Integrated Compound Management

Integrated Compound Management
using Daylight
TM
, Java
TM

and Oracle
®


The GNF Compound Management System Project

Elena Rodriguez, GNF

Steven Wilkens, GNF

Chris Palmer, MVLLC

Jack Crawford, MVLLC

Elena Rodriguez, Steven Wilkens,
Chris Palmer & Jack Crawford

MUG ’02 Conference • Santa Fe, NM

2

Initial GNF Compound
Management Challenges


No compound
registry

–
File
-
based

–
No searching
capability


No automated
plate tracking

–
Error prone

–
Manual entry


No project
management

–
Lack of tracking and
scheduling


Problems with
scalability

–
Reliability of
underlying systems

–
Manual process
bottlenecks


Elena Rodriguez, Steven Wilkens,
Chris Palmer & Jack Crawford

MUG ’02 Conference • Santa Fe, NM

3

Imminent Challenges


Growth of
compound collection



Increased
screening throughput



Migration from
384 to 1536

storage format



Establishment of GNF
Lead Discovery effort



Spin
-
off company

support

Elena Rodriguez, Steven Wilkens,
Chris Palmer & Jack Crawford

MUG ’02 Conference • Santa Fe, NM

4

Desired Objectives


Capture and maintain compound collection
in secure, scalable, electronic format


Design and implement web
-
based
information management tools in order to:

–
Make intelligent business decisions based on
current collection status

–
Make intelligent scientific decisions based on

cheminformatics data

Elena Rodriguez, Steven Wilkens,
Chris Palmer & Jack Crawford

MUG ’02 Conference • Santa Fe, NM

5

Goal: The GNF
I
nformation
M
anagement
C
enter


GRS
: GNF Registration System

–
Secure, scalable, searchable corporate registry


PRS
: Plate Reformatting System

–
Transactional data capture for core facility process


CLS
: Container Locator System

–
Enterprise
-
wide container management


CRS
: Compound Request System

–
Operational component of lead follow
-
up process

Elena Rodriguez, Steven Wilkens,
Chris Palmer & Jack Crawford

MUG ’02 Conference • Santa Fe, NM

6

GNF Compound Flow

96DW Plates

PRS

SD File Load

GRS

Structure
Searching and
Library Querying

Synthesis Design

ChemDraw

Precursor Selection

Reagent Selector

Synthesis

IRORI SynthMan

Virtual Library
Construction

Afferent

High Density
Storage

CLS

High Throughput
Screening

Follow
-
up
Requests

CRS

Elena Rodriguez, Steven Wilkens,
Chris Palmer & Jack Crawford

MUG ’02 Conference • Santa Fe, NM

7

G
NF
R
egistration
S
ystem


Built on DayCart!


Batch load of SD files, library based


One
-
off registration


Structure searching


Compound library comparison


Foundation for compound follow
-
up


Elena Rodriguez, Steven Wilkens,
Chris Palmer & Jack Crawford

MUG ’02 Conference • Santa Fe, NM

8

Elena Rodriguez, Steven Wilkens,
Chris Palmer & Jack Crawford

MUG ’02 Conference • Santa Fe, NM

9

Elena Rodriguez, Steven Wilkens,
Chris Palmer & Jack Crawford

MUG ’02 Conference • Santa Fe, NM

10

Elena Rodriguez, Steven Wilkens,
Chris Palmer & Jack Crawford

MUG ’02 Conference • Santa Fe, NM

11

Elena Rodriguez, Steven Wilkens,
Chris Palmer & Jack Crawford

MUG ’02 Conference • Santa Fe, NM

12

Elena Rodriguez, Steven Wilkens,
Chris Palmer & Jack Crawford

MUG ’02 Conference • Santa Fe, NM

13

Elena Rodriguez, Steven Wilkens,
Chris Palmer & Jack Crawford

MUG ’02 Conference • Santa Fe, NM

14

Elena Rodriguez, Steven Wilkens,
Chris Palmer & Jack Crawford

MUG ’02 Conference • Santa Fe, NM

15

GNF Plating Operation

Elena Rodriguez, Steven Wilkens,
Chris Palmer & Jack Crawford

MUG ’02 Conference • Santa Fe, NM

16

P
late
R
eformatting
S
ystem

Elena Rodriguez, Steven Wilkens,
Chris Palmer & Jack Crawford

MUG ’02 Conference • Santa Fe, NM

17

Elena Rodriguez, Steven Wilkens,
Chris Palmer & Jack Crawford

MUG ’02 Conference • Santa Fe, NM

18

Elena Rodriguez, Steven Wilkens,
Chris Palmer & Jack Crawford

MUG ’02 Conference • Santa Fe, NM

19

C
ontainer
L
ocator
S
ystem

Elena Rodriguez, Steven Wilkens,
Chris Palmer & Jack Crawford

MUG ’02 Conference • Santa Fe, NM

20

C
ompound
R
equest
S
ystem


On
-
line ordering of
follow
-
up material


Linked to GRS and
PRS data

Elena Rodriguez, Steven Wilkens,
Chris Palmer & Jack Crawford

MUG ’02 Conference • Santa Fe, NM

21

Development Team


Genomics Institute of the
Novartis Research
Foundation (GNF)

–
Steven Wilkens

–
Elena Rodriguez

–
Kristina Burow

–
Jeff Janes

–
Kaisheng Chen

–
Jared Ek

–
Paul Calvin

–
Christina Guintu

–
Dennis Theodoropoulos



Managed Ventures LLC

–
Jack Crawford

–
Chris Palmer

–
Robert Bamford

–
Chris Novak

–
Brad Ziola

–
Kim Collins

–
Ben Chang


Special thanks to:

–
Jack Delany, Daylight

–
Michael Tennant, Syrrx

–
Alberto Gobbi, Anadys

–
Bernd Rhode, Novartis


Elena Rodriguez, Steven Wilkens,
Chris Palmer & Jack Crawford

MUG ’02 Conference • Santa Fe, NM

22

Technology Stack

JVM

JInfoNe
t

Marvin

ChemDraw

jChem jKlustor

Java Servlets

Web Services

Daylight Toolkit

Apache Tomcat


Solaris • Linux

Oracle8i & 9i • DayCart Cartridge

Elena Rodriguez, Steven Wilkens,
Chris Palmer & Jack Crawford

MUG ’02 Conference • Santa Fe, NM

23

Demonstration


Chris Palmer

Managed Ventures LLC