| Q: | What is Daylight software used for? | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| A: | Chemical information processing. Storage, retrieval, and display of chemical structures and other data and manipulation of that data in a network environment. Formulation and implementation of "chemical intelligence". High performance searching even for large databases. Our mission: to provide high performance chemical information processing tools to those who need them; to provide chemical information systems capable of handling all of the chemical information in the world. (Examples: minoxidil in medchem00, Beta-Aspartate-Hydroxamate in wdi004.) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Q: | How is Daylight software better or different than other competing software? | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| A: | A toolkit-based approach (since ~1990) facilitating cross-platform multi-vendor interoperabiltiy over local and large networks. Rigorous and public chemical information languages and algorithms facilitating the open communication of chemical information and knowledge. Foremost and primary among these languages is SMILES, a simple, comprehensive, unique-ifyable nomenclature for chemistry, invented by Dave Weininger. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Q: | Huh? You mean SMILES is a Daylight invention? You've got to be kidding me. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| A: | You bet your aspartame-analogs. And SMILES has steadily gained acceptance and popularity and become an industry standard. Other Daylight languages include SMARTS, for flexible substructure pattern matching, Thor DataTrees (TDTs) for data, and Reaction SMILES. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Q: | What do you mean by "toolkit-based" exactly? | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| A: | The Daylight Toolkits are programming libraries of functions comprising a well defined and supported API -- application programming interface -- suitable for commercial software developers and code-happy rapid-prototyping computational chemists alike. The full power and functionality of Daylight software is made available at the toolkit interface. In some respects, many of the Daylight applications are simply examples of Daylight Toolkit programs. In addition, many Daylight applications can be employed as tools, and integrated with other software to create custom solutions. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Q: | So... is this an expert system? A neural network? A genetic algorithm? | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| A: | No, but these things could be written using the toolkits. Daylight provides a "chemical information processing infrastructure" with many basic and advanced features built-in, but is infinitely customizable to accomodate the needs of users. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Q: | I don't really want to do any programming, and why should I? You are the software company. What can your application software do out of the box? | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| A: |
Well, here's an example, a scenario. Let's say you have a file of 500,000
compounds with associated data. You can convert them to Daylight TDTs,
create a Daylight database. In so doing you find that there are 30,000
duplicate structures; these will be merged automatically thanks to the
uniquification of SMILES. 40,000 are stereoisomers; these will be
merged also, with the stereoisomeric SMILES retained along with their
respective associated data. A handful of corporate IDs are
discovered to be ambiguous. You can also:
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| Q: | Impressive. I'm almost convinced. Say, does it run on a PC? | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| A: |
Yes, if the PC is running Linux.| Q: |
Does it run on a PC running Windows?
| A: |
Short answer: No. | Longer answer: No, but insofar as PC's run browsers, you can run it "from a PC". Also, there is a Remote Toolkit for toolkit programming on Windows (or MacOS). Note also a MacOS-X port is in development. Q: |
So what platforms does Daylight run on? What hardware do I need?
| A: |
| The Merlinserver requires enough physical RAM to store all searchable data "pools". For a typical 500,00 structure database, perhaps 200MB of additional RAM. Multiple CPUs will improve search speed. Q: |
Does Daylight sell databases too?
| A: |
Yes, Daylight publishes and distributes databases authored and
maintained by other organizations. We convert these datasets to
Daylight format, often adding data such as clustering data and 3D
coordinates. There is a growing list:
Medchem
(BioByte/Pomona),
World Drug
Index (Derwent),
Spresi and
SpresiReact (InfoChem),
ACD
(MDLIS), the
Maybridge catalog,
AsInEx catalog,
InterBioScreen catalog,
and others. For more info see our
website.
| Q: |
Let's see how you'll answer this one: What is Daylight's greatest weakness?
| A: |
Daylight has focused on its toolkits, not its user interfaces.
Early on, the need to learn SMILES was an activation energy barrier
which discouraged many potential users. Still, in many ways, we expect
more effort and savvy from the user, but we believe the effort is
justified and well rewarded.
| Q: |
My company uses Oracle to store biological data. Can I integrate a
Daylight system with Oracle?
| A: |
Yes. DayCart (TM), released with Daylight 4.71 (Sept.'00), is the
Daylight-chemistry-cartridge for Oracle. Stay tuned for more info
later in this meeting.
| Q: |
Who else has Daylight partnered with?
| A: |
Over the years, Daylight has partnered with several other
companies such as ModGraph, Informix, CAS, MSI, Netgenics,
and Synopsys, to integrate products and improve their
overall usefulness for users. See our partners page for the current list.
Moreover, as described, Daylight's toolkit-based
architecture facilitates software integration, and can be
done by anyone.
| Q: |
Can Daylight handle reactions?
| A: |
Yes. The Reaction Toolkit was introduced in 1996, and the Reaction
SMILES language was introduced to describe reactions consisting of
reactants, agents and products. Reactions are fully integrated into
the Daylight system, and reactions can be searched powerfully and
flexibly. Reaction transforms, encoded as SMIRKS, allow the toolkit to
implement "virtual chemistry", enabling a wide range of programmatic
possibilities, from virtual combinatorial libraries to reaction
expert systems. (References: 1.
Daylight Theory Manual, 2.,
Reaction Talk, MUG '97 [J. Delany]).
| Q: |
How about the Monomer Toolkit -- what does that do?
| A: |
The Monomer Toolkit was introduced in 1993 to support combinatorial
chemistry, with languages Chuckles, Chortles and Charts. Monomers are
user-configureable molecular building blocks. Combinatorial mixtures
can be specified for oligomeric or scaffold-based libraries and stored
in a database. Enumeration is thus avoided and speed and
efficiency enhanced. Monomer Toolkit capability is built into the
database servers and clients, however, no user-friendly library
building application currently exists.
(References: 1.
Daylight Theory Manual), 2.
White Paper on Daylight Combinatorics, C. James, 1996.)
| Q: |
So what's new at Daylight these days?
| A: |
Stay tuned!
| Q: |
Who is the
Daylight Krewe?
| A: |
|
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| Term | Description | Note |
|---|---|---|
| SMILES | molecule language | also see the SMILES Home Page |
| SMARTS | substructure search language | also see the SMARTS related FAQ pages |
| Reaction SMILES | reaction language | |
| Reaction SMARTS | reaction search language | |
| SMIRKS | reaction transform language | |
| THOR | chemical DBMS | THesaurus Oriented Retrieval, works in conjunction with Merlin |
| Merlin | chemical DBMS | works in conjunction with Thor |
| TDT | Thor Data Tree | usually smiles-rooted, with ambiguous and overlapping identifiers |
| MCL | Merlin Control Language | serial Merlin client |
| Chuckles,Chortles,CHARTS | combinatorial languages for molecules, mixtures and searches | Monomer Toolkit |
| Fingerprint | 2D molecular bitmap | used for similarity and clustering |
| DayCart | Daylight/Oracle Chemistry Cartridge | alternative to Thor/Merlin |
| Contrib | free source code | mostly toolkit programs, many very useful |
| CEX | Chemical EXchange | chemical information exchange protocol, open-source |
| Graffeo | Our favorite coffee | Beverly Hills and San Francisco |
Daylight Chemical Information Systems Inc.