Workflows

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Showing 13 results. Use the filters on the left and the search box below to refine the results.
Type: Taverna 2 Tag: cabig Licence: by-sa
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Workflow Lymphoma type prediction based on microar... (7)

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Scientific value Using gene-expression patterns associated with DLBCL and FL to predict the lymphoma type of an unknown sample. Using SVM (Support Vector Machine) to classify data, and predicting the tumor types of unknown examples. Steps Querying training data from experiments stored in caArray. Preprocessing, or normalize the microarray data. Adding training and testing data into SVM service to get classification result.

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

Credits: User Wei Tan User Ravi User Stian Soiland-Reyes

Workflow Using CQL to query protein sequence data (1)

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To query protein sequence infomation out of 3 caGrid data services: caBIO, CPAS and GridPIR Adapted from http://www.myexperiment.org/workflows/600

Created: 2009-05-07

Credits: User Stian Soiland-Reyes

Attributions: Workflow Using CQL to query protein sequence data

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Workflow caDSR Data service query in caGrid (3)

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This workflow is used as an example in this wiki article: https://wiki.cagrid.org/display/knowledgebase/How+to+Create+CaGrid+Workflow+Using+Taverna+2   Tested with Taverna 2.1.2 as of 6/10/2010

Created: 2010-05-25 | Last updated: 2010-06-11

Credits: User Wei Tan

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Workflow Support-Vector-Machine (SVM) based data cl... (2)

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Support-Vector-Machine based data classificationSupport-Vector-Machine based data classification using genePattern SVM service, the input should be in genePattern STATML format.

Created: 2010-05-24 | Last updated: 2010-05-24

Credits: User Wei Tan

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Workflow An example workflow with WSRF service (1)

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An example workflow with WSRF service The service used is http://sidgrid.ci.uchicago.edu:8100/wsrf/services/CounterService The service is included in Globus toolkit installation (ws-core). If the it is down you can host your own and modify the workflow definition file to point to your own. The workflow first creates a counter instance and adds the value 10 for two times to the same counter. Therefore the result should be 20.

Created: 2009-07-28

Credits: User Wei Tan User Stian Soiland-Reyes

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Workflow genePattern data preprocessing (2)

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preprocess data set using genePattern preProces service, the input should be in genePattern STATML format. Configuration parameters can be adjusted by changing the default preprocess data set using genePattern preProces service, the input should be in genePattern STATML format.preprocess data set using genePattern preProces service, the input should be in genePattern STATML format. Configuration parameters can be adjusted by changing the string constants.

Created: 2010-05-24 | Last updated: 2010-05-24

Credits: User Wei Tan

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Workflow caArray data retrieving (1)

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Query all the gene expression data in a caArray experiment. Returns a evenly divided gene expression data set with corresponding class information. They ca be later used as training and test data set in many classification algorithms.Query all the gene expression data in a caArray experiment. Returns a evenly divided gene expression data set with corresponding class information. They can be later used as training and test data set in many classification algorithms.

Created: 2009-11-23

Credits: User Wei Tan

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Workflow Principle Component Analysis (PCA) over mi... (1)

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Principle Component Analysis (PCA) over microarray data. Data is uploaded through caGrid transfer ultility.

Created: 2010-09-10 | Last updated: 2010-09-10

Credits: User Wei Tan

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Workflow Testing caBIG workflow (1)

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An example workflow to test the installation of caGrid Workflow Suite and the submission of a workflow to a caGrid workflow service.

Created: 2010-08-17 | Last updated: 2010-08-17

Credits: User Wei Tan

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Workflow A simple CQL query workflow in caGrid (1)

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1. CQL is a language to query data from caGrid/caBIG services. This workflow is tested with Taverna 2.1.2 and the caGrid Workflow Suite downloadable from http://www.mcs.anl.gov/~wtan/t2/. 2.More information regarding CQL can be found from http://wiki.cagrid.org/display/dataservices. 3. Sample input (95) is provided in the workflow. It is to query all the hybridization data within a microarray experiment whose id is 95.

Created: 2010-05-24 | Last updated: 2010-05-25

Credits: User Wei Tan

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