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 ESC001ESC002ESC003ESC004 ESC001ESC001-ESC001ESC002-ESC001ESC003-ESC001ESC004-ESC001 ESC002ESC001-ESC002ESC002-ESC002ESC003-ESC002ESC004-ESC002 ESC003ESC001-ESC003ESC002-ESC003ESC003-ESC003ESC004-ESC003 ESC004ESC001-ESC004ESC002-ESC004ESC003-ESC004ESC004-ESC004 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. Software Design Abstraction is good for software engineers Its bad for scientists - Specialisation Scientists Comp-Science

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

11. Experiment Modelling Visual platform

12. 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 JChem/Marvin JChem Standardize Reactor

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

14. Chemical Viewer

15. Integration Steps 1.Add Viewers to ValueType 2.Implement RebuildLocal in Viewer protected void rebuildLocal(JPanel jPanel) { buildGUI(); … } protected void buildGUI() { mainPanel = new MViewPane(); mainPanel.setEditable(2); mainPanel.setM(0, ChemicalUtility.emptyMolecule); }

16. Integration Steps 3.Load Data (SMILES) from model public void load() { super.unregisterWithContext(); // dont 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(); }

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

18. Executable

19. 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); }

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

21. Parallel Synthesis Reactants Products

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

23. Chemical Intelligence BeforeAfter Applying Chemical Business rules for representation

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

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

26. Other Edge plugins Fitting and charting

27. 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

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