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Showing 16 results. Use the filters on the left and the search box below to refine the results.
Tag: cagrid User: Wei Tan 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

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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. Scientific value To query protein sequence information out of 3 caGrid data services: caBIO, CPAS and GridPIR. To analyze a protein sequence from different data sources. Steps Querying CPAS and get the id, name, value of the sequence. Querying caBIO and GridPIR using the id or name obtained from CPAS.    

Created: 2008-12-05 | Last updated: 2009-07-14

Credits: User Wei Tan

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Workflow hierarchical microarray clustering (1)

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To illustrate our caGrid plug-in’s application, we tested it with a microarray hierarchical clustering workflow that involves services hosted at multiple institutions. Microarrays are a high-throughput technology used to measure the expression of tens of thousands of genes in different tissues or cells. Scientists represent the data from each microarray via a vector (profile) in which each element represents a gene’s expression level. They use clustering analysis to identify sim...

Created: 2008-12-05 | Last updated: 2008-12-05

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 caDSR metadata query in caGrid (1)

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This workflow shows the coordinated use of two services in CaGrid, i.e., the caDSR (Cancer Data Standards Repository) and EVS (Enterprise Vocabulary Services) services. caDSR is to define a comprehensive set of standardized metadata descriptors for cancer research terminology used in information collection and analysis. EVS provides resources and services to meet NCI needs for controlled terminology, and to facilitate the standardization of terminology and information systems across the Insti...

Created: 2008-12-05 | Last updated: 2008-12-05

Credits: User Wei Tan

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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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Blob Output of the lymphoma prediction workflow (on Ubunt...

Created: 2009-04-23 20:06:51

Credits: User Wei Tan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

testing on Ubuntu Linux 8.0.4 + Java 1.5_16

File type: XML

Comments: 0 | Viewed: 46 times | Downloaded: 29 times

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Blob Output of the lymphoma prediction workflow

Created: 2009-04-23 17:37:16 | Last updated: 2011-09-03 21:56:29

Credits: User Wei Tan

Attributions: Workflow Lymphoma type prediction based on microarray data

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Output of the lymphoma prediction workflow at http://www.myexperiment.org/workflows/746?version=1. It shows the lymphoma type prediction results. It contains lymphoma type predictions for 38 samples and there is only one error (on testSample_4).

File type: XML

Comments: 0 | Viewed: 36 times | Downloaded: 30 times

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Blob Input CQL of the lymphoma prediction workflow

Created: 2009-04-23 17:25:04 | Last updated: 2011-09-03 21:57:43

Credits: User Wei Tan

Attributions: Workflow Lymphoma type prediction based on microarray data

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Input CQL of the lymphoma prediction workflow at http://www.myexperiment.org/workflows/746?version=1. It is only for the purpose of illustration and  NOT needed to run the workflow since the input has already been embedded.

File type: XML

Comments: 0 | Viewed: 56 times | Downloaded: 29 times

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