Integrated Compound Management

indexadjustmentInternet and Web Development

Nov 13, 2013 (3 years and 7 months ago)

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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