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Network-member 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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Blob Input CQL of the lymphoma prediction workflow

Created: 23/04/09 @ 17:25:04 | Last updated: 23/04/09 @ 17:28:24

Credits: User Wei Tan

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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Blob Output of the lymphoma prediction workflow

Created: 23/04/09 @ 17:37:16

Credits: User Wei Tan

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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Blob Output of the lymphoma prediction workflow (on Ubuntu Linux)

Created: 23/04/09 @ 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

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Workflows (15)
Taverna 1

Original Uploader

Workflow caDSR metadata query in caGrid (v1)

Created: 05/12/08 @ 17:45:17 | Last updated: 05/12/08 @ 18:20:25

Credits: User Wei Tan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Tanwei-gt4
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

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Taverna 1

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Workflow hierarchical microarray clustering (v1)

Created: 05/12/08 @ 18:31:53 | Last updated: 05/12/08 @ 20:33:37

Credits: User Wei Tan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Cagrid-sample2
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...

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Taverna 1

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Workflow Using CQL to query protein sequence data (v1)

Created: 05/12/08 @ 22:03:03 | Last updated: 14/07/09 @ 19:32:17

Credits: User Wei Tan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Cql
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.    

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Taverna 2

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Workflow Lymphoma type prediction based on microarray data (v7)

Created: 11/05/10 @ 19:04:30 | Last updated: 11/05/10 @ 19:04:32

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

_lymphoma_type_prediction_based_on_microarray_data_
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: 0.0 / 5 (0 ratings) | Versions: 7 | Reviews: 0 | Comments: 0 | Citations: 2

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Taverna 2

Original Uploader

Workflow Using CQL to query protein sequence data (v1)

Created: 07/05/09 @ 14:28:59

Credits: User Stian Soiland-Reyes

Attributions: Workflow Using CQL to query protein sequence data

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

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Taverna 2

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Workflow An example workflow with WSRF service (v1)

Created: 28/07/09 @ 17:24:05

Credits: User Wei Tan User Stian Soiland-Reyes

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Wsrf
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.

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Taverna 2

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Workflow caDSR Data service query in caGrid (v3)

Created: 25/05/10 @ 19:16:58 | Last updated: 11/06/10 @ 04:50:15

Credits: User Wei Tan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

_untitled_
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

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Taverna 2

Original Uploader

Workflow caArray data retrieving (v1)

Created: 23/11/09 @ 18:09:47

Credits: User Wei Tan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Caarray_data_retrieving
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.

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Taverna 2

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Workflow genePattern data preprocessing (v2)

Created: 24/05/10 @ 22:42:38 | Last updated: 24/05/10 @ 22:42:39

Credits: User Wei Tan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Caarray
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.

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Taverna 2

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Workflow Support-Vector-Machine (SVM) based data classification (v2)

Created: 24/05/10 @ 22:34:31 | Last updated: 24/05/10 @ 22:34:32

Credits: User Wei Tan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

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Taverna 2

Original Uploader

Workflow Query caArray data service and retrieving files (v2)

Created: 24/05/10 @ 22:55:57 | Last updated: 24/05/10 @ 22:55:58

Credits: User Wei Tan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Query_caarray_data_service_and_retrieving_files_
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)

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Taverna 2

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Workflow Invoke caGrid FQP securely and use credential delegation (v1)

Created: 11/05/10 @ 20:21:58 | Last updated: 11/05/10 @ 20:22:40

Credits: User Wei Tan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Federated_query_using_dcql_and_credential_delegation
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:/...

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Taverna 2

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Workflow Invoke a secured caGrid service: caTissue (v1)

Created: 24/05/10 @ 23:41:56 | Last updated: 24/05/10 @ 23:48:29

Credits: User Wei Tan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

_untitled_
Invoke a secure caGrid service, i.e., caTissueCore, to query all the cell specimen. 1. This workflow is tested with Taverna 2.1.2 and the caGrid Workflow Suite plugin downloadable from http://www.mcs.anl.gov/~wtan/t2/. 2. Sample input is embedded in the workflow file. 3. You need a caGrid username/password to invoke it. Find more regarding caGrid security from http://wiki.cagrid.org/display/gaards/.

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Taverna 2

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Workflow A simple CQL query workflow in caGrid (v1)

Created: 24/05/10 @ 23:52:05 | Last updated: 25/05/10 @ 19:20:30

Credits: User Wei Tan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

_untitled_
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.

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Taverna 2

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Workflow Testing caBIG workflow (v1)

Created: 17/08/10 @ 18:24:05 | Last updated: 17/08/10 @ 19:45:34

Credits: User Wei Tan

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

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