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Instant JChem

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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  1. Instant JChem INFORMATICS MATTERS Informatics solutions for drug discovery

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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)

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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.

  13. 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

  14. Query extensions • Overlap analysis • Compare one set of structures with another • Federated search • Run a structure search across multiple structure tables at once

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. IJC Development curve • Rapid development since Jan 2006 start

  21. Future developments • Development is rapid and accelerating • capacity is being doubled (2007 Q1 vs 2008 Q1) • User feedback drives future development

  22. Further information • Web pages & Download • http://www.chemaxon.com/instantjchem • Licensing • sales@chemaxon.com • Support forum • http://www.chemaxon.com/forum/forum62.html • Animations • http://www.chemaxon.com/anim/ijc.html

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