instant jchem 2009 us + eu seminars confidential. copyright© 2009 chemaxon kft, informatics matters...

Instant JChem 2009 US + EU SeminarsConfidential . Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd

Instant JChemInstant JChem Seminar series Q1 2009


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


Product map


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


1. Simple and flexible deployment


2. Create and manage structure databases


3. Import/export/merge/edit data


4. Build tabular and form based reports


5. Run combined structure and data searches


6. Structure based predictions


7. Manage relational data


8. Access sophisticated chemistry features


9. Collaborate with other users


10. Extensible


Typical usage scenarios

How customers are typically using IJC


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


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


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


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


Customer A

Mid size, multi-site biotech wants to manage multiple commercial content db’s (SD and RD files) as discrete db’s while giving users the ability to search all simultaneously

Features

• Administrator prepares everything for users

• Upgrading content is easy

• Unlimited numbers of content


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


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)


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


IJC developments

short and medium term


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


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


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


IJC server: current architecture

Local DB

IJC Client Database

Remote DB

Oracle cartridge


IJC server: server architecture

IJC

IJC Client

Database

IJC Server

Web Apps

Web services

Services API

Oracle cartridge


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


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


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)


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


Thank you

• ChemAxon: www.chemaxon.com

• IJC: www.chemaxon.com/instantjchem/

• Forum: www.chemaxon.com/forum/forum62.html

• Questions?

instant jchem 2009 us + eu seminars confidential. copyright© 2009 chemaxon kft, informatics matters...

Documents

chemaxon kft

eu seminars confidential

ijc slide

data export data slide

relational data slide

discussion slide

mysql data

structure databases