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  • 1. Solutions for Cheminformatics November 200 8 Migration from ISIS environment Szabolcs Csepregi et al
  • 2. Migration - Topics
    • ChemAxon - Product Overview
    • F rom Isis/Host and MDL Direct to JChem Cartridge
    • Alternatives to Cheshire (Standardizer)
    • From ISIS/Base to Instant JChem
    • From ISIS for Excel To JChem for Excel
    • Migrating Custom A pplications
    • ChemAxon Web Services
    • Appendix: ChemAxon for Developers (Resources)
  • 3. Product Map
  • 4. ChemAxon Embedded - examples
    • Workflow
      • Pipeline Pilot, Inforsense, and KNIME.
    • ELN
      • Agilent, Contur, DeltaSoft, Kinematic, etc.
    • SAR
      • Spotfire, Synaptic Science, Omniviz
    • Databases
      • Aureus, GVK, Jubilant Biosys, Patcore
    • Web
      • Thomson Reuters, Wiley, Houghton Mifflin, Cengage, Prentice Hall, Collaborative Drug Discovery, RCSB PDB, BindingDB, NIH/NLM ChemIDPlus, Molport etc
  • 5. The Marvin family MarvinSketch MarvinView MarvinSpace Available as Java applets for HTML pages and Java beans for standalone apps (full API) Structure, query & reaction editing Individual and structure table visualization Publication quality macromolecule visualization MarvinSketch/View http:// www.chemaxon.com/MarvinSketch_View.ppt MarvinSpace http:// www.chemaxon.com/MarvinSpace.ppt
  • 6. Marvin D evelopment Histor y 1998 Applets, Molfiles, stereo support, Windows, Unix SMILES , SMARTS, PDB, Rgroups , isotopes, shortcuts, Marvin Beans Ball and stick JPG, PNG, SVG, Cut&Paste with Isis/ChemDraw, 2D cleaning , (de)aromatization, reaction drawing 2000 1999 SDF, RDF, XYZ animations, CML, templates, compressed formats, Swing, 3D models 2001 Mac support, signed applets, Java Web Start, atom mapping Partial charge, p K a , log P / log D , 3D optimi z ation , radicals , abbreviated groups Marvin file format, enhanced stereo , shapes, text boxes, multiple groups, link nodes, TPSA, recursive SMARTS , D onor/Acceptor , electron arrows, 200 4 2003 200 5 Tautomers , resonance , lone pairs , conformers, 3D sketching , MarvinSpace , Topology ana l y s i s , presentation quality graphics , .. . 2006 More Plugins, more R-groups, EMF, PDF and Mol2, Improved property storage in MRV, SDfiles and Rdfiles. .NET support in MarvinBeans. 2002 2007 Structure to name , Coordinati on compounds, Polymer drawing, OLE , Markush enumeration plugin Configurations 2008 Name to structure , OLE 2 , Chemical Terms Customizable GUI
  • 7. Calculator Plugins Calculator Plugins h ttp://www.chemaxon.com/Calculator_Plugins.ppt
    • Elemental Analysis
    • IUPAC Name
      • Standard IUPAC Name
    • Protonation
    • pKa, Major Microspecies, Isoelectric Point
    • Partitioning
    • logP, logD
    • Charge
    • Charge, Polarizability, Orbital Electronegativity
    • Isomers
    • Tautomerization, Resonance, Stereoisomer
    • Conformation
    • Conformer, Molecular Dynamics
    • Geometry
    • Topology Analysis, Geometry, Polar Surface Area (2D), Molecular Surface Area (3D)
    • Markush enumeration
    • Other
    • Hydrogen Bond Donor-Acceptor, Huckel Analysis, Refractivity
    A vari e ty of structure based calculations are available from the Marvin GUI, cxcalc command line tool and the API. The calculations are widely used within several JChem tools and are available as functions of Chemical Terms expressions.
  • 8. Chemical Naming
    • Structure to Name/ Name to structure
    • Supported nomenclatures :
    • Chains, Monocycles/ Traditional names with and without heteroatom/ Spiro ring systems/ Ethers/ Common characteristic groups, Ionic compounds/ Unlimited number of atoms and rings/ All atom types /Stereochemistry/ etc.
    • Usage:
    • drag&drop or copy&paste to MarvinSketch
    • Label updated in real-time
    • Automatic format recognition
    • Batch from command line
  • 9. JChem family JChem Base JChem Cartridge Instant JChem Fast substructure and similarity searching Tight Oracle SQL integration Desktop application for scientist ChemAxon’s proprietary database structure Arbitrary database structure Access local and remote databases
  • 10. JChem development history 2000 Oracle , MySQL, SQLServer, Access, hashed fingerprints , substructure and similarity search DB2, PostgreSQL, Rgroup searching R eaction searching , fragmentation, r eact ion processing , standardization, pharmacophore s , screening 2002 2001 Clustering , diversity 2003 R-decomposition , R- enumeration , reaction library , custom fingerprints, random s y nthesis , link nodes … 2005 2006 T automer search , Instant JChem reaction similarity, Library MCS , GUI for Standardizer/ Reactor … 2007 Calculated columns, Installer, Tautomer Duplicate filtering, Query tables, Markush tables , Speed enhancements for JChem Cartridge , form design, relational data for Instant JChem ... C artridge , enhanced stereo searching, recursive SMARTS , Chemical Terms , virtual s y nthesis 2004 2008
    • Position variation queries,
    • Instant JChem :
    • - Federated search,
    • - Cartridge support ...
    • JChem for Excel
  • 11.
