Instant jchem
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Instant JChem. INFORMATICS MATTERS Informatics solutions for drug discovery. 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.

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Instant JChem

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Instant jchem

Instant JChem

INFORMATICS

MATTERS

Informatics solutions for drug discovery


Instant jchem is

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


Aims of instant jchem

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


Key strengths

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


Database creation

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:

http://www.chemaxon.com/conf/JChem_Base.ppt


Import and export

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)


Calculations and predictions

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:

    • 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 of ChemAxon’s Chemical Terms:http://www.chemaxon.com/jchem/doc/user/ChemicalTerms.html


Chemical business rules standardizer

Chemical business rules - Standardizer

  • Control the way structures are handled

  • Nitro group representation

  • Counter-ions

  • Explicit hydrogen atoms

  • Tautomers

For more information about structure canonicalization: http://www.chemaxon.com/conf/Standardizer.ppt


Grid view

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


Form view

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


Flexible display options

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 sub-structure highlighting and alignment to query structure


Relational data

Relational data

  • Relational data can be displayed in master-detail 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.


Query

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: http://www.chemaxon.com/conf/Structural_Search.ppt


Query extensions

Query extensions

  • Overlap analysis

    • Compare one set of structures with another

  • Federated search

    • Run a structure search across multiple structure tables at once


List and query management

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


Markush search and enumeration

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


Deployment

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


Multi user environments

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


Licensing

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


Ijc development curve

IJC Development curve

  • Rapid development since Jan 2006 start


Future developments

Future developments

  • Development is rapid and accelerating

    • capacity is being doubled (2007 Q1 vs 2008 Q1)

  • User feedback drives future development


Further information

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


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