Workflows in this Topic

untitled (1)

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Created: 2008-01-28

Credits: Agbiotec

Probeset_id_2_Swissport_id.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

gene_info_to_gene_name.xml (1)

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Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

get_best_best_neighbors_by_gene (1)

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Search the best-best neighbor of a gene in all organisms. Example of input: gene_id: eco:b0002 offset: 1 limit: 10

Created: 2008-10-02

Credits: Franck Tanoh

Blast against ENSEMBLE Danio_rerio_Genome (1)

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This workflow invokes the blast service provided at www.bioinformatics.nl, written by Pieter Neerincx. The workflow takes as input a database name (Danio_rerio_Genome for Zebra Fish for example) and a set of sequences in fasta format. The blast service is invoked (using polling) and the result is a tab separated blast report.   To run this workflow, a certificate to access www.bioinformatics.nl needs to installed (Some services use an SSL connection). Look at the link below how to ins...

Created: 2008-10-15 | Last updated: 2008-10-15

Credits: Wassinki

COVE Workflow (1)

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This workflow reads data from a netCDF file and sends out a message to COVE (collaborative ocean visualization environment). COVE reads the netCDF data and renders that.  

Created: 2008-10-21 | Last updated: 2008-10-21

Credits: Trident

NetCDFDiff (1)

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This WF reads two netCDF files to two hyper cube data structures. Then this workflow uses the HyperCubeDiffTransform activity to perform difference operation between the values of a netCDF variable read from the two files. The WF generates a difference cube as output.

Created: 2008-10-21

Credits: Trident

NETCDFMean (1)

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This WF reads a netCDF file to a hyper cube data structure. Then this WF applies the mean transform to a variable in the netCDF file. The calculated mean is produced as part of the output.

Created: 2008-10-21

Credits: Trident

XSL Transform (1)

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This WF downloads a web page and converts the content from HTML to XSL.

Created: 2008-10-21

Credits: Trident

MiscanMod (1)

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Created: 2009-03-27 | Last updated: 2009-04-23

Credits: Robert Muetzelfeldt

LINTUL crop model (1)

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Created: 2009-04-01

Credits: Robert Muetzelfeldt

Taverna rendering of the PAN-STARRS workfl... (1)

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Example inputs: CSVRootPath = /Users/paolo/Documents/myGRID/OPM/PC3/SampleData/J062941 JobID:J062941  

Created: 2009-04-30

Credits: Paolo

snpNeighbours (1)

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My first Taverna workflow:  the input is the SNP "rs25". The Web Services invoked finds its position on the human genome and find its neighbours at 100bp. The XML result is then saved to a local file. The web services used here are under developpement and might be turned off in a near future.

Created: 2009-05-14 | Last updated: 2009-05-14

Credits: PL

t ... (2)

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Created: 2009-08-21 | Last updated: 2009-10-09

Credits: Ctindal

Tutorial Taverna (1)

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Created: 2010-02-26 | Last updated: 2010-02-26

Credits: Rodriguez

OpenTox Apply Model On Dataset (3)

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Apply a model to predict a dataset

Created: 2010-05-11 | Last updated: 2010-05-11

Nucleotide frequency workflow (2)

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No description

Created: 2010-05-13 | Last updated: 2010-11-12

Credits: wabi

For loop sample for Trident v1.2 (1)

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  Please refere following link for more information http://tridentworkflow.codeplex.com/Project/Download/FileDownload.aspx?DownloadId=138916

Created: 2010-08-19 | Last updated: 2010-08-24

Credits: Trident

Replicator Activity sample for Trident v1.2 (1)

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The objective of this workflow is to explain the working of the Replicator activity in the Trident application. For detailed description of the worklfow please refer the following document. Sample Description

Created: 2010-09-03 | Last updated: 2010-09-03

Credits: Trident

IfEls Activity sample for Trident v1.2 (v1) (1)

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The objective of this workflow is to explain the working of the If Else activity in the Trident application.  For more information on how to use the if else sample. Please refere the following document. IfElse-Sample Details

Created: 2010-09-03 | Last updated: 2010-09-03

Credits: Trident

Sample for explaining the feature: - Type ... (1)

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The objective of this workflow is to explain the working of the Type Initializer in the Trident application.   For detailed information on type initializer and how it can be used please refer the following document:- http://tridentworkflow.codeplex.com/Project/Download/FileDownload.aspx?DownloadId=138922  

Created: 2010-09-03 | Last updated: 2010-09-03

Credits: Trident

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

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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

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

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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

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

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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

Change Class Distribution of Your Training... (1)

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This example process shows how to change the class distribution of your training data set (in this case the training data is what ever comes out of the "myData reader"). The given training set has a distribution of 10 "Iris-setosa" examples, 40 "Iris-versicolor" examples and 50 "Iris-virginica" examples. The aim is to get a data set which has the class distribution for the label, lets say 10 "Iris-setosa", 20 "Iris-versicolor" and 20 "Iris-virginica. Beware that this may change some propert...

Created: 2011-01-21 | Last updated: 2011-01-21

Read files from Directory (1)

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This workflow reads files from a given directory, based on a known file extension (e.g. .txt), and then outputs the contents of each file in a single value/single list.