    • Features
    • Fast and sophisticated searching ( chemical and non-chemical data, Chemical Terms filter, many options )
    • Custom standardization
    • Calculated columns
    • Combinatorial Markush structure tables
    • Interfaces
    • Integration with most relational database engines
    • JChem Cartridge for tight Oracle SQL integration
    • JSP integration – open source web example
    • Desktop-ready through Instant JChem
    JChem Base Structural Search http:// www.chemaxon.com/Structural_Search.ppt JChem Base http:// www.chemaxon.com/JChem_Base.ppt DB2
  • 12. Searching in combinatorial Markush structures
    • Combinatorial Markush structure registration and search
    • Markush features handled in search & enumeration:
      • R-groups (nesting to any depth)
      • Atom lists , b ond lists
      • Position variation bond
      • Link nodes
    • Compatible Markush enumeration plugin
    • Not all query features supported
    • Detailed description :
    • http://www.chemaxon.com/product/markush_search.html
  • 13. JChem Cartridge for Oracle
    • Access JChem functionality via SQL functions
    • All search features of JChem Base
    • JChem index for chemical data in arbitrary database structure
    • C hemical filters and property predictors using Chemical Terms
    • Standardization ( structure canonicalization) during registration
    • Structure format conversions
    • 2D, 3D image generation
    • Library enumeration using virtual reaction s and Markush structures
    JChem Cartridge http:// www.chemaxon.com/JChem_Cartridge.ppt
  • 14. Instant JChem Desktop application for local and remote chemical database management, search and structure based prediction
    • Simply connect to external databases and share your native database simultaneously
    • Powerful search functionalities
    • Scalable – explore large datasets (10 6 +)
    • Dynamically predict properties using Calculator Plugins
    • Apply canonicalization rules for import and viewing
    • Wide import / export options
    • Merge data sets into a single set
    • Very active development – what do you want to do?
    Instant JChem: http://www.chemaxon.com/conf/Instant_JChem.ppt
  • 15. JChem for Excel
    • Microsoft Excel integrated solution for Marvin and JChem functionality
    • Use Excel’s powerful features: Functions, Sorting, Filtering, Charts…
    • Implemented in C# .NET, and Visual Studio
      • P roof that ChemAxon APIs can be used in a Java-less .NET environment
    • Easy to install and deploy
    • UNDER DEVELOPMENT
  • 16. Canonicalization with Standardizer Standardizer http:// www.chemaxon.com/Standardizer.ppt
    • Structure canonicalization
      • Mesomers
      • Tautomers
      • Solvent and counter ion removal
      • Aromatization, dearomatization
      • Explicit/implicit hydrogen conversion
      • Stoichiometry expansion
      • Stereo manipulations
      • 2D cleaning
      • Template based cleaning
    • Custom rules
    • Availability
      • JChem Base , Cartridge & IJC
      • API (Java and .NET)
      • Batch processing
      • GUI
  • 17. Drug discovery tools JKlustor Screen Profiling, analysis, diversity Virtual screening by topological descriptors Fragmenter Reactor Library profiling and reactant generation Virtual reactions and synthesis
  • 18. Migration - Topics
    • ChemAxon - Product Overview
    • F rom Isis/Host and MDL Direct to JChem Cartridge
    • Alternatives to Cheshire (Standardizer)
    • From ISIS/Base to Instant JChem
    • From ISIS for Excel To JChem for Excel
    • Migrating Custom A pplications
    • ChemAxon Web Services
    • Appendix: ChemAxon for Developers (Resources)
  • 19. Contents
    • A short introduction of JChem Cartridge
    • MDL/Symyx features in JChem
    • Migration from MDL/Direct and ISIS/Host
    • Migration case studies and user feedback
  • 20. Purpose of JChem Cartridge
    • Access JChem functionality using SQL:
      • SELECT count(*) FROM nci WHERE jc_contains(structure, 'Brc1cnc2ccccc12') = 1
      • Access JChem in any programming environment offering Oracle connectivity ( .NET , Java, Perl, PHP, Python, Apache mod_plsql...)‏
    • Execute SQL queries efficiently using extensible indexes
      • Precompute chemical information on structures by creating jc_idxtype indexes:
      • CREATE INDEX jcxnci ON nci(structure) INDEXTYPE IS jc_idxtype
      • The jc_idxtype implementation scans the indexed column for eligible structures in one single performance-optimized operation: domain index scan
  • 21. Features of JChem Cartridge
    • Adds chemistry knowledge into the SQL language of Oracle (SELECT, INSERT, UPDATE, ...)‏
    • Substructure, superstructure, exact structure, similarity searching
    • Fast: typically 1 0k hits in 3M structures within a second
    • Complex chemical expressions using the Chemical Terms language that includes logP, p K a , ...
    • Automatic property calculation during registration
    • Standardization (canonicalization) during registration
    • Structure format conversions (MRV, Molfile, SDfile, RDfile, SMILES, CML, etc.)‏
    • 2D, 3D image generation
    • Structure enumeration using reaction rules
    • Interaction with Oracle optimizer
  • 22.
