|An Introduction to Daylight|
Abstract: General and fundamental aspects of Daylight as a chemical information company are presented. The company mission and goals are formalized. The foundation of technological achievements is presented in some detail, and require only basic knowledge of chemistry. A line of products, including a programming interface, applications, and databases are exhibited. The scope, advantages, and disadvantages of Daylight are revealed.
The Big Picture
What is Daylight?
Daylight Chemical Information Systems, Inc. (Daylight CIS) is a software company with a mission to provide high performance chemical information processing tools.
Daylight's goal is to provide the best known computer algorithms for chemical information processing to those who need them; to provide chemical information systems capable of handling all of the chemical information in the world. We provide these algorithms in two ways: as a programmer's library, known as the Daylight ToolkitTM, and as ready-to-use programs built on the Daylight Toolkit.
Who are the people behind Daylight?
Daylight was cofounded by Yosi Taitz (CEO) and Dave Weininger (President) and incorporated in 1987.
Yosi directs the Corporate Office in Mission Viejo, CA.
Dave and Jack Delany (CTO) lead the Research & Development Office in Santa Fe, NM.
John Bradshaw heads European Operations in Cambridge, UK.
How does Daylight shine?
Daylight utilizes state of the art computing technology in several areas to provide high performance and forward mobility in a rapidly changing computing world. Daylight users solve many problems in chemistry, including predicting properties of a molecule, maintaining and searching databases of chemical properties, and deducing structure from chemical properties. Furthermore, everyone benefits from contributed applications, which are free, donated programs built on the Daylight Toolkit.
Points of Interest
How did Daylight start?
Dave invented the Simplified Molecular Input Line Entry System (SMILES). SMILES is a simple yet comprehensive chemical nomenclature. At that time, Yosi consulted for National Semiconductor and was involved in stacked memory board design. The compactness of SMILES and the high capacity memory boards where joind when Dave approached Yosi with the idea to store all of chemistry in RAM.
Daylight was born.
Whoa! SMILES is a Daylight invention?
Sort of. Development of SMILES was initiated by Dave, at the Environmental Research Laboratory, U.S.E.P.A., Duluth, MN; the design was completed at Pomona College in Claremont, CA. It was embodied in the Daylight Toolkit with the assistance of Cedar River Software. SMILES as a molecular representation has steadily gained acceptance, popularity, and become an industry standard. A related language, SMARTS, was developed for the purpose of describing patterns (as a subgraph) in a molecule (as a graph).
Table 1: Daylight Languages Language Purpose Descriptive Features SMILES 1, 2, 3, 4 representation of molecules atoms, bonds, branches, rings, fragments, isotopes, double bond orientation, tetrahedral chirality, general chirality, aromaticity, tautomers SMARTS search for molecules atoms, bonds, logical operators, recursion
What about advanced chemical nomenclature?
Daylight nomenclature has expanded to include substructure searching, reaction processing, and combinatorial chemistry.
Table 2: Daylight Advanced Languages Language Purpose Descriptive Features Reaction SMILES 5, 6 representation of reactions reactants, agents, and products Reaction SMARTS 5, 6 search for reactions reactants, agents, and products SMIRKS description of reaction transforms reactants, agents, and products CHUCKLES, CHORTLES, & CHARTS 7, 8 representation of monomers, mixtures, and searching for them monomers, mixtures, and searching
Anything else I should know about?
In additional to Daylight nomenclature, some terms are Daylight savvy.
Table 3: Daylight Terminology Term Definition Example Use THOR 9 THesaurus-Oriented Retreival chemical database system retrieve a compound data by identifier TDT THOR Data Tree data structure for chemical database system MERLIN 9 high-speed exploratory data analysis discover structurally similar compounds MCL MERLIN Control Language automate search Fingerprint concise structural descriptor accelerate search and enable clustering Contrib repository of Daylight open-source freeware solve problem by writing less code DayCart integration of Daylight into Oracle database server environment extend Oracle clients and servers with new chemistry capabilities Contrib repository of Daylight open-source freeware solve problem by writing less code CEX Chemical EXchange mechanism for interprocess communication transfer information independent of machine, architecture and language
Programming, Applications, and Databases
I'm a programmer and develop applications. How can I leverage your technology?
The Daylight Toolkit offers a robust Application Program Interface (API) in the form of programmer libraries. The objects and entry points are well-defined and widely used. Wrappers are available in C, FORTRAN, PERL, and other languages.
I'm not a programmer. What applications do you provide?
Daylight provides applications for various tasks, including data retrieval, substructure search, properties calculation, Postscript printing, molecular editing, and web browsing.
What about contributed software?
Contributed software, also known as Contrib, are developed by Daylight users to solve problems. Perhaps the problem is easy, and sharing the application will simply save someone programming time. Perhaps the problem is difficult, and sharing the program with others will make application better. Some examples of Daylight Contrib include generation of stereochemical SMILES, characterization of the commonalities among groups of structures, evolution of virtual libraries, and a PERL wrapper.
Can I use my data with the Daylight system?
