http://www-ai.cs.uni-dortmund.de/SOFTWARE/TaCl/index.html

Created: 2011-11-17 | Last updated: 2011-11-17

Compare OCR result of original and BW vers... (1)

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 Use the word based edit distance to compare the OCR result of the original and a binarised version of an image

Created: 2011-11-15 | Last updated: 2011-11-15

Credits: perdalum IMPACT-myGrid-Hackathon

Attributions: Calculate edit distance based on words

Associate a Shock at Earth with Flare and ... (2)

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Using start date and end date all shock events at Earth are backpropagated to the Sun. Arround the time all flares (above certain levels) and cmes are assoicated. The possition of the flare and speed of the CME are used to forward propagate the event to Mars.

Created: 2011-11-15 | Last updated: 2012-07-20

Credits: Anja Le Blanc David PS

Connect flare events with proton events on... (4)

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This workflow uses flares listed in the goes_sxf_flare list, checks wether this flare is connected to Earth via the Parker spiral, and looks for proton events at earth listed in the goes_proton_event list. The flare listing and the proton listing is combinded into a VOTable output.

Created: 2011-11-15 | Last updated: 2012-05-15

Credits: Anja Le Blanc