    • jc_compare : substructure/similarity/exact searching combined with Chemical Terms expressions
    • jc_matchcount : number of occurences of the query structure in the target
    • jc_evaluate : Chemical Terms evaluation
    • jc_molweight : molecular weight
    • jc_formula : molecular formula
    • jc_react : structure enumeration based on virtual reactions
    • jc_standardize : structure canonization
    • jc_molconvert : conversion to different formats (image generation is supported)
    • jc_tanimoto : similarity search
    • jcf.hitColorAndAlign : substructure coloring and alignment
    • Similarity search example displaying ID, SMILES code, and molweight:
    • SELECT cd_id, cd_smiles, cd_molweight FROM my_structures WHERE jc_tanimoto (cd_smiles, 'CC(=O)Oc1ccccc1C(O)=O') >= 0.8;
    Operators and functions
  • 23. Structure search features
    • Wide range of query atoms
    • Query properties
    • R-group queries
    • Full SMARTS support
    • Coordination compounds
    • Link nodes
    • Position variation
    • Pseudo atoms
    • Lone pairs
    • Relative stereo
    • Reaction search features
    • Hit coloring
    See detailed information on structure search: www.chemaxon.com/conf/Structural_Search.ppt
  • 24. S earch options
    • Chemical Terms filter constraint
    • Tautomer search
    • sp hybridization state check
    • Stereo on/off
      • Ignore charge/isotope/radical/valence/mixture brackets
      • Vague bond matching modes: „or aromatic”; ignore bond types
      • Inverse hit list
    • Maximum search time / number of hits
    • SQL SELECT statement for pre-filtering
    • Ordering of results
    • etc.
  • 25. Compatibility and integration
    • File formats:
      • SMILES
      • MDL molfile (v2000 and v3000)
      • MDL SDF
      • RXN
      • RDF
      • MRV
      • IUPAC name, InChI
    • Operating systems:
      • Windows
      • Linux
      • Solaris
      • HP-UX
      • etc.
    DB engines : Oracle versions 9i R2 or above for alternative RDBMS systems, see the JChem Base presentation : http:// www.chemaxon.com/JChem_Base.ppt
  • 26. Index parameters
    • Index parameters affect:
      • Fingerprint attributes
      • Standardizer configuration
      • Table space and storage options of the index table
    • Examples:
    • Standardization by stripping hydrogens and using basic aromatization:
      • CREATE INDEX jcxnci ON nci(structure) INDEXTYPE IS jc_idxtype PARAMETERS('STD_CONFIG=dehydrogenize:optional..aromatize:b')‏
    • Add structural keys to fingerprint for more efficient substructure searching (structural keys are defined in table stfp_keys):
      • CREATE INDEX jcxnci ON nci(structure) INDEXTYPE IS jc_idxtype PARAMETERS('STRUCTURALFP_CONFIG=select structure from stfp_keys')‏
  • 27. Supported Column Types
    • VARCHAR2 : typically for short formats, e.g. SMILES
    • CLOB
    • BLOB
    for longer formats, e.g. MDL molfile, Marvin (mrv)
  • 28. MDL Feature Compatibility
    • Generic atom types and bond types
    • Atom query properties
    • Atom Lists/ not lists
    • Aliases
    • Pseudo atoms
    • Atom values
    • Group and brackets
      • Abbreviated groups
      • Multiple groups
      • Repeating units
      • Polimers
      • Mixtures
      • Attached Data
    • Link Nodes
    • R-groups, R-logic
    • Stereochemistry
      • Chiral flag
      • Parity
      • Double bond stereo
      • Enhanced stereo (abs/end/or)
      • inv/ret
    • Reacting center on bonds
    • Reaction mapping
    • Topology (ring/chain)
    • Option for ISIS-like look
    • Others…
    The learning curve of chemists familiar with ISIS is very short. After having some practice, Marvin is reported a more productive drawing environment. The most of the MDL features are available in Marvin and JChem, and many others not available in MDL technology.
  • 29. MDL Feature Compatibility
    • Polymer search (coming in 5.2)
    • A ttached data S-group search (coming in 5.2)
    • 3D special features
    • Exact change flag (reaction)
    What is missing:
  • 30. Migration from MDL/Direct cartridge
    • 2 alternatives:
      • JChem indexes need to be created on structure columns of existing tables, or
      • Structural data migrated to new tables with JChem Cartridge indexes
    • The MDL/Direct SQL operators need to be changed to JChem operators in all uses.
    • Non-chemistry tables: no need for migration
  • 31. Migration from ISIS/Host
    • Molecule source need to be accessible for JChem:
      • Through exporting SD/Rdfiles from ISIS and importing into new tables with JChem index, or
      • Setting option in ISIS/Host to include molfile in RCG tables, and:
        • Use SQL to insert mol field into JChem tables, or
        • Add JChem index on original tables
    • ISIS/Host interfaces need to be rewritten to use SQL only, referencing JChem operators.
    • Hviews and GUI-s need to be replaced separately. (See further slides later.)
    • Non-chemistry tables: no need for migration
  • 32. An Independent Comparison
    • FMC migrated from MDL® ISIS/Base ISIS/Host to ChemAxon’s JChem. They later published their detailed scientific comparison.
    • Used 1.8 million vendor compounds to create a testing database
    • Prepared 115 different query structures for comparison
    • 51 simple sub-structure search
    • 51 similarity search
    • 64 complex search
    • Identical search hits in almost all cases, major differences result from MDL’s incorrect aromatic bond definitions in case of 5 member aromatic rings. ChemAxon's approach is the chemically correct and their performance is higher (faster).
  • 33. Identical Results
  • 34. Differences
  • 35. Vague Bonds
    • For the sake of perfect compatibility with MDL searching ChemAxon provides vague bond options to retrieve results according to MDL systems.
