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2012 ACS Skolnik Symposium - ChemSpotlight
- 1. Automated Molecular DataExtraction using Open Babel & ChemSpotlight: The Semantic Desktop Prof. Geoff Hutchison Department of Chemistry University of Pittsburgh geoffh@pitt.edu ACS CINF: Skolnik Symposium 21 August 2012 http://hutchison.chem.pitt.edu
- 2. “ I can plugmy iPod into any computer and it will recognize my music and give me all sorts of metadata: artist, title, type of music... Why can’t I read the chemical metadata off my chemistry files? ” — Prof. Henry S. Rzepa (Imperial College) Spring 2005 ACS Meeting, San Diego, CA
- 3. Pre-History: Chem://Dig Index files, websites Based on Chem MIME Find files on extension Perceive chemistry Database Store Search, Filter Retrieval H. Rzepa et al. New J. Chem (2002) 26 p. 656
- 4. Open Babel Open Babel (Started 2001) Free, open source chemical toolbox Cross-platform: Win, Mac, Linux... Both user-tools & C++ library Interfaces in Python, Perl, Ruby, Java, C# Supports chemistry, bioinformatics, solid-state… 100+ file formats and variants http://openbabel.org/ O’Boyle et al. J. Cheminf. 2011, 3:33
- 5. Chemical Database? 1. Some way to store data (Organize it) 2. Index it 3. Search / filter 4. Visualize results
- 6. ChemSpotlight: Indexing Architecture ~300 lines + + of code Spotlight Open Babel http://chemspotlight.openmolecules.net/
- 7. ChemSpotlight: “Un” Database Use the system-wide search database No (Visible) Database! Index files in-place Includes textual data (e.g., chemical names, formulas, etc.) Multiple retrieval and filtering interfaces (i.e., any third-party search tool works) http://chemspotlight.openmolecules.net/
- 8. So What’s Stored/ Perceived Formula, mass, SMILES, InChI net_sourceforge_openbabel_Formula = C21H36N7O8S Fingerprints, number of atoms, bonds, residues PDB, SDF keywords, properties Calculation keywords: kMDItemComment = "Gaussian 09 #n B3LYP/6-31G(d) Opt" Calculation results (HOMO, LUMO, Dipole Moment) net_sourceforge_chemspotlight_DipoleMoment = 3.5
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- 11. How Do WeVisualize? “QuickLook” previews New code ~800 lines Generate SDF, PDB, CIF (if needed) Pass off to ChemDoodle Web Components Pseudo-3D, interactive JS + HTML5 … or SVG generation from Open Babel http://web.chemdoodle.com/
- 12. Organic Heterojunction SolarCells light Transparent Electrode + p-type material Circuit - n-type material Reflective Electrode
- 13. Organic Heterojunction SolarCells ΔE ≥ Exciton Binding Energy e- Optical Excitation light hν Cathode Transparent Electrode Hole Electron Conducting Effective + p-type material Conductor Polymer Heterojunction Circuit - n-type material (Nanoparticle) Bandgap Reflective Electrode Anode h+
- 14. Pipeline Model forFinding New Molecules Monomers >106 Possible Structures Electronic ~9 minutes Properties Optical Properties Synthetic Score J Phys Chem C 2011 vol. 115 pp. 16200 ...
- 15. Pipeline Model forFinding New Molecules Monomers >106 Possible Structures Fast Electronic ~9 minutes Screening Properties Optical Properties Synthetic Slower Score J Phys Chem C 2011 vol. 115 pp. 16200 ...
- 16. New Genetic AlgorithmApproach Rather than directly driving & wait for calc results Check Spotlight for new results “What are top HOMO energies?” Update GA, generate new candidates, submit new jobs
- 17. Scaling Up thePolymer Solar Search S 0 2nd Gen. Search: 680 Monomers LUMO Energy (eV) −1 2800+ Fragments Search Space: −2 500+ million oligomers ~9 minutes per core −3 −9.5 −9.0 −8.5 −8.0 −7.5 −7.0 −6.5 HOMO Energy (eV)
- 18. Take-Home Messages “Big Data” is a Big Headache ChemSpotlight & Un-Databases Work! Keep data as native files w/separate index Integrate into user-friendly tools Sell to users: “What’s in it for me?” Indexing, retrieval Improved workflows
- 19. Marcus Hanwell Pitt / Kitware Dr. Noel O’Boyle Casey Campbell U.C. Cork, Ireland Pitt (2010)