MUG'02 -- 26 Feb - 01 Mar 2002 -- Santa Fe, NM

Intro to Daylight - MUG '02 Edition
A History of Innovations

Jeremy Yang
InnovationDateVersionComments
  • SMILES
  • CLogP
  • SMARTS
  • THOR
  • Merlin
  • Fingerprints
  • Depict
    		•  1983-89 3.1-3.54 (Medchem) Many algorithms and technologies, SMILES formost among them, were first developed and published at the MedChem Project, Pomona College. Al Leo and Dave collaborated to create ClogP. Dave and Art were coding in Fortran on VAX/VMS. Tanimoto similarity c/o Peter Willett, et al. Canonicalization of SMILES. Isomeric SMILES. SMILES papers: 0 ('86)  1 ('88)  2 ('89)  3 ('90)
  • Aladdin
    		•  1990 3.62 3D Searching using SMARTS and ACL, Aladdin Control Language, which enabled a rigorous language based query specification. Collaboration with Abbott Labs, Yvonne Martin and John Van Drie.
  • C/unix port
  • IP-client/server Thor and Merlin
  • oopish programming toolkit
    		•  1991 4.1 Complete rewrite of the core toolkits in C, by Cedar River Software ( Jeremy and Jeff Scofield). Most hard coded limits disappear due to malloc() replacing static Fortran arrays. The new toolkit object model facilitates rapid application development to follow. Networked DBMS evolve past mainframe/terminal model. Thor record-locking and other enterprise features developed by Craig James in collaboration with Glaxo, John Bradshaw and Rashmi Mistry.
  • Clustering Package
    		• 1992 4.2 Jarvis-Patrick clustering based on fingerprints. Impressively fast clustering of large datasets, again thanks to compactness of SMILES and fingerprints and shameless use of RAM. Highly customizable.
  • PrintPackage
    		• 1993 4.31 PostScript output for structures and data.
  • Remote Toolkit
    		• 1993 4.31 Toolkit server for PCs: toolkits for native PC and Mac applications via network. Help from Novartis ( Bernd Rohde, Alberto Gobbi).
  • Rubicon
    		• 1993 4.32 Distance geometry and SMARTS based conformation invention and analysis. Based on Jeff Blaney's DGEOM.
  • Program Object Toolkit

    		•  1995 4.41 Access to programs as toolkit objects
  • Parallelized Clustering

    		•  1995 4.41 Cluster millions in a day! (Multiple processes, not multithreaded/reentrant yet -- but working on it.)
  • Monomer Toolkit
  • Chuckles, Chortles and Charts
    		• 1995 4.41 Combinatorial chemistry: define monomers with monomer-SMILES, multimers with Chuckles, and mixtures with Chortles, then search with Charts. Ideal for regular, exhaustive oligomeric and scaffold based combinatorial mixtures. Grew from Chiron collaboration (Blaney, Siani).
  • MCL
    		• 1995 4.41 Merlin Control Language - scripted queries for batch searching.
  • Parallelized Merlin Searching

    		•  1996 4.42 Via program object merlinsmartstalk
  • DayCGI
    		• 1996 4.42 Web programming paradigm with examples, including smi2gif, which creates GIF structure on the fly from SMILES.
  • DayPerl
    		• 1996 4.42 Perl toolkit wrapper. Programming for the masses! Thanks Alex Wong.
  • Reaction Toolkit
  • Reaction SMILES
  • Reaction SMARTS
  • SMIRKS
    		•  1997 4.51 Store and search reactions using Reaction SMILES and Reaction SMARTS. Define and effect transformations using SMIRKS, facilitating virtual chemistry, virtual libraries. Guided by collaboration with Bernd Rohde.
  • 64-bit port*
    		•  1998 4.61 *SGI toolkits, merlinserver only
  • JavaGRINS
    		• 1998 4.61 Java applet, graphical molecular editor for SMILES. Later enhanced to write SMARTS.
  • DayCart
    		• 2000 4.71 The Daylight Chemistry Cartridge for Oracle. Endows Oracle with Daylight capabilities including: sub/super-structure search, similarity search, canonical smiles, extensible program object interface. Multiple collaborators.
  • Linux port
    		• 2000 4.71 RedHat supported, but others work too
  • 34-bit Thor
    		• 2000 4.71 16GB data file limit, increased from 2GB
  • ????
    		• 2002- 4.81, 4.82, 4.91... Stay tuned!

    Some other introductions to Daylight:

    MUG'02 -- 26 Feb - 01 Mar 2002 -- Santa Fe, NM
    Daylight Chemical Information Systems Inc.
    info@daylight.com