  • 36. Technical Comparison
    • Supported Platforms
      • ISIS®: Sun Solaris, Windows Servers
      • JChem: Sun Solaris, Windows Servers, Linux, Irix, MAC
    • Supported Databases
      • ISIS: Oracle
      • JChem: Oracle, MySQL, SQL Server, PostgreSQL, Access, DB2
    • Processing SD Files
      • ISIS: 31 hours, Pipeline Pilot & ISIS
      • JChem: 11 hours, JChem
    • Technology Transparency
      • ISIS®: Unclear Data/Table Structures
      • JChem: Clear Understanding of
        • Flow of Data
        • Structure of Data
        • Execution Process
      • Native Oracle Tables and Procedures
    • Performance
      • ISIS®: Slow similarity search
      • JChem: Fast similarity search
  • 37. Comparison Conclusions
    • Technical Conclusion
      • Clear and straightforward understanding of data representation and system architecture
      • Integrated system
      • Quicker and less error-prone
      • Less hassle for software development
      • From technical point of view, ChemAxon is favorable
    • Business Conclusion
      • ChemAxon was the better choice
  • 38. Migration Experience Questionnaire
    • Five companies were interviewed about their JChem Cartridge migration experiences in the form of a questionnaire containing 14 questions.
    • A UK based service/biotech company
    • A Swedish biotech company
    • A US branch of a Swiss pharmaceutical company
    • A Japanese pharmaceutical company
    • A US branch of a Japanese pharmaceutical company
  • 39. Migration Experience
    • 1. What was the platform you used before the migration?
      • All systems were run using the Daycart cartridge on Linux servers
      • MDL Cartridge running on Sun Solaris
      • Daycart
      • We used ISIS/Host as a server, the client was ISIS/Base customized using ISIS/PL
      • Daylight and IDBS Chembridge
    • 2. How long did it take to migrate?
      • Very simple, hardly any time at all, just a few hours to uninstall old cartridge, install new cartridge and build indexes. Then modify a few SQL statements in the code to use the new cartridge functions.
      • It took a full weekend to switch over and convert all old databases.
      • Since we use SQL for structure searches, the actually change in the application code are few. Code changes takes about 1 day. However, we spent at least two weeks to compare the daylight and jcart.
      • It took 1 year for planning, and another 1 year for designing and developing the system. 1-year-migration time includes all of the operation that is needed. That means our technical people worked for this project 1 year. We migrated the data structure of HView, but the form was re-designed in order to fit our existing (wet) workflow.
      • Two months
  • 40. Migration Experience
    • 3. How many technical people were required in the migration process?
      • It was fairly simple so just one developer with all round programming, database, and chemistry knowledge.
      • One person
      • 2 people
      • 6 technical people. 2 were contacting with users. For the system design, 11 users were involved from chemistry, HTS, eADME groups.
      • 1.5
    • 4. Why did you decide on leaving the previous platform? (problems)
      • Purely the cost. We found the Daycart system to be very good, very stable, fast, and the API was well thought out. However, it was just too expensive for us.
      • Old technology not offering new functionality. High cost, in particular for new licenses.
      • Daycart (at least at that time) did not take MOL query, not all query structures could be correctly presented as smiles/smarts.
      • Two main reasons were the maintainance cost, and the accessibility. We had to suppress the raising system (software) cost, and at the same time we had to enlarge the number of users and client PCs from which we could use DB system.
      • Cost, maintenance and risk
  • 41. Migration Experience
    • 5. What alternative platforms were considered/evaluated?
      • Prior to selecting ChemAxon we looked at all the cartridges available at the time
      • The Accord cartridge was also evaluated. Some others did not qualify for evaluation.
      • None
      • Accord (Accelrys), and ChemOffice (Cambridge Soft) were two major alternatives.
      • Symyx/MDL Direct Oracle cartridge
    • 6. Why did you choose ChemAxon technology? (advantages)
      • Cost was a major factor, but also because we felt we could work with ChemAxon to develop the tools further as we wanted to use them. A very open approach. Another reason was that all the tools we needed were available from a single vendor, i.e. Oracle cartridge for searching, and sketching and viewing tools.
      • Almost as good as Accord but with better impact on improvement and support.
      • Marvin Sketch and JCart represent the molecules in MOL using exactly the same backend library. MOL is used instead of smiles/smarts. Much faster search. Price is good .
      • We could keep the cost lowest by using ChemAxon, and more than that, the affinity for the web technology was favorable to our future vision of the cheminformatics system.
      • The greatest advantage is the low cost and great support. We have always had MDL/Direct cartridge, but the greatest advantage is the low cost and stellar support speaks specifically to ChemAxon.
  • 42. Migration Experience
    • 7. What were the most problematic issues occurred during the migration? (negative impressions)
      • Understanding the finer points of all the search functions / options i.e. precisely how things like aromaticity, stereochemistry, etc. are handled. We've also had to spend time considering how to restandardise structures and how to rewrite SQL. When doing a straight forward structure search (i.e. benchmarking), the JChem cartridge performs very well against other systems such as Daylight, however, if you want to incorporate joins between tables can considerably affect the query times even when using what we call ChemAxon SQL.
      • Structure matching bugs in the cartridge and undocumented actions needed to be performed.
      • JCart installation was not so smooth 3 years ago. Much better now. Most of the problem and issues are because some structures are interpreted different between the two software. Some are Daylight bugs and others are jchem bugs. JChem has fix all their share.
      • There were little problem, what I remember is that the response was slower than expected when the chemical object was included in the page.
      • Identifying all the integration points.
  • 43. Migration Experience
    • 8. How could you overcome in these difficulties? (resolutions)
      • We spent a lot of time experimenting with the different functions/options so we completely understand what they do.
      • The structure search bugs was overcome by rewriting the registration procedures, undocumented actions were overcome by hard work.
