INTRODUCTION TO DAYLIGHT

A 3 day course

• Class schedule
• Files for course
• Orientation and disclaimers
• Documentation/reference list
• SUMnet - our network environment
• System Administration Information (DHCP)

I. Daylight Basics - day one

1. SMILES

2. SMARTS

3. SMIRKS (Reaction Transforms)

4. Thor Data Trees (TDTs)

5. Fingerprints

1. Database Applications (Thor, Merlin, thorfilters, etc.)

2. Other Applications (PCModels, Clustering Package, Rubicon, etc.)

3. Web Applications

• Documentation/reference list

II. Daylight Administration - day two

  A. Installation

  B. Clients & Servers

  C. Security

  D. Customization

  E. Databases

DayCart: Jack Delany

Special Topic: State of Cheminformatics

III. Daylight Toolkits - day three

  A. Overall Capabilities

  B. The Toolkit view

  C. Programming languages

  D. Programming tools and environments

  E. The functions

  F. Contrib examples

  G. Web development

  H. Examples

  Special Topics:

1. 3rd Party GUI's and Other Applications - Ragu Bharadwaj

2. Daylight and Discovery - John Bradshaw - Download PPT file

Lab Activities - Intro to Daylight

I. Daylight Basics - Languages and Applications

1. SMILES Practice- Compose SMILES, Isomeric SMILES, and Reaction SMILES from depictions, self test w/ smipractice.cgi.
2. SMARTS Practice - Compose SMARTS for described chemical target substructures / functional groups. Recursive and disconnected SMARTS. Self test using depictmatch.cgi.
3. TDT Retrieval and editing with xvthor - running xvthor and experimenting with its various features.
4. Structural, Non-Structural, and Reaction Searching - exploratory data analysis techniques with Merlin including Reaction SMILES and SMARTS
5. Thorfilters/Sthorman - thorlookup, thorlist, etc. also generating poscript with prado from printpackage
6. PCModels/PCFilters - running xvpcmodels, clogp and cmr in various modes.
7. Cluster Package - generating a clustered dataset, jarpat, listclusters, showclusters, etc.
8. Rubicon - generating 3D coordinates for a TDT file
9. DayCGI and MCL - using the web applications, JavaGrins, and the daycgi Wizard program to generate an MCL script.

II. Daylight Administration

1. Software Installation - automated script or manual process
2. Database Installation - add and verify data
3. Customization of Installation - via environment variables, dy_profile.opt, dy_sysprofile.opt and command line
4. Security of Servers - secure server access via passwords using sthorman
5. Security and Customization of Databases - auxilliary databases, passwords, file paths, read-only, caching
6. Server Starting and Stopping - manually, automatically, and at boot
7. Database Design - specifying a new datatype
8. Database Creation - using sthorman and thormake
9. Database Building - automating with scripts
10. Database Loading - with sthorman and thorload
11. Provide Data for Searching - create a Merlin Pool with merlinload, sthorman
12. Search Configuration - selecting datafields for loading a Merlin Pool
13. Web Tools Cconfiguration - dcgi_env.sh, httpd aliases and script aliases
14. DayCart - using SQL*Plus to explore the Daylight/Oracle chemistry cartridge

III. Daylight Toolkits

1. Compiling and modifying cansmi.c - Creating a development environment, compiling and linking with a makefile, modifying cansmi.c to count atoms and bonds in the molecule.
2. Compiling the contrib code - adding a new program to a makefile
3. Reaction toolkit basics - adding reactions to cansmi.c
4. Exploring reaction functionality - with various contrib programs.
5. Transforms - Using and understanding transforms with react.cgi; using and understanding transforms with react.c and enumerate.c
6. Creating a CGI - in /daycgi/, to run one Daylight application
7. Compiling, running, analyzing, and modifying some example code - recommended contrib programs for experimentation
8. PROJECTS - selected projects of interest to students