Absolutely. If you want to use Daylight products with your data, we have the tools to make your custom THOR database. Also, there are Contrib databases, such as the biological compounds with screening data from the National Cancer Institute.
Platforms and Partners
What platforms do you support?
SUN Solaris 2.5, 2.6, & 2.7 SGI Irix 6.4 & 6.5 Red Hat Linux 6.1 & 6.2 (x86)
Hey! What about Macintosh and MS-Windows?
We offer the Remote ToolkitTM for programming from Macintosh and 16- and 32-bit MS-Windows systems. The Remote Toolkit requires connection to a server on one of the supported platforms. Of course, our web-based interfaces are accessible from Macintosh and MS-Windows via a browser.
Can I integrate the Daylight system with Oracle?
Yes. In cooperation with Oracle, Daylight has created DayCartTM, the Daylight Chemistry Cartridge. Oracle users should feel right at home.
Who is partnered with Daylight?
Daylight has partnered with many other companies to integrate products and improve their overall usefulness for users. Moreover, Daylight's toolkit-based architecture facilitates software integration, and many collaborations occur with users.
Products and Databases
Where do I go for more information?
The Daylight website at http://www.daylight.com is a rich source of information and covers the product line. Email email@example.com for business and firstname.lastname@example.org for technical inquiries.
What is SMILES?
A: a simple yet comprehensive chemial nomenclature
C: Benny Hill trademark
What is Reaction SMILES?
A: SMILES extentions for reactions
B: Oc1ccccc1.CC(=O)O > SOCl2 > CC(=O)Oc1ccccc1
C: Benny Hill grin with raised eyebrows
What is SMARTS?
A: a SMILES-related language for describing patterns in a molecule
C: stockpiling petro before the strike
What is Reaction SMARTS?
A: SMARTS extentions for reactions
B: Oc1cc[$(c),$(n)]cc1.CC(=O)O > SOCl2 > CC(=O)Oc1cc[$(c);$(n)]cc1
C: stockpiling petro during the strike
What is SMIRKS?
A: a SMILES-related language for describing reaction transforms
B: [O:1][c:2]1[c:3][c:4][$([c:5]);$([n:5])][c:6][c:7]1.[C:8][C:9](=[O:10])[O:11] > [S:12][O:13][Cl:14]2 > [C8:][C:9](=[O:10])[O:1][c:2]1[c:3][c:4][$([c:5]);$([n:5])][c:6][c:7]1
C: expression your friend makes when you drink his beer
What is CHUCKLES?
A: a language for representation of monomers
C: Dave's response to "Do you adore Microsoft?"
What is CHORTLES?
A: a language for representation of mixutes
C: Yosi's response to "Is DayCart free?"
What is CHARTS?
A: a language for searching monomers and mixtures
C: black market medical records
What is THOR?
A: THesaurus-Oriented Retreival chemical database system
B: constant time lookup, independant of database size
C: Turkey & Ham On Rye
What is a TDT?
A: THOR Data Tree
C: Terrible Driving Tourist
What is MERLIN?
A: a program for high-speed exploratory data analysis
B: really fast, even on huge data sets
C: a program for high-speed peeling tires, made by Firestone
What is MCL?
A: MERLIN Control Language
B: Create column of datatype P function AVERAGE named "Mean(LogP(o/w))".
C: Monty Python's John CLease
What is a Fingerprint?
A: a concise structural descriptor
C: evidence found on keyboard
What is DayCart?
A: tools for integration of Daylight into Oracle database server environment
B: select * from rxn where reactant(smiles, 'Oc1ccccc1') = 1;
C: daytime food stand
What is Contrib?
A: repository of Daylight open-source freeware
B: Chiralify, Stigmata, GoForth, DayPerl, and much more.
C: helping out with the groceries
What is CEX?
A: Chemical EXchange mechanism for interprocess communication
B: sob = cx_create_string(NULL, "Hello world!");
C: reason to get married
What is the scope of Daylight products?
Daylight's scope is the representation of all chemistry. All of Daylight's chemical algorithms expand up to the total size of chemistry. If we had only 10 molecules in the world, we'd simply look at all of them in order find the one you want. Since there are millions of molecules and growing, we've approached chemical information with algorithms that scale extremely well.
What are the advantages of Daylight products?
The canonicalization of SMILES allows identifiers to be retrieved in constant time, independent of database size. SMILES is a semantically well-defined language and parses accurately and efficiently. The Object Oriented Programming-ish (OOP-ish) interface of the Daylight Toolkit is independent of the application, word size, and system architecture, exhibiting perseverance for over 10 years, and is expected to continue to thrive without change for many years to come. The Daylight Toolkit provides a chemical-information infrastructure allowing programmers to get directly to their unique chemical problems and achieve project completeness without reinventing the wheel. Companies can express their corporate advantage using the Daylight Toolkit. Daylight's client-server database system provides network database access, evolving beyond the mainframe model.
What are the disadvantages of Daylight products?
At this time, Daylight doesn't provide specialized applications.
In a nutshell, what's the bottom line?
We're tool makers. We provide hammer and nails, you're the builder the mansion.