1. Instant JChem 2009 US + EU Seminars Confidential. Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd Instant JChem Instant JChem Seminar series Q1 2009

2. Instant JChem 2009 US + EU Seminars Confidential. Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd Topics Welcome and thanks Brief introduction of ChemAxon and the IJC seminar 10 things that best describe IJC Typical usage scenarios User presentation IJC developments, short and medium term Demos Questions and discussion

3. Instant JChem 2009 US + EU Seminars Confidential. Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd Product map

4. Instant JChem 2009 US + EU Seminars Confidential. Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd 10 things that describe IJC Simple and flexible deployment Create and manage structure databases Import/export/merge/edit data Build tabular and form based reports Run combined structure and data searches Structure based predictions Manage relational data Access sophisticated chemistry features Collaborate with other users Extensible

5. Instant JChem 2009 US + EU Seminars Confidential. Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd 1. Simple and flexible deployment

6. Instant JChem 2009 US + EU Seminars Confidential. Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd 2. Create and manage structure databases

7. Instant JChem 2009 US + EU Seminars Confidential. Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd 3. Import/export/merge/edit data

8. Instant JChem 2009 US + EU Seminars Confidential. Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd 4. Build tabular and form based reports

9. Instant JChem 2009 US + EU Seminars Confidential. Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd 5. Run combined structure and data searches

10. Instant JChem 2009 US + EU Seminars Confidential. Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd 6. Structure based predictions

11. Instant JChem 2009 US + EU Seminars Confidential. Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd 7. Manage relational data

12. Instant JChem 2009 US + EU Seminars Confidential. Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd 8. Access sophisticated chemistry features

13. Instant JChem 2009 US + EU Seminars Confidential. Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd 9. Collaborate with other users

14. Instant JChem 2009 US + EU Seminars Confidential. Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd 10. Extensible

15. Instant JChem 2009 US + EU Seminars Confidential. Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd Typical usage scenarios How customers are typically using IJC

16. Instant JChem 2009 US + EU Seminars Confidential. Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd Build your own database Create database and add tables from within IJC Local DBs (personal use) Oracle or MySQL DBs (shared use) Import data Make SD file data accessible to you and others Canonicalize (chemical business rules) Enter/Edit data Report data (Build forms, tables etc.) Search data Export data

17. Instant JChem 2009 US + EU Seminars Confidential. Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd Report from existing database Tables already exist in Oracle or MySQL Data typically accessed in read-only mode Tables and columns need to be promoted into IJC so that they can be used Administrator typically prepares data and forms for others to use DBA may have performed magic in the database – IJC will not understand all types of magic Reporting, searching and export features of IJC still apply

18. Instant JChem 2009 US + EU Seminars Confidential. Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd Share data between sites/organisation Allows sharing and collaboration between multiple sites or organisations Shared database Copy and distribute local databases Allows control over how data will be seen No need to import data No assumption about what software other party has Forms, formatting, queries, lists etc. can be pre-defined

19. Instant JChem 2009 US + EU Seminars Confidential. Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd Customise Build your own extensions on top of the IJC APIs Fill in the missing bits Add functionality particular to your needs Let us know what you are doing! You might be doing something useful to others We might be able to help We need to know what bits of IJC should be extensible

20. Instant JChem 2009 US + EU Seminars Confidential. Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd Customer A Mid size, multi-site biotech wants to manage multiple commercial content dbs (SD and RD files) as discrete dbs while giving users the ability to search all simultaneously Features Administrator prepares everything for users Upgrading content is easy Unlimited numbers of content

21. Instant JChem 2009 US + EU Seminars Confidential. Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd Customer B Small start-up biotech looking for fast, enterprise wide deployment of IT infrastructure for all discovery data and interfaces. Features Use IJC as a simple chemistry and assay management tool Tables created and data input via IJC Access control restricts who can do what Small amounts of DBA magic also involved

22. Instant JChem 2009 US + EU Seminars Confidential. Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd Customer C Large biotech/CRO wants to stop re-inventing and supporting the wheel for project data while having flexibility to extend/customise Features For all in-house scientists Provide data to their customers using IJC (confidence in customers view of received data)

23. Instant JChem 2009 US + EU Seminars Confidential. Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd Commercials Flavors Personal – free, but local database only Calculations pack – all calculator plugins Enterprise – shared databases Enterprise + JChem API Add-ons Standardizer Calculator plugins Markush Name to structure (Reactor) Licenses Annual or perpetual

24. Instant JChem 2009 US + EU Seminars Confidential. Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd IJC developments short and medium term

25. Instant JChem 2009 US + EU Seminars Confidential. Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd Synchronisation with JChem releases Starting late 2008 IJC releases aim to be synchronised with Marvin/JChem releases Allows you to work with latest versions of Marvin/JChem and use IJC on the same data We release IJC version within a day or two of the Marvin/JChem release These are minor patch releases (e.g. 2.4.1, 2.4.2…) with mostly bug fixes Major feature releases every 6 -9 months, hopefully in sync with Marvin/JChem major releases

26. Instant JChem 2009 US + EU Seminars Confidential. Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd Next Major IJC release Expected end Q2 2009 Major features: IJC server URL fields Schema editor improvements Reactor integration Probably in sync with Marvin/JChem 5.3

27. Instant JChem 2009 US + EU Seminars Confidential. Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd IJC server: key benefits Searching on server Reduced memory footprint on client Faster searching Faster startup time Model does not have to be initialized on each client startup Improved security Build web apps and web services around IJC data

28. Instant JChem 2009 US + EU Seminars Confidential. Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd IJC server: current architecture Local DB IJC ClientDatabase Remote DB Oracle cartridge

29. Instant JChem 2009 US + EU Seminars Confidential. Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd IJC server: server architecture IJC IJC Client Database IJC Server Web Apps Web services Services API Oracle cartridge

30. Instant JChem 2009 US + EU Seminars Confidential. Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd URL fields Images, HTML, documents Access as: Static URL Dynamic URL DB column Display in form and grid view Allows: Pulling in data from external sources Handling new data types Drill out to external sites

31. Instant JChem 2009 US + EU Seminars Confidential. Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd Schema editor improvements Improved DB administration console Data tree editor and schema editor merged to single component Easier to use Add support for additional database features e.g. database views

32. Instant JChem 2009 US + EU Seminars Confidential. Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd Reactor integration Perform chemically feasible syntheses in IJC Draw generic reaction and enumerate Enumerate using pre-defined reaction scheme Reaction based enumeration in an IJC DB Reactants come from IJC table Restrict reactants to a particular list of compounds Products written to IJC table Calculate properties of the generated products ChemAxon reaction library Defines reactivity and selectivity rules etc. Currently 145 reactions (being extended)

33. Instant JChem 2009 US + EU Seminars Confidential. Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd Future releases 3.1 Fine grain security Custom roles Table and column level access control Calculated fields Future Charting/visualisation More field + widget types Copy between databases Better reporting of assay data (e.g. from Activity Base) More chemistry features

34. Instant JChem 2009 US + EU Seminars Confidential. Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd Thank you ChemAxon: www.chemaxon.comwww.chemaxon.com IJC: www.chemaxon.com/instantjchem/www.chemaxon.com/instantjchem/ Forum: www.chemaxon.com/forum/forum62.htmlwww.chemaxon.com/forum/forum62.html Questions?