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.

1. Instant JChem
Tim Dudgeon
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Solutions for Cheminformatics

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
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3. New in the last year
• Improved Query
• List and query management
• Improved deployment features
• Improved collaboration
• Marvin/JChem 5
• New licensing system
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4. Improved Query
• Form based query
• Improved query builder
• Query by example
• Federated search
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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
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6. Thank you for your attention!
For more information please visit
www.chemaxon.com
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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
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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
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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
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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)
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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
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12. Coming in IJC 2.4
• Cartridge support
• Calculated fields
• Improved printing
• Name import (using name2structure)
• Relational data export
• Various UI/Usability improvements
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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
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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
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15. Improved printing
• Better and more flexible printing
– Prettier printing
– Multi page printing
– Headers, footers….
• Based on Jasper Reports engine
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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
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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
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18. IJC server
IJC Client Database
Local DB
Remote DB
3 tier
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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
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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)
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21. Thank you for your attention!
For more information please visit
www.chemaxon.com
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