Instant J Chem: one-stop information hub for medicinal chemists: US UGM 2008

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Instant JChem is ChemAxon's desktop solution for chemistry. We will present the recent developments which have been primarily in improving the ability to deploy Instant JChem to a large community of users, and for those users to share information. We will also describe the functionality that is currently under development.

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Instant J Chem: one-stop information hub for medicinal chemists: US UGM 2008

  1. 1. Instant JChem Tim Dudgeon 1 Solutions for Cheminformatics
  2. 2. What is Instant JChem? • Desktop application for chemists and biologists • Cross platform – Windows, Mac OSX, Linux – Oracle, MySQL, Derby • Simple but powerful – Exploit the power of the Marvin and JChem toolkits – Advanced computational chemistry usable by chemists – Simple to deploy • Supports collaboration and sharing • Extensible – Modular – Public API • Under continual development – User led development – Rapid development curve 2
  3. 3. New in the last year • Improved Query • List and query management • Improved deployment features • Improved collaboration • Marvin/JChem 5 • New licensing system 3
  4. 4. Improved Query • Form based query • Improved query builder • Query by example • Federated search 4
  5. 5. List and query management • Hit list is created when query is run and query is recorded • Lists and previously run queries can be re-run • Lists and queries can be made permanent • List logic on hit lists • List can be manually edited, imported, exported • Queries can be restricted to a particular list 5
  6. 6. Thank you for your attention! For more information please visit www.chemaxon.com 6
  7. 7. Improved deployment features • Java Web Start – Once click launch from a web page – Deploy to your own server • Shared projects – Central configuration of a project and all its contents – Simple deployment to all your users • Support for LDAP authentication – Centralised authentication and authorization 7
  8. 8. Collaboration features • Sharing • IJC URLs – Views – Define access to a • form view particular view + • grid view list/query – Lists – Distribute the URL (e.g. – Queries via email) • Ownership: – User clicks on link: – Private • IJC opens – Public • View opens – Shared • List/Query is applied 8
  9. 9. Marvin/JChem 5 • MarvinSketch 5.0 • Query and Markush table types • Markush enumeration • Code assist for chemical terms expressions • Improved mol formula sorting • Various functions moved to Marvin/JChem API implementations – Structure file parsing – Hit display – JChem Search options 9
  10. 10. License management • New license management system – License management same as for all CXN tools – New license for IJC Calculations Pack (includes all calculator plugins + standardizer for local use) • Centralised license deployment (using HTTP server) 10
  11. 11. Miscellaneous • Export to Excel • Import and export of InChI format • Better error reporting during import • Form printing • Editable chemical terms favourites • Improved relational data management • Support for Java 1.6 11
  12. 12. Coming in IJC 2.4 • Cartridge support • Calculated fields • Improved printing • Name import (using name2structure) • Relational data export • Various UI/Usability improvements 12
  13. 13. Oracle cartridge support • Support for JChem cartridge – Index on existing JChemBase table – Index on text column of standard table • Will improve ability to connect IJC to existing cartridge environment • Benefits – Supports very large database tables – Structure search operates in Oracle – Much reduced memory footprint on client – Faster start up 13
  14. 14. Calculated fields • New field type that automatically generates values: – assay1 / assay2 [mathematical operations] – wt_grams * 10000 [unit conversions] – avg(assay_table.kit_kinase_ic50) [aggregate functions] – date() [auditing] • Database generated values using functions and/or triggers 14
  15. 15. Improved printing • Better and more flexible printing – Prettier printing – Multi page printing – Headers, footers…. • Based on Jasper Reports engine 15
  16. 16. Future • 3.0 (end of year) – More field and widgets types – IJC server • 3.x – Visualisation (graphs/charts) – Reactor – LibMCS – R-group analysis – Screening • Pharmacophores, BCUTs and other metrics – Assay data 16
  17. 17. New field types and widgets • Short term (3.0) – Images (png, gif…) – Documents (PDF, Word…) presented as hyperlinks – “URL fields” – ability to define field content as a URL e.g. http://yourserver.com/nmrspectra/${cpd_id}.png • Longer term (3.x) – Calculator plugin fields • conformers/tautomers/stereoisomers • pKa/logD plots – Graph widgets • scatter plots, histograms, pie charts… – Spectra (JCAMP-DX) – Dose response curves 17
  18. 18. IJC server IJC Client Database Local DB Remote DB 3 tier 18
  19. 19. IJC server key benefits • Searching performed on server • Reduced memory needs on client • Larger database sizes • Reduced need for synchronising upgrades of client • Faster initialization of connections on startup • Improved security • Improved collaboration • Other mechanisms of access e.g. web applications 19
  20. 20. Content for IJC • Do you want to see content provided for IJC? • Do you have content that you would like to provide to IJC users? • Commonly used content – ACD – Suppliers DBs • Maybridge, Chembridge, Sigma Aldridge, Fluka, Otava, Key Organics, BioFocus… – WDI – MDDR – Beilstein – Wombat – Patent data (Markush) 20
  21. 21. Thank you for your attention! For more information please visit www.chemaxon.com 21 21

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