1. CICC Chemical Compound Mining Workflows Jungkee (Jake) Kim Community Grids Laboratory

2. 10/06/2006CICC Project Meeting XML files A Workflow for Big Red Demo I Big Red is one of fastest supercomputers Mining chemical compounds found on research paper texts and showing them in 3D graphics PubMed Abstracts OSCAR3 SMILES Extraction Converting the format Molecular & Quantum Mechanics Converting to pictures Generating HTML script Text files SMILES SDF files SDF files POV, JPG files

3. A Workflow for Big Red Demo II Final HTML pages

4. 10/06/2006CICC Project Meeting A Workflow for Big Red Demo III PubMed abstracts –555,007 PubMed abstracts of 2005 – 2006 (part) –1,000 abstracts per node distributed (Simple parallelism) 511 nodes X 1,000 input abstracts used for the demo OSCAR3 –A Cambridge tool which extracts chemical information from text and produces an XML instance highlighting the chemical information –Used a revised version for convenient batch processing (some incompatibility to BigRed architecture) SMILES extraction –Extracting SMILES elements from OSCARs XML output files –Unique SMILES list within a batch

5. 10/06/2006CICC Project Meeting A Workflow for Big Red Demo IV Generating 3D formats –Converting from SMILES to SDF format –Molecular Mechanics program: mengine (MM engine) –No Quantum Mechanics (QM) in the demo Converting 3D formats to pictures –Persistence of Vision Raytracer (POV-Ray): converting SDF to POV –Another program which converts the POV files to JPEG format Generating HTML script –Showing those graphic files in an HTML page

6. Bigger Picture for the Workflow NIH PubMed Database OSCAR Text Analysis POV-Ray Parallel Rendering Initial 3D Structure Calculation Toxicity Filtering Cluster Grouping Docking Molecular Mechanics Calculations Quantum Mechanics Calculations IUs Varuna Database NIH PubChem Database Big Red Demo High Throughput Screening (HTS) Data Organization and Flagging