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User: Wei Tan
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Name: Wei Tan Joined: Monday 07 July 2008 @ 19:35:32 (GMT) Last seen: Saturday 21 January 2012 @ 03:14:24 (GMT) Email (public): wtan [at] us.ibm.com Website: http://www.ci.uchicago.edu/~wtan/ Location: Hawthorne, United States |
Wei Tan has been credited 19 times Wei Tan has an average rating of: 5.0 / 5 (1 rating in total) for their items |
Description/summary not set
Other contact details:
https://researcher.ibm.com/researcher/view.php?person=us-wtan
Interests:
scientific workflow, service oriented architecture, grid computing, Petri net
Field/Industry: Education & Research
Occupation/Role(s): Research Staff Member
Organisation(s):
IBM T. J. Watson Research Center
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Created: 23/04/09 @ 17:25:04 | Last updated: 03/09/11 @ 21:57:43
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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.
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Created: 23/04/09 @ 17:37:16 | Last updated: 03/09/11 @ 21:56:29
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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).
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Created: 23/04/09 @ 20:06:51
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
testing on Ubuntu Linux 8.0.4 + Java 1.5_16
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Created: 10/09/10 @ 23:45:05 | Last updated: 10/09/10 @ 23:51:03
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Principle Component Analysis (PCA) over microarray data. Data is uploaded through caGrid transfer ultility.
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Created: 17/08/10 @ 18:24:05 | Last updated: 17/08/10 @ 19:45:34
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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.
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Created: 14/08/10 @ 06:02:00 | Last updated: 14/08/10 @ 06:03:20
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
preprocess data before it is sent to any GenePattern services.
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Created: 24/05/10 @ 23:41:56 | Last updated: 05/11/10 @ 21:04:04
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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Created: 11/05/10 @ 20:21:58 | Last updated: 05/11/10 @ 21:06:29
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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...
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Created: 24/05/10 @ 22:55:57 | Last updated: 24/05/10 @ 22:55:58
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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)
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Created: 24/05/10 @ 22:34:31 | Last updated: 24/05/10 @ 22:34:32
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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.
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Created: 24/05/10 @ 22:42:38 | Last updated: 24/05/10 @ 22:42:39
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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.
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Created: 23/11/09 @ 18:09:47
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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.
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Created: 28/07/09 @ 17:24:05
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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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Created: 05/12/08 @ 22:03:03 | Last updated: 14/07/09 @ 19:32:17
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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.
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Created: 05/12/08 @ 18:31:53 | Last updated: 05/12/08 @ 20:33:37
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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...
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Created: 24/05/10 @ 23:52:05 | Last updated: 25/05/10 @ 19:20:30
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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.
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Created: 11/05/10 @ 19:04:30 | Last updated: 11/05/10 @ 19:04:32
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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.
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Created: 25/05/10 @ 19:16:58 | Last updated: 11/06/10 @ 04:50:15
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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
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Created: 05/12/08 @ 17:45:17 | Last updated: 05/12/08 @ 18:20:25
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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...
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