      • Wait until major bugs in JChem are fixed. We live with about 0.01% of inconsistencies and work it out later.
      • The needless chemical objects were replaced by pictures.
      • Availability and quick turn around to patch any
    • 9. Did you expect any other problem, that did not occur? (positive impressions)
      • We though there may be problems running two different cartridges on the same table but this worked fine
      • Not really. Most MDL features were available in JChem. This was one of the selection criteria, particularly important for chemical registration.
      • No
      • We expected that the transfer of the existing data might be problematic, and that the system change might be inconsistent with existing 'wet' workflow. That was why we organized 11 users as a system designing team, and I think the team worked well.
      • Migration went very smooth
  • 44. Migration Experience
    • 10. What additional components were purchased together with the JChem Cartridge?
      • Most of them!
      • Descriptor calculations.
      • None. User probably should consider plug-ins for calculating HBD, HBA, logp, psa, etc. We did not because we need to stick to CLOGP in order to be consistent with the rest of the company.
      • Standardizer.
      • Standardizer.
    • 11. How much technical support did you need from ChemAxon for the migration?
      • Initially quite a lot, though the products have been developed a lot since then. We haven't required much support for structure migration, but we've also migrated a load of SMIRKS and we've needed support for that mainly because of the way in which they were handled in the old system (non-standard).
      • A few needed support cases where filed on the support forum and fairly quickly resolved.
      • Lots, we had close communication with dev team during the migration.
      • Our technical people sent e-mail several times to your support team.
      • Little.
  • 45. Migration Experience
    • 12. Were/Are you satisfied with the ChemAxon support?
      • Yes. Support has always been good.
      • Yes very satisfied. The support has always been very fast and accurate.
      • Yes.
      • Yes.
      • Yes.
    • 13. Did the migration reach its original goals?
      • So far, yes! The systems are up and running.
      • Yes.
      • Yes.
      • Yes.
      • Yes.
  • 46. Migration Experience
    • 14. Are you satisfied with the performance/functions of the ChemAxon powered system?
      • The number of functions available and flexibility of the JChem tools is excellent, and allows us to develop very interesting and useful drug discovery software for our scientists.
      • Yes.
      • Yes.
      • Yes.
      • Yes.
  • 47. Useful migration resources ChemAxon's Marvin & JChem (v 3.1.3) vs. MDL® ISIS/Draw ISIS/Host (v 4.0) Seong Jae Yu, David Roush*, Usha Ganesh, Young Moon, Henry Liu, FMC Corp. http://www.chemaxon.com/conf/FMC_ChemAxon_JCHEM_Cart_xnotes.ppt User Group Meeting presentations: http://www.chemaxon.com/UGM/ugm_land.html
  • 48. Migration - Topics
    • ChemAxon - Product Overview
    • F rom Isis/Host and MDL Direct to JChem Cartridge
    • Alternatives to Cheshire (Standardizer)
    • From ISIS/Base to Instant JChem
    • From ISIS for Excel To JChem for Excel
    • Migrating Custom A pplications
    • ChemAxon Web Services
    • Appendix: ChemAxon for Developers (Resources)
  • 49. Cheshire Alternatives from ChemAxon
    • What is Cheshire?
    • “ Cheshire is a scripting language that enables you to write scripts to validate, modify, or gather information about chemical structures, such as molecules and reactions.”
    • What alternatives can ChemAxon offer?
    • ChemAxon’s Java API (also available from .NET)
    • Chemical Terms
    • Standardizer
  • 50. Java API for Cheminformatics from ChemAxon ChemAxon’s class library consists of more than 1500 chemistry related classes tuned for usability and high performance.
  • 51. Chemical Terms charge () and match ( amine ) or match ( hydrazine ) Chemical Terms offers more than a hundred popular chemistry functions opening up the power of cheminformatics for those scientists who focus on quick results instead of the details of programming and scripting. The integration of Chemical Terms makes make chemistry applications smarter and more customizable.
  • 52. Standardizer for Batch Conversion Standardizer is a batch conversion utility providing many useful and customizable functions for the canonicalization of chemical structures and restoration renovation chemical information in structures from older databases.
