Tag Results

Items tagged with "cabig" (20)

Note: some items may not be visible to you, due to viewing permissions.


Files (3)
Uploader

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

Tags:

Uploader

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

Tags:

Uploader

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

Tags:

Groups (1)
Owner

Network-member caBIG: cancer Biomedical Informatics Grid

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

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.

0 shared items   |   1 announcements

Tags:

Latest announcement:: : caBIG: cancer Biomedical Informatics Grid

Workflows (16)
Uploader

Workflow caDSR metadata query in caGrid (1)

Thumb
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

Uploader

Workflow hierarchical microarray clustering (1)

Thumb
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

Uploader

Workflow Using CQL to query protein sequence data (1)

Thumb
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

Uploader

Workflow Lymphoma type prediction based on microar... (7)

Thumb
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

Workflow Using CQL to query protein sequence data (1)

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

Created: 2009-05-07

Credits: User Stian Soiland-Reyes

Attributions: Workflow Using CQL to query protein sequence data

Uploader

Workflow An example workflow with WSRF service (1)

Thumb
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.

Created: 2009-07-28

Credits: User Wei Tan User Stian Soiland-Reyes

Uploader

Workflow caDSR Data service query in caGrid (3)

Thumb
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

Created: 2010-05-25 | Last updated: 2010-06-11

Credits: User Wei Tan

Uploader

Workflow caArray data retrieving (1)

Thumb
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

Uploader

Workflow genePattern data preprocessing (2)

Thumb
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

Uploader

Workflow Support-Vector-Machine (SVM) based data cl... (2)

Thumb
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

Uploader

Workflow Query caArray data service and retrieving ... (2)

Thumb
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)

Created: 2010-05-24 | Last updated: 2010-05-24

Credits: User Wei Tan

Uploader

Workflow Federated query using DCQL and credential ... (2)

Thumb
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...

Created: 2010-05-11 | Last updated: 2010-11-05

Credits: User Wei Tan

Uploader

Workflow Invoke a secured caGrid service: caTissue (2)

Thumb
No description

Created: 2010-05-24 | Last updated: 2010-11-05

Credits: User Wei Tan

Uploader

Workflow A simple CQL query workflow in caGrid (1)

Thumb
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.

Created: 2010-05-24 | Last updated: 2010-05-25

Credits: User Wei Tan

Uploader

Workflow Testing caBIG workflow (1)

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

Created: 2010-08-17 | Last updated: 2010-08-17

Credits: User Wei Tan

Uploader

Workflow Principle Component Analysis (PCA) over mi... (1)

Thumb
Principle Component Analysis (PCA) over microarray data. Data is uploaded through caGrid transfer ultility.

Created: 2010-09-10 | Last updated: 2010-09-10

Credits: User Wei Tan

What is this?

Linked Data

Non-Information Resource URI: http://alpha.myexperiment.org/tags/1068


Alternative Formats

HTML
RDF
XML