instant j chem - introduction and latest
DESCRIPTION
Overview of Instant JChem (structure database management, search and prediction), use cases and upcoming features in 3.0 and beyondTRANSCRIPT
Instant JChem 2009 US + EU SeminarsConfidential . Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd
Instant JChemInstant JChem Seminar series Q1 2009
Instant JChem 2009 US + EU SeminarsConfidential . 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
Instant JChem 2009 US + EU SeminarsConfidential . Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd
Product map
Instant JChem 2009 US + EU SeminarsConfidential . 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
Instant JChem 2009 US + EU SeminarsConfidential . Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd
1. Simple and flexible deployment
Instant JChem 2009 US + EU SeminarsConfidential . Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd
2. Create and manage structure databases
Instant JChem 2009 US + EU SeminarsConfidential . Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd
3. Import/export/merge/edit data
Instant JChem 2009 US + EU SeminarsConfidential . Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd
4. Build tabular and form based reports
Instant JChem 2009 US + EU SeminarsConfidential . Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd
5. Run combined structure and data searches
Instant JChem 2009 US + EU SeminarsConfidential . Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd
6. Structure based predictions
Instant JChem 2009 US + EU SeminarsConfidential . Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd
7. Manage relational data
Instant JChem 2009 US + EU SeminarsConfidential . Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd
8. Access sophisticated chemistry features
Instant JChem 2009 US + EU SeminarsConfidential . Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd
9. Collaborate with other users
Instant JChem 2009 US + EU SeminarsConfidential . Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd
10. Extensible
Instant JChem 2009 US + EU SeminarsConfidential . Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd
Typical usage scenarios
How customers are typically using IJC
Instant JChem 2009 US + EU SeminarsConfidential . 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
Instant JChem 2009 US + EU SeminarsConfidential . 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
Instant JChem 2009 US + EU SeminarsConfidential . 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
Instant JChem 2009 US + EU SeminarsConfidential . 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
Instant JChem 2009 US + EU SeminarsConfidential . Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd
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
Instant JChem 2009 US + EU SeminarsConfidential . 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
Instant JChem 2009 US + EU SeminarsConfidential . 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)
Instant JChem 2009 US + EU SeminarsConfidential . 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
Instant JChem 2009 US + EU SeminarsConfidential . Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd
IJC developments
short and medium term
Instant JChem 2009 US + EU SeminarsConfidential . 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
Instant JChem 2009 US + EU SeminarsConfidential . 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
Instant JChem 2009 US + EU SeminarsConfidential . 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
Instant JChem 2009 US + EU SeminarsConfidential . Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd
IJC server: current architecture
Local DB
IJC Client Database
Remote DB
Oracle cartridge
Instant JChem 2009 US + EU SeminarsConfidential . 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
Instant JChem 2009 US + EU SeminarsConfidential . 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
Instant JChem 2009 US + EU SeminarsConfidential . 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
Instant JChem 2009 US + EU SeminarsConfidential . 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)
Instant JChem 2009 US + EU SeminarsConfidential . 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
Instant JChem 2009 US + EU SeminarsConfidential . Copyright© 2009 ChemAxon Kft, Informatics Matters Ltd
Thank you
• ChemAxon: www.chemaxon.com
• IJC: www.chemaxon.com/instantjchem/
• Forum: www.chemaxon.com/forum/forum62.html
• Questions?