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Items tagged with "cancer research" (10)

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Workflows (8)

Taverna 1 Original Uploader Wei Tan	caDSR metadata query in caGrid (v1) Created: 05/12/08 @ 17:45:17 \| Last updated: 05/12/08 @ 18:20:25 Credits: Wei Tan License: Creative Commons Attribution-Share Alike 3.0 Unported License 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... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 92 times \| Downloaded: 36 times Tags (7): cabig \| cadsr \| cagrid \| cancer research \| globus \| grid service \| metadata	View Download (v1)
Taverna 1 Original Uploader Wei Tan	hierarchical microarray clustering (v1) Created: 05/12/08 @ 18:31:53 \| Last updated: 05/12/08 @ 20:33:37 Credits: Wei Tan License: Creative Commons Attribution-Share Alike 3.0 Unported License 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... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 185 times \| Downloaded: 75 times Tags (8): cabig \| cagrid \| cancer research \| clustering \| gene expression \| globus \| grid service \| microarray	View Download (v1)
Taverna 1 Original Uploader Wei Tan	Using CQL to query protein sequence data (v1) Created: 05/12/08 @ 22:03:03 \| Last updated: 14/07/09 @ 19:32:17 Credits: Wei Tan License: Creative Commons Attribution-Share Alike 3.0 Unported License 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 181 times \| Downloaded: 56 times Tags (9): cabig \| cabio \| cagrid \| cancer research \| cpas \| globus \| grid service \| gridpir \| protein	View Download (v1)
Taverna 2 Original Uploader Wei Tan	Lymphoma type prediction based on microarray data (v7) Created: 11/05/10 @ 19:04:30 \| Last updated: 11/05/10 @ 19:04:32 Credits: Wei Tan Ravi Stian Soiland-Reyes License: Creative Commons Attribution-Share Alike 3.0 Unported License 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. Rating: 5.0 / 5 (1 rating) \| Versions: 7 \| Reviews: 0 \| Comments: 0 \| Citations: 3 Viewed: 610 times \| Downloaded: 235 times Tags (11): cabig \| cagrid \| cancer research \| classification \| gene expression \| globus \| grid service \| lymphoma \| lymphoma workflow \| microarray \| support vector machine	View Download (v7)
Taverna 2 Original Uploader Stian Soiland-Reyes	Using CQL to query protein sequence data (v1) Created: 07/05/09 @ 14:28:59 Credits: Stian Soiland-Reyes Attributions: Using CQL to query protein sequence data License: Creative Commons Attribution-Share Alike 3.0 Unported License To query protein sequence infomation out of 3 caGrid data services: caBIO, CPAS and GridPIR Adapted from http://www.myexperiment.org/workflows/600 Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 155 times \| Downloaded: 69 times Tags (10): cabig \| cabio \| cagrid \| cancer research \| cpas \| globus \| grid service \| gridpir \| protein \| sequence	View Download (v1)
Taverna 2 Original Uploader Wei Tan	caDSR Data service query in caGrid (v3) Created: 25/05/10 @ 19:16:58 \| Last updated: 11/06/10 @ 04:50:15 Credits: Wei Tan License: Creative Commons Attribution-Share Alike 3.0 Unported License 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 Rating: 0.0 / 5 (0 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 79 times \| Downloaded: 62 times Tags (5): cabig \| cadsr \| cancer research \| example \| grid service	View Download (v3)
Taverna 2 Original Uploader Wei Tan	genePattern data preprocessing (v2) Created: 24/05/10 @ 22:42:38 \| Last updated: 24/05/10 @ 22:42:39 Credits: Wei Tan License: Creative Commons Attribution-Share Alike 3.0 Unported License 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 59 times \| Downloaded: 31 times Tags (5): cabig \| cagrid \| cancer research \| functional workflow \| microarray	View Download (v2)
Taverna 2 Original Uploader Wei Tan	Principle Component Analysis (PCA) over microarray data (v1) Created: 10/09/10 @ 23:45:05 \| Last updated: 10/09/10 @ 23:51:03 Credits: Wei Tan License: Creative Commons Attribution-Share Alike 3.0 Unported License Principle Component Analysis (PCA) over microarray data. Data is uploaded through caGrid transfer ultility. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 39 times \| Downloaded: 23 times Tags (7): caarray \| cabig \| cagrid \| cagrid-transfer \| cancer research \| microarray \| pca	View Download (v1)

Files (2)

Uploader:

Wei Tan

Input CQL of the lymphoma prediction workflow

Created: 23/04/09 @ 17:25:04 | Last updated: 03/09/11 @ 21:57:43

Credits: Wei Tan

Attributions: 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

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 14 times | Downloaded: 12 times

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Uploader:

Wei Tan

Output of the lymphoma prediction workflow

Created: 23/04/09 @ 17:37:16 | Last updated: 03/09/11 @ 21:56:29

Credits: Wei Tan

Attributions: 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

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