myExperiment - Tags

Workflows (14)

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	caArray data retrieving (v1) Created: 23/11/09 @ 18:09:47 Credits: Wei Tan License: Creative Commons Attribution-Share Alike 3.0 Unported License 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 3 \| Citations: 0 Viewed: 48 times \| Downloaded: 19 times Tags (8): caarray \| cabig \| cagrid \| functional workflow \| gene \| globus \| grid service \| microarray	View Download (v1)
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	Support-Vector-Machine (SVM) based data classification (v2) Created: 24/05/10 @ 22:34:31 \| Last updated: 24/05/10 @ 22:34:32 Credits: Wei Tan License: Creative Commons Attribution-Share Alike 3.0 Unported License Support-Vector-Machine based data classificationSupport-Vector-Machine based data classification using genePattern SVM service, the input should be in genePattern STATML format. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 106 times \| Downloaded: 49 times Tags (5): cabig \| cagrid \| classification \| functional workflow \| support vector machine	View Download (v2)
Taverna 2 Original Uploader Wei Tan	Query caArray data service and retrieving files (v2) Created: 24/05/10 @ 22:55:57 \| Last updated: 24/05/10 @ 22:55:58 Credits: Wei Tan License: Creative Commons Attribution-Share Alike 3.0 Unported License need to install Taverna 2 caGrid integration suite from http://www.mcs.anl.gov/~wtan/t2/ and get a cagrid Dorian account (see http://wiki.cagrid.org/display/caGrid13/Home) Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 21 times \| Downloaded: 25 times Tags (6): caarray \| cabig \| cagrid \| cagrid-transfer \| cql \| microarray	View Download (v2)
Taverna 2 Original Uploader Wei Tan	Federated query using DCQL and credential delegation (v2) Created: 11/05/10 @ 20:21:58 \| Last updated: 05/11/10 @ 21:06:29 Credits: Wei Tan License: Creative Commons Attribution-Share Alike 3.0 Unported License CDS_Activity issues an EPR of the delegated credential. FQP uses this EPR to fetch the actual delegated credential from CDS and uses it to invoke multiple data services (the query activity) on behalf of the invoker. CDS_Activity issues an EPR of the delegated credential. FQP uses this EPR to fetch the actual delegated credential from CDS and uses it to invoke multiple data services (the query activity) on behalf of the invoker. Need to install Taverna 2 caGrid integration suite from http://ww... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 16 times \| Downloaded: 11 times Tags (5): cabig \| cagrid \| credential delegation \| security \| t2	View Download (v2)
Taverna 2 Original Uploader Wei Tan	Invoke a secured caGrid service: caTissue (v2) Created: 24/05/10 @ 23:41:56 \| Last updated: 05/11/10 @ 21:04:04 Credits: Wei Tan License: Creative Commons Attribution-Share Alike 3.0 Unported License No description Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 17 times \| Downloaded: 17 times Tags (7): cabig \| cagrid \| catissue \| cql \| globus gsi \| security \| specimen	View Download (v2)
Taverna 2 Original Uploader Wei Tan	A simple CQL query workflow in caGrid (v1) Created: 24/05/10 @ 23:52:05 \| Last updated: 25/05/10 @ 19:20:30 Credits: Wei Tan License: Creative Commons Attribution-Share Alike 3.0 Unported License 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. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 31 times \| Downloaded: 10 times Tags (5): cabig \| cagrid \| cql \| hybridization \| microarray	View Download (v1)
Taverna 2 Original Uploader Wei Tan	Testing caBIG workflow (v1) Created: 17/08/10 @ 18:24:05 \| Last updated: 17/08/10 @ 19:45:34 Credits: Wei Tan License: Creative Commons Attribution-Share Alike 3.0 Unported License An example workflow to test the installation of caGrid Workflow Suite and the submission of a workflow to a caGrid workflow service. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 15 times \| Downloaded: 22 times Tags (4): cabig \| cagrid \| example \| workflow service	View Download (v1)
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)

Groups (1)

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Wei Tan

caBIG: cancer Biomedical Informatics Grid

Unique name: cabig Created: Tuesday 24 November 2009 @ 04:42:32 (GMT)

caBIG® stands for the cancer Biomedical Informatics Grid®. caBIG® is an information network enabling all constituencies in the cancer community – researchers, physicians, and patients – to share data and knowledge. The caBIG group in myExperiment is a community for caBIG workflow developers and users.

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Latest announcement:: : caBIG: cancer Biomedical Informatics Grid

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Files (3)

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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

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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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