  • 53. Standardizer Actions Aromatize Dearomatize Add Explicit Hydrogens Remove Explicit Hydrogens Clean2D Clean3D Transform Wedge Clean Clear Isotopes Remove Fragments Remove R-groups Neutralize Tautomerize Mesomerize Set Absolute Stereo Remove Absolute Stereo Convert Wedge Interpretation Convert Double Bonds Clear Stereo Alias to Group, Alias to Atom Contract Group Expand Group Ungroup Expand Stoichiometry Map Reaction Unmap
  • 54. Counting Groups – Cheshire Counting O=S=O groups in Cheshire
  • 55. Counting Groups – Java API Counting any functional groups with ChemAxon’s Java API Counting O=S=O groups in Chemical Terms
  • 56. Adding Explicit Hydrogens - Cheshire Adding explicit hydrogens and cleaning the molecule in Cheshire
  • 57. Adding Explicit Hydrogens – Java API Adding explicit hydrogens and cleaning the molecule with ChemAxon’s Java API
  • 58. Adding Explicit Hydrogens – Standardizer Adding explicit hydrogens and cleaning the molecule with Standardizer The same in command line
  • 59. Group Conversions – Cheshire Conversion of neutral form of nitro to the ionic one in Cheshire
  • 60. Group Conversions – Java API Conversion of neutral form of nitro to the ionic one with ChemAxon’s Java API
  • 61. Group Conversions – Standardizer The same in command line Conversion of neutral form of nitro to the ionic one in Standardizer
  • 62. Structure Checker Framework
    • ValenceChecker
    • AromaticityChecker
    • OverlappingAtomsChecker
    • OverlappingBondsChecker
    • CrossedDoubleBondChecker
    • WigglyDoubleBondChecker
    • WedgeBondsChecker
    • BondLengthChecker
    • BondAngleChecker
    • AliasChecker
    • PseudoAtomChecker
    • AbbreviatedGroupChecker
    • MultiComponentChecker
    • QueryChecker
    • MoleculeChargeChecker
    • RadicalChecker
    • IsotopeChecker
    • ExplicitHydrogenChecker
    • StereoDoubleBondChecker
    • TetrahedralStereoAtomChecker
    • UnspecifiedStereoDoubleBondChecker
    • ChiralFlagChecker
    • CovalentSaltChecker
    • FerroceneChecker
    • CumulatedRingBondChecker
    • UnbalancedReactionChecker
    • MultistepReactionChecker
    • AtomMapChecker
    • MissingAtomMapChecker
    • AtomMapStyleChecker
    • RgroupQueryChecker
    • MarkushChecker
    • 3DCoordinateChecker
    • MolfileChecker
    • RxnfileChecker
    • SmilesChecker
    • SmartsChecker
    • InchiChecker
    • PeptideSequenceChecker
    • CmlChecker
    • PdbChecker
    The new Structure Checker framework will provide plenty of validation and correction functions to detect and repair defective or unpreferred structures.
  • 63. Summary
    • ChemAxon’s Java API provides similar freedom and flexibility to Cheshire for programmers to develop chemistry functions for any tears like web clients, desktop applications, server systems and Oracle stored procedures.
    • Java is a standard language with worlwide community, rich resources and lots of well educated developers. (The ChemAxon Java API is also accessible from .NET.)
    • Chemical Terms provides more than a hundred high level, ready to use functions substituting dozens of lines of complex Cheshire code.
    • Chemical Terms expressions can directly be used in database filters, virtual reactions, pharmacophore definitions or other cheminformatics applications.
    • Standardizer is an easy to use batch tool and graphical interface for chemists to create conversion rules without writing a single line of code.
    • The upcoming Structure Checker will provide and extensible set of quick “problem detection” functions that can be integrated in any applications and will be added to Marvin and Standardizer as well.
  • 64. Migration - Topics
    • ChemAxon - Product Overview
    • F rom Isis/Host and MDL Direct to JChem Cartridge
    • Alternatives to Cheshire (Standardizer)
    • From ISIS/Base to Instant JChem
    • From ISIS for Excel To JChem for Excel
    • Migrating Custom A pplications
    • ChemAxon Web Services
    • Appendix: ChemAxon for Developers (Resources)
  • 65. Instant JChem is…
    • An “out of the box” desktop application designed for biologists and chemists
    • A modular platform for developing chemistry applications
  • 66. Instant JChem lets users…
    • Create or connect to existing structure databases
    • Easily manage relational data
    • Import/export/merge/edit data
    • Build forms for reporting
    • Run combined structure + data searches
    • Perform structure based predictions
    • Access sophisticated chemistry features
    • Collaborate with other users
  • 67. Feature comparison to ISIS/Base Feature ISIS/Base Instant JChem Databases Local + Oracle (differences in steroechemistry and calculations etc.). Local + Oracle + MySQL (no differences in local and remote db functionality). Forms Form builder. Form builder. Tabular view Limited. Comprehensive. Relational data Hview DataTree. Deployment Installer only. Installer or Java Web Start. Many deployment features. Collaboration Limited. Many collaboration and sharing features. Scalability & performance Limited, especially for local DBs. Good.
  • 68. IJC Architecture
    • Built on modular platform
      • Allows easy extension by ChemAxon, customers and 3 rd parties
      • Strong enforcement of APIs
    • API
      • Allows extension
      • IJC functionality is built upon these APIs
  • 69. Current architecture Local DB IJC Client Database Remote DB Oracle cartridge
  • 70. IJC server architecture IJC IJC Client Database IJC Server Services API IJC server due Q1 2009 Oracle cartridge Web Apps Web services
  • 71. Migration issues: general Database artefacts IJC is currently table based. Access to views, synonyms etc. is currently being added. Use of database links has not been investigated yet, but no particular problems expected . Security model
    • Current implementation provides basic access control:
    • Read-only
    • Read-write
    • Edit database model
    • Users can create forms/lists etc. even in read-only mode, but can’t modify data that affects other users.
    Security integration LDAP is probably the most suitable, but the security implementation is quite flexible and customisable.
  • 72. Migration issues: migration of ISIS DBs Hview vs. Data Tree No direct conversion, so this would currently need to be done manually, though some automation is potentially possible. Data Tree is modelled on the same approach as Hview, so migration in most cases should be relatively simple. Forms No direct import from ISIS, but creating IJC forms is very simple and fast. Customisation Currently no equivalent to ISIS/PL. ISIS applications with complex logic may be more suited as IJC extensions, or as standalone web or JWS applications.
