Transcript Instant JChem

Instant JChem
INFORMATICS
MATTERS
Informatics solutions for drug discovery
Instant JChem (IJC) — April 2008
Confidential . Copyright© 2008 ChemAxon Kft, Informatics Matters Ltd
Instant JChem is…
• An “out of the box”
desktop application
designed for biologists
and chemists
• A fast and scalable
database application
for chemistry
• A modular platform for
developing future
chemistry applications
Instant JChem (IJC) — April 2008
Confidential . Copyright© 2008 ChemAxon Kft, Informatics Matters Ltd
Aims of Instant JChem
• Provide a desktop alternative to current
applications such as ISIS, Accord etc.
• Easy to install, manage and update
• Maintain an open modular extensible platform to
allow new functionalities to be continually added
(by users, ChemAxon and ChemAxon partners)
• Integrate other ChemAxon toolkits upon demand
• Client led development
• Fully documented and supported
• Localizable
Instant JChem (IJC) — April 2008
Confidential . Copyright© 2008 ChemAxon Kft, Informatics Matters Ltd
Key strengths
• Ease of deployment in multi user environment
• Flexible deployment options
• Simple and easy to use
• Fast and scalable
• Easy to create form and table based reports
• Powerful search functionality
• Powerful chemistry functionality
• Import, export and merge capabilities
• Modular and extensible
Instant JChem (IJC) — April 2008
Confidential . Copyright© 2008 ChemAxon Kft, Informatics Matters Ltd
Database creation
• Create databases in seconds
• Multiple databases can be
open
• Local and remote databases
supported
• Derby, Oracle, MySQL
• Customize by defining
additional fields
• Support for relational data
• Support for multiple structure
table types
• Molecule, Reaction, Query,
Markush, Any Structures
For
more
information
about database handling and search:
Instant
JChem (IJC)
— April 2008
Confidential . Copyright© 2008 ChemAxon Kft, Informatics Matters Ltd
http://www.chemaxon.com/conf/JChem_Base.ppt
Import and export
• Flexible options for defining
how to import files into the
database
• Merge data from multiple files
into one dataset
• Export wizard allows data to be
exported to files
• Standard file formats supported
such as SD & RD files and
Daylight smiles
• Support for multiple encodings
(e.g. Japanese text)
Instant JChem (IJC) — April 2008
Confidential . Copyright© 2008 ChemAxon Kft, Informatics Matters Ltd
Calculations and predictions
• Add calculated or predicted
properties using chemical terms
fields
• Values automatically updated
when structures edited or added
• Wide range of functions available
• Examples:
–
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logP/logD
pKa
H-bond donor/acceptors
Lipinski rule of 5
Bioavailability
IUPAC Name
• Can be used as filters for
searches
For more information about structure based prediction and other
functions
ChemAxon’s
Chemical Terms:
Instant JChem (IJC)of
— April
2008
Confidential . Copyright© 2008 ChemAxon Kft, Informatics Matters Ltd
http://www.chemaxon.com/jchem/doc/user/ChemicalTerms.html
Chemical business rules - Standardizer
• Control the way
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For
more
information
about structure canonicalization:
Instant
JChem (IJC)
— April 2008
Confidential . Copyright© 2008 ChemAxon Kft, Informatics Matters Ltd
http://www.chemaxon.com/conf/Standardizer.ppt
structures are
handled
Nitro group
representation
Counter-ions
Explicit hydrogen
atoms
Tautomers
Grid View
•
A chemically aware table
suitable for very large data
sets
•
Multiple views can be open
and visible at any one time
•
Data in the table can be
sorted, queried and
formatted
•
Structure changes update
predicted properties
dynamically
•
Various display options are
possible
Instant JChem (IJC) — April 2008
Confidential . Copyright© 2008 ChemAxon Kft, Informatics Matters Ltd
Form view
• Custom forms can be
designed.
• Relational data can be
displayed
• “Snap to edges” aids
form design
• Form Widgets are
bound to data fields
• Form widgets
expected to become
major extension point
• Extensible widgets
and renderers
Instant JChem (IJC) — April 2008
Confidential . Copyright© 2008 ChemAxon Kft, Informatics Matters Ltd
Flexible display options
• Views can be
configured to format
data according to
users needs
• Here options for
structure display are
being specified
• Support for 2D and
3D structure display
• Support for substructure
highlighting and
alignment to query
structure
Instant JChem (IJC) — April 2008
Confidential . Copyright© 2008 ChemAxon Kft, Informatics Matters Ltd
Relational data
• Relational data can be
displayed in masterdetail forms
• Relational models can
be built using the
Schema and Data Tree
editors
• “Relationships” modelled
on (and use) database
foreign key constraints
• Import of relational data
from MDL’s RDF format
files.