Created: 2011-02-03 | Last updated: 2011-02-03

Credits: Paul Fisher

Diabetes_workflow (1)

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No description

Created: 2011-03-31 | Last updated: 2011-03-31

Credits: Munasultan Banu

[untitled] (1)

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This workflow allows the user to search for processes that are involved with a certain gene. Using microarray-files (CEL-files), consisting of wild type and KO mice to which a stimulant is induced, the user can get an idea of the processes involved. (This is done using the global test and the literature weighted global test.) The results are then given as a text-file. Warning: workflow is not working (needs some revisions), all input is currently hardcoded! (You will have to change the file...

Created: 2011-04-26 | Last updated: 2011-04-26

Credits: Dennis Leenheer

Example for external tools with gzip and g... (1)

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This workflow is self-contained. It has a fixed URL from which a text file is downloaded (output as Original_file). That file is gzipped (output as Compressed_File) and then gunzipped again (output as Decompressed_File). The workflow wraps external tools from taverna.nordugrid.org and needs a beta version of Taverna 2.3 or later.

Created: 2011-05-18 | Last updated: 2011-05-18

Credits: Steffen Möller Alan Williams

The NOTCH2 workflow (1)

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Analysis of the exome sequencing data for the following article: Nat Genet. 2011 Mar 6;43(4):306-8. Truncating mutations in the last exon of NOTCH2 cause a rare skeletal disorder with osteoporosis. Isidor B, Lindenbaum P, Pichon O, Bézieau S, Dina C, Jacquemont S, Martin-Coignard D, Thauvin-Robinet C, Le Merrer M, Mandel JL, David A, Faivre L, Cormier-Daire V, Redon R, Le Caignec C. using knime4bio

Created: 2011-09-06 | Last updated: 2011-09-06

Credits: PL

City weather information (1)

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Get the weather forcast of the day for you city. Info display: wind, visibility, temperature, sky conditions and pressure. The default value is my home town. To find out any supported city run the 'Get cities by country name' workflow

Created: 2011-09-14 | Last updated: 2011-09-14

Credits: Wdsnellg

Instance Selection and Prototype Based Rul... (1)

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Example of Instance selection chain (Requires Instance Selection and Prototype Based Rules plugin): Beafore training kNN we do instance selection based on cascade of instance selection algorithms. Here ENN algorithm is followed by CNN algorithm. Instance selection algorithms form PRules plugin works as View on original ExampleSet

Created: 2011-11-05

Sample IMPACT hackathon workflow (1)

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Workflow that implements the Use Case for Group 2 at the IMPACT/Taverna hackathon. What it does is to take the URL of a TIFF image and compute the Levenshtein difference between the OCR output of the uncompressed version with various ones compressed at various bit rates.

Created: 2011-11-14 | Last updated: 2012-06-19

Credits: Donal Fellows

workflow in systems (1)

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Created: 2012-01-12

Credits: Ahmed hosny

A heuristic measure for detecting undesire... (2)

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The workflow takes TIFF image instances as input, applies a list of JP2 compression parameter values, executes OCR using an open source OCR engine, evaluates the results, and creates a diagram visualising the results. Dependencies on external tools for the tool service components: Tesseract ImageMagick Kakadu Gnuplot Dependencies on external Java libraries of beanshells: Apache commons lang

Created: 2012-02-06 | Last updated: 2012-03-09

Credits: Sven

Define Associated Regions and Genes (2)

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Defines regions and genes from associated SNPs A JAVA MySQL connector is required to run the workflow and must be placed in the $TAVERNA_HOME/lib directory.

Created: 2012-02-08 | Last updated: 2012-05-09

Credits: Paul martin

Parse QuickGO "proteinList" file format (2)

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Parse QuickGO "proteinList" file format. http://www.ebi.ac.uk/QuickGO/reference.html

Created: 2012-02-20 | Last updated: 2013-07-10

Credits: Rafael C. Jimenez

Migrate Pipeline Workflow (1)

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Migrate estimates effective population sizes and past migration rates between n population assuming a migration matrix model with asymmetric migration rates and different subpopulation sizes. Migrate uses maximum likelihood or Bayesian inference to jointly estimate all parameters.     Workflow Usage & Specifications Migrate can use the following data types: •Sequence data using Felsenstein's 84 model with or without site rate variation, •Single nucleotide poly...

Created: 2012-03-08

Credits: Pipeline

Hadoop Large Document Collection Data Prep... (1)

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Workflow for preparing large document collections for data analysis. Different types of hadoop jobs (Hadoop-Streaming-API, Hadoop Map/Reduce, and Hive) are used for specific purposes. The *PathCreator components create text files with absolute file paths using the unix command 'find'. The workflow then uses 1) a Hadoop Streaming API component (HadoopStreamingExiftoolRead) based on a bash script for reading image metadata using Exiftool, 2) the Map/Reduce component (HadoopHocrAvBlockWidthMapR...

Created: 2012-08-17 | Last updated: 2012-08-18

Credits: Sven

Tesseract 2.04 Basic Workflow (1)

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 Elementary workflow for execution on the on-line DAE platform. (requires an uncompressed tiff image URL as input or will fail otherwise)

Created: 2012-10-16

Credits: Bart Lamiroy

Ocrad 0.19 Basic Workflow (1)

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Elementary OCR workflow for execution on the on-line DAE platform. Implement v0.19 of the ocrad OCR engine. (requires an PGM or PMB input image URL) 

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

Credits: Bart Lamiroy