  • 73. Hview vs. Data Tree: standard tables master_table master_table_id col1 col2 col3 detail_table detail_table_id master_table_id cola colb colc * ISIS Hview HVIEW my_data TREE master DEVICE oracle USERNAME scott PASSWORD tiger TNAME master_table TREE detail DEVICE oracle USERNAME scott PASSWORD tiger TNAME detail_table LINK master (master_table_id) over detail (master_table_id) One-to-many relationship IJC Data Tree
  • 74. Hview vs. Data Tree: Mol + Rxn tables < RC tables> inventory inventory_id molregno cola colb colc * ISIS Hview HVIEW cpds_inv TREE compounds DEVICE chemicaldb USERNAME CPD/CPD PASSWORD TNAME compounds TREE inventory DEVICE oracle USERNAME scott PASSWORD tiger TNAME inventory LINK compounds (molregno) over inventory (molregno) IJC Data Tree compounds molregno structure [jc_index] inventory inventory_id molregno cola colb colc *
  • 75. Migration options Simple local or Host based databases used primarily for searching/reporting Migrate to IJC ISIS/Base application with complex application logic but standard (Hview based) data structure (e.g. registration applications) Create custom IJC extension module built upon IJC API (much of the existing IJC functionality is essentially done this way) Application with complex data model and logic Either: Create standalone web application or: Create standalone JWS application or: Create custom IJC module that defines its own data access API.
  • 76. Migration: local ISIS databases
    • Analyse data hierarchy
    • Export data as SDF/RDF
    • Import into IJC
    • Build forms
    • Maybe possible to automate by writing COM application to read data from ISIS and write to Oracle database.
  • 77. Migration: ISIS/Host databases
    • Analyse database tables and Hview
    • Migrate RCG tables to JChem table(s)
    • Connect IJC to the database
    • Promote tables/columns/foreign keys into IJC
    • Assemble IJC Data Tree
    • Build forms
    • May be possible for some automation.
  • 78. Migration - Topics
    • ChemAxon - Product Overview
    • F rom Isis/Host and MDL Direct to JChem Cartridge
    • Alternatives to Cheshire (Standardizer)
    • From ISIS/Base to Instant JChem
    • From ISIS for Excel To JChem for Excel
    • Migrating Custom A pplications
    • ChemAxon Web Services
    • Appendix: ChemAxon for Developers (Resources)
  • 79. JChem for Excel
    • Microsoft Excel integrated solution for Marvin and JChem functionality
    • Use Excel’s powerful features: Functions, Sorting, Filtering, Charts…
    • Implemented in C# .NET, and Visual Studio
      • P roof that ChemAxon APIs can be used in a Java-less .NET environment
    • Easy to install and deploy
    • UNDER DEVELOPMENT
  • 80. ISIS for Excel to JChem for Excel
    • Import ISIS SARTables (January 2009)
      • Workbook exported from ISIS for Excel
    • Migration of standard ISIS Workbooks?
  • 81. Migration - Topics
    • ChemAxon - Product Overview
    • F rom Isis/Host and MDL Direct to JChem Cartridge
    • Alternatives to Cheshire (Standardizer)
    • From ISIS/Base to Instant JChem
    • From ISIS for Excel To JChem for Excel
    • Migrating Custom A pplications
    • ChemAxon Web Services
    • Appendix: ChemAxon for Developers (Resources)
  • 82. Custom Applications
    • Java Applications
      • Swing
    • .NET Applications
      • JNBridge: Commercial Java - .NET Proxy
      • Byte Code to IL (.NET binary) translation ( IKMV )
        • Open Source, very good performance
        • No full GUI support at the moment, but coming
        • JChem for Excel is built using IKVM
    • Web Based Applications
      • JSP, ASP.NET, AJAX
    • SOAP
  • 83. Custom Components
    • Plans to release custom components
      • Java Swing
      • AJAX Examples
      • .NET
        • Visual Studio integrated
        • Windows Forms (from JChem for Excel),WPF?
        • ASP.NET
        • ASP.NET AJAX, MVC
  • 84. .NET Integration Enhancements
    • Problem : ChemAxon API uses Java Classes, not familiar to .NET developers
    • Higher Level .NET wrappers, components
      • Properties, Events
      • Search results in DataSet, IDataReader
      • LINQ, IEnumerable interfaces
      • GUI Components: DataGridView, Property Grids, Components for Search
  • 85. Custom Application Migration and Development
    • Resources and experience for migrating custom ISIS(Host - Base) based applications
      • ISIS Forms to other applications
      • Procedural Language (ISIS/PL)
    • Consultation
      • Help with custom application development on ChemAxon platform
      • Both in-house (CXN) staff and partner companies are available
      • Custom/prioritised improvements of ChemAxon products
  • 86. Migration - Topics
    • ChemAxon - Product Overview
    • F rom Isis/Host and MDL Direct to JChem Cartridge
    • Alternatives to Cheshire (Standardizer)
    • From ISIS/Base to Instant JChem
    • From ISIS for Excel To JChem for Excel
    • Migrating Custom A pplications
    • ChemAxon Web Services
    • ChemAxon for Developers (Resources)
  • 87. Web Services
    • Extends ChemAxon functionality to Web applications
    • Enables interoperability from multiple programming languages with SOAP Protocol
    • Allows migration of existing web applications to ChemAxon services
    • Encourages creation new web applications
  • 88. Service Modules
    • Application Building Blocks
      • DB Searching
        • Substructure, Similarity, Exact, etc.
      • Molecular Standardization
      • Clustering and Diversity
    • Chemically Intelligent Tools
      • Shorthand Chemical Terms and Calculator Plugins
        • Lipinski Rule of 5, pK a , logP, logD, etc.
      • Molecular Format Conversion
      • Image Generation
  • 89. SOAP Protocol
    • SOAP protocol used by most major web application languages
    • Programming languages
      • Java
      • .Net (C#, ASP.net)
    • Scripting languages
      • JavaScript
      • Perl
      • Python
    • Etc.
