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