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Modelling experiments

Modelling experiments. Using Teranode XDA and Chemaxon Andrew Lemon and Robert Shell. Agenda. Issues with capturing experiments Integrating Chemaxon Futures Acknowledgements. Experiments. Protocol Design* Data capture* Automated data capture Data Analysis and reduction* Conclusion

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Modelling experiments

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  1. Modelling experiments Using Teranode XDA and Chemaxon Andrew Lemon and Robert Shell

  2. Agenda • Issues with capturing experiments • Integrating Chemaxon • Futures • Acknowledgements

  3. Experiments • Protocol Design* • Data capture* • Automated data capture • Data Analysis and reduction* • Conclusion • Review and Publication • Search and report data Diversity from synthesis to Preclinical testing

  4. Protocols

  5. Data capture • Spreadsheets • Formula to link cells in 2D • =A3 & “-” & B2 ESC001-ESC001 • Modelling difficult and error prone • Expansion difficult

  6. Protocol Modelling • Need to model the experiment • Parameterise the dimensionality

  7. Protocol Modelling • Need to model the experiment • Parameterise the dimensionality

  8. Protocol Modelling • Cope with runtime modification • ‘Stuff’ happens • Still track data

  9. Modelling Chemistry • How can we model real experiments? • Instruments • Data • What about chemical information?

  10. Experiment Modelling • Visual platform

  11. JChem/Marvin JChem Standardize Reactor Integration Requirements • Support specialist data types • Structure, Reaction • Access to raw data • SDF, RDF, CTFile, Smiles • Provide processing capabilities • Chemical Business rules • Enumeration • Not compromise the platform architecture • Java plugin architecture • Reasonable cost implication • Be compatible with other software • Responsive vendor (support, enhancements, innovation) • Good pedigree

  12. Teranode API • Value Type • Custom Viewer • Large Panels • Dialogs • Small single line/cell views • Executables • Import • Export • Custom Processes

  13. Chemical Viewer

  14. Integration Steps • Add Viewers to ValueType • Implement RebuildLocal in Viewer protected void rebuildLocal(JPanel jPanel) { buildGUI(); … } protected void buildGUI() { mainPanel = new MViewPane(); mainPanel.setEditable(2); mainPanel.setM(0, ChemicalUtility.emptyMolecule); }

  15. Integration Steps • Load Data (SMILES) from model public void load() { super.unregisterWithContext(); // don’t trigger refresh try { data = new ChemData(getProperty().getOutputString()); mainPanel.setM(0,data.getMolecule()); } catch (Exception e) { mainPanel.setM(0,ChemicalUtility.emptyMolecule); log.warn("Failed to read in molecule", e); } super.registerWithContext(); }

  16. Executable • File Importers • Structure Transformations • Standardize • Reactor • Searching • Filters • SSS • public Executable getExecutable() • { • if (executable==null) • { • executable = new • StandardizerExecutable(); • } • return executable; • }

  17. cd Exec ChemAxon API StandizeViewer ViewerPanel + rebuildLocal(JPanel) : void + rebuildLocal(JPanel) : void StandarizeValueType MViewPane AbstractStringValueType + setM(Molecule) : void StandizeData - destination: Property run - source: Property - transform: String Standardizer RunAllExecutable StandarizeExecutable MolImporter Teranode API + importMol(String) : Molecule Executable

  18. Implementation protected void executeLocal(GraphObject graphObject) throws Exception { Property property = m_executeEvent.getExecutableProperty(); String value = property.getOutputString(); Node node = (Node) graphObject; StandardizerData data = new StandardizerData(node,value); Standardizer standardizer = new Standardizer(data.getRules()); // Read Chemistry from source clean and save to destination ChemicalData chem = new ChemicalData(data.getSource()); Molecule cleaned = standardizer.standardize(chem.getMolecule()); chem.setMolecule(cleaned); data.getDestination().setValueString(chem.toString(), node); }

  19. Chemaxon • Well designed Object Model • Quickly get to chemistry terms not objects • Leverage domain knowledge • Faster programming • Robust • Documented • Supported • Forums • Interested! • Active Development

  20. Parallel Synthesis Reactants Products

  21. Enumerated Products Reactants Reaction Products Combinatorial Chemistry • Layout reagents on synthesis plates • Apply the reaction • Enumerate the products • All within a single workflow

  22. Before After Chemical Intelligence Applying Chemical Business rules for representation

  23. Chemical Intelligence Structural Filtering Split a list of Amines into Primary Secondary, Tertiary and Quaternary Amines Filter by Structure

  24. Integrated Chemistry • Data access • Chemical Indexing and searching • Integrated Chemical Intelligence • Web-based Query and Reporting Marvin Reactor JChem

  25. Other Edge plugins • Fitting and charting

  26. Futures • Integrate more Chemaxon components • PhysChem Predictors • Cluster analysis • Reporting • Structure searching within Semantic webstore • Integration components to databases • ID/Structure lookup • Integration of screening data • SAR reports etc

  27. Acknowledgements • Chemaxon Software Collaboration • Teranode Software Collaboration • European Agent • The Edge Software Consultancy • Robert Shell More information? http://www.edgesoftwareconsultancy.com/ andrew@edgesoftwareconsultancy.com

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