  • 90. AJAX Example
  • 91. Migration of Existing Web Apps
    • ChemAxon Web Services can be called from existing web services
    • ChemAxon Web Services can directly replace specific functionality
    • Migrate using Security Standards
      • WS-Security, WS-Security Policy
      • Integrate with existing authentication services (e.g. LDAP, Active Directory)
  • 92. Creation of New Web Apps
    • Standard WSDL files allow for automated client side code generation (Python, Perl, Java, C#, etc.)
    • AJAX provides asynchronous and desktop application performance
    • Easily integrate with Marvin applets
  • 93. Migration - Topics
    • ChemAxon - Product Overview
    • F rom Isis/Host and MDL Direct to JChem Cartridge
    • Alternatives to Cheshire (Standardizer)
    • From ISIS/Base to Instant JChem
    • From ISIS for Excel To JChem for Excel
    • Migrating Custom A pplications
    • ChemAxon Web Services
    • Appendix: ChemAxon for Developers (Resources)
  • 94. API and Compatibility
    • Java API ( Marvin GUI included)
    • Marvin Applets for web applications
    • .NET API over JNBridge ( Marvin GUI included)
    • Native .NET solution under development ( Marvin GUI included)
    • API from SQL: JChem Cartridge for Oracle
    • SOAP interface (Python, C, .NET, ... over SOAP) under development
    • AJAX interface under development ( Marvin GUI included)
    • Instant JChem highly configurable + Java API
    • Integration: Pipeline Pilot, KNIME, Spotfire, ...
  • 95. Java API
    • Direct manipulation of structures
    • Format conversions, name<=>structure, image generation
    • Structure searching with/without DB access
    • Standardization of structures
    • Property calculations
    • Reaction modelling (enumeration)
    • Clustering
    • Sketcher, 2D/3D viewers (Marvin family)
    • Etc
    • JChem API
  • 96. Marvin Applets for Web Applications
    • All relevant browsers (IE, FF, Safari, ...)
    • Manipulation from HTML page (from JavaScript)
    • Catching drawing events in JavaScript
    • Can be used from .NET applications using the web browser control
    • Marvin demo
    • MarvinSketch Applet Examples
    • MarvinView Applet Examples
    • MarvinSpace Applet Examples
  • 97. .NET API Over JNBridge
    • Tight integration with .NET
    • Full Java API is mirrored in .NET
    • Marvin GUI components are also supported
  • 98. Native .NET S olution
    • Translating the non-GUI elements to Java binary to .NET binary (using IKVM)
    • Building a thin .NET GUI for Marvin and other tools over the core.
    • Advantages
    • Pure .NET solution, Java is not needed to be installed
    • No license issue
    • No performance overhead of proxying
    • under development
  • 99. JChem Cartridge for Oracle
    • API from Oracle SQL
    • All features needed for structure handling and searching
    • Fast searching, insertion, and indexing
    • Special features:
      • Standardization of structures is tied with structure tables
      • Property calculations
      • Format conversions, name<=>structure, image generation
      • Reaction and Markush based structure enumeration
      • Markush libraries in structure tables (coming soon)
  • 100. SOAP Interface
    • Web services interface to most functionalities
    • Bridges to Python, C, Perl, .NET, Java using WSDL
    • Enables both remote and local access to ChemAxon functionalities
    • under development
  • 101. AJAX GUI
    • AJAX components for web applications
    • Customization using CSS and XSL
    • Accesses SOAP interface
    • Structure searching, database handling example
    • Fast and rich GUI
      • Floating windows
      • Scrolling through large database without paging
    • Marvin Applets are integrated
    • under development
  • 102. Instant JChem for Developers
    • Sharable forms, queries, lists
    • URL-s to sharable items - Demos
    • Instant JChem API
  • 103. Integrations
    • Several software vendors integrated ChemAxon components
    • Pipeline Pilot
    • KNIME (by Infocom)
    • Spotfire
    • Aureus
    • Integrity (Thomson)
    • O thers : (Agilent, Tripos, Symyx, Deltasoft, GVK, Wiley, Genedata, Contur, Inforsense, Kinematik, Houghton Mifflin , Kelaroo, Patcore, Cengage, Prentice Hall, Crossfire Beilstein, etc)
  • 104. Visit other technical presentations ChemAxon Overview http:// www.chemaxon.com/conf/ChemAxon_Overview.ppt MarvinSketch/View http:// www.chemaxon.com/MarvinSketch_View.ppt MarvinSpace http:// www.chemaxon.com/MarvinSpace.ppt Calculator Plugins h ttp://www.chemaxon.com/Calculator_Plugins.ppt Structural Search http:// www.chemaxon.com/Structural_Search.ppt JChem Base http:// www.chemaxon.com/JChem_Base.ppt Instant JChem http:// www.chemaxon.com/conf/Instant_JChem.ppt JChem Cartridge http:// www.chemaxon.com/JChem_Cartridge.ppt Standardizer http:// www.chemaxon.com/Standardizer.ppt Screen http:// www.chemaxon.com/Screen.ppt J Klustor http:// www.chemaxon.com/JKlustor.ppt Fragmenter http:// www.chemaxon.com/Fragmenter.ppt Reactor http:// www.chemaxon.com/Reactor.ppt
  • 105. Find out more
    • Product descriptions & links
      • www.chemaxon.com/products.html
    • Forum
      • www.chemaxon.com /forum
    • Presentations and posters
      • www.chemaxon.com /conf
    • Download
      • www.jchem.com/licensefrset.html
  • 106.
    • Thank you for your attention !