Instant JChem (IJC) — April 2008
Confidential . Copyright© 2008 ChemAxon Kft, Informatics Matters Ltd
Query
• Form based query and
query builder provide
alternative ways of defining
queries
• Complex queries are
rapidly executed even with
millions of structures
• Indexes can be added to
improve performance
• Relational and AND and
OR type queries can be
specified
• Filter results with chemical
terms expressions
• Alignment and
substructure highlighting in
results
For
more
information
on search features:
Instant
JChem (IJC)
— April 2008
Confidential . Copyright© 2008 ChemAxon Kft, Informatics Matters Ltd
http://www.chemaxon.com/conf/Structural_Search.ppt
Query extensions
• Overlap analysis
– Compare one set of
structures with
another
• Federated search
– Run a structure
search across
multiple structure
tables at once
Instant JChem (IJC) — April 2008
Confidential . Copyright© 2008 ChemAxon Kft, Informatics Matters Ltd
List and Query Management
• Queries can saved and
re-executed
• Lists of results can be
saved and restored
• Queries can be restricted
to a list of entries
• List and queries can be
copied or shared
between users
• Lists can be combined
with Intersection, Union,
XOR, A not B logic
Instant JChem (IJC) — April 2008
Confidential . Copyright© 2008 ChemAxon Kft, Informatics Matters Ltd
Markush search and enumeration
• Markush table type for
storing Markush
structures
– Combinatorial libraries
– Patents
• Perform structure
searches against the
Markush structures
• Enumerate a Markush
structure
– Full enumeration
– Random enumeration
– Enumerate within context
of a query structure
Instant JChem (IJC) — April 2008
Confidential . Copyright© 2008 ChemAxon Kft, Informatics Matters Ltd
Deployment
1. Traditional installer
• Updated modules can be
downloaded and installed
• Allows you to keep up to
date with the latest
features and fixes
• Customers can configure
their own update center
• Distribute your own
plugins
2. Java Web Start
• Zero install option
• Deployable at customer’s
site
Instant JChem (IJC) — April 2008
Confidential . Copyright© 2008 ChemAxon Kft, Informatics Matters Ltd
Multi-user environments
• Pre-configured settings for multi-user
environments
• Centralised deployment through Java Web Start
• Centralised project and connection configuration
• Centralised license management
• Multi-user databases
• Access control
• Sharing of views, queries, lists
• ‘IJC URLs’: click on a hyperlink in web/email and:
• IJC opens (installing if necessary)
• Open the specified view
• Apply the specified query or list
Instant JChem (IJC) — April 2008
Confidential . Copyright© 2008 ChemAxon Kft, Informatics Matters Ltd
Licensing
• ‘Personal’ (no license required)
• Free for commercial and academic users
• Local databases only - no search limitations
• Default standardization included (custom standardization
requires standardizer license)
• Most chemical terms functions require calculator plug-in
licenses
• Markush features need licenses
• ‘Enterprise’ (requires license)
• Shared databases (Oracle and MySQL)
• Multi-user collaboration
• ‘Calculations pack’ (requires license)
• All calculator plugins
• Standardizer
• Only for use in a local database
Instant JChem (IJC) — April 2008
Confidential . Copyright© 2008 ChemAxon Kft, Informatics Matters Ltd
IJC Development curve
• Rapid development since Jan 2006 start
IJC 1.0
Nov 2006
IJC 2.0
Aug 2007
IJC 2.1
Sep 2007
IJC 2.2
Jan 2008
IJC 2.3
Apr 2008
Database creation
Local and remote DBs
File import/export
Query
Spreadsheet view
Overlap analysis
Form view
Relational data
Advanced query
Multi user access
Security
API
List management
Query management
Form based query
Shared views, lists,
queries
Federated search
LDAP based security
Export to Excel
Java Web Start
Form printing
Marvin/JChem 5.0
Shared projects
IJC URLs
Markush features
Instant JChem (IJC) — April 2008
Confidential . Copyright© 2008 ChemAxon Kft, Informatics Matters Ltd
Future developments
• Development is rapid and accelerating
– capacity is being doubled (2007 Q1 vs 2008 Q1)
• User feedback drives future development
Functionality
Architecture
ChemAxon tools
Applications
More field types (esp.
biological types)
More display widgets
Calculated fields
Charting & visualisation
Conditional formatting
IJC server
Improved API
Scripting
Pivoted data
JChem cartridge
Reactor
LibMCS
JKlustor
Marvin Space
R-group analysis
New licensing system
Chemical Registration
Assay data management
Virtual screening
Library design
Instant JChem (IJC) — April 2008
Confidential . Copyright© 2008 ChemAxon Kft, Informatics Matters Ltd
Further information
• Web pages & Download
• http://www.chemaxon.com/instantjchem
• Licensing
• [email protected]
• Support forum
• http://www.chemaxon.com/forum/forum62.html
• Animations
• http://www.chemaxon.com/anim/ijc.html
Instant JChem (IJC) — April 2008
Confidential . Copyright© 2008 ChemAxon Kft, Informatics Matters Ltd