building services for bci with taverna
DESCRIPTION
Building Services for BCI with Taverna. Jungkee (Jake) Kim Community Grids Laboratory. Two Taverna Demos. BCI Clustering Demo Based on David Wild’s BCI Clustering Program WWMM Demo (Optional to show) Based on Peter Murray-Rust’s World Wide Molecular Matrix (WWMM) Workflow. BCI Clustering. - PowerPoint PPT PresentationTRANSCRIPT
Building Services for BCI with Taverna
Jungkee (Jake) Kim
Community Grids Laboratory
1/27/2006 CICC project meeting
Two Taverna Demos
• BCI Clustering Demo– Based on David Wild’s BCI Clustering
Program• WWMM Demo (Optional to show)
– Based on Peter Murray-Rust’s World Wide Molecular Matrix (WWMM) Workflow
1/27/2006 CICC project meeting
BCI Clustering
• Barnard Chemical Information (BCI) Clustering: A process of automatic classification of the chemical structures in a dataset, on the basis of similarities between them.
• Our Current Usage– Generating a fingerprint file from a SMILES
structure file. (*.smi -> *.scn)– Clustering a finger print file with Divkmeans. (*.scn -> *.dkm)
1/27/2006 CICC project meeting
Client-Server Architectures
ServerClient
BCI Clustering
WSDL based Service
ANTWrapper
AXISW.S.
Taverna
1/27/2006 CICC project meeting
Services to Provide in BCI Demo
• Taverna Client– Local Text File Read– Local Text File Write– Concatenate Two Strings
• Web Services in the Server– BCI Clustering Launched by the ANT wrapper– Text file read and send it to the Client– Read text strings and save them to a text file
1/27/2006 CICC project meeting
Flow Chart of BCI Demo
SMILEfile
Read a Dataset
Sendthe Dataset
BCImakebits
BCIdivkm
DKMfile
Fingerprintfile
Writethe Dataset
DKMfile
1/27/2006 CICC project meeting
Workflow for BCI Demo
String Constant Local Processor Web Services
1/27/2006 CICC project meeting
Input for BCI Demo
1/27/2006 CICC project meeting
Output from BCI Demo
1/27/2006 CICC project meeting
Services in WWMM Demo
• Download Crystallographic Information Files (CIF’s) from ACTA Crystallographica site
• Taverna Client Input– Year List– Month List– Journal Section– Local Download Directory Path
Workflow for WWMM Demo
String Constant
Local Processor
Bean Shell
CDK-Taverna Services
Input for WWMM DemoYearList 2003 2004
MonthList 05 06
Journal e
DownloadDirPath D:\NIHTemp
Running the WWMM Workflow
1/27/2006 CICC project meeting
Results of the WWMM Workflow
Blank Screen!Blank Screen! (8 minutes for this case)
1/27/2006 CICC project meeting
Fetched Files from WWMM Demo
• Paper Files of Acta Crystallographica Section E• These files are input of CIF2CML workflow