1

Instant JChem

Tim Dudgeon

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

3

New in the last year

• Improved Query

• List and query management

• Improved deployment features

• Improved collaboration

• Marvin/JChem 5

• New licensing system

4

Improved Query

• Form based query

• Improved query builder

• Query by example

• Federated search

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

6

Thank you for your attention!

For more information please visit

www.chemaxon.com

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

8

Collaboration features

• Sharing– Views

• form view

• grid view

– Lists

– Queries

• Ownership:– Private

– Public

– Shared

• IJC URLs

– Define access to a

particular view +

list/query

– Distribute the URL (e.g.

via email)

– User clicks on link:

• IJC opens

• View opens

• List/Query is applied

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

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)

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

12

Coming in IJC 2.4

• Cartridge support

• Calculated fields

• Improved printing

• Name import (using name2structure)

• Relational data export

• Various UI/Usability improvements

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

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

15

Improved printing

• Better and more flexible printing

– Prettier printing

– Multi page printing

– Headers, footers….

• Based on Jasper Reports engine

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

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

18

IJC server

Local DB

IJC Client Database

Remote DB

3 tier

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

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)

21

Thank you for your attention!

For more information please visit

www.chemaxon.com

21