Transcript Building an Electronic Research Habitat at ETC Peter Condron 2008 ChemAxon European UGM PUBLIC Who ? • The Experimental Therapeutics Centre (ETC) was founded in 2007 with.

Building an Electronic
Research Habitat at
ETC
Peter Condron
2008 ChemAxon European UGM
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Who ?
• The Experimental Therapeutics Centre (ETC)
was founded in 2007 with the mission to
– engage in early stage drug discovery and
development
– develop innovative research tools for clinical analysis
– set-up public-private partnerships to facilitate the
advancement of drug candidates.
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Singapore
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GSK
Health Sciences
Authority (HSA)
Institute of Bioengineering
& Nanotechnology
Experimental
Therapeutics Centre
Novartis (NITD)
Bioinformatics
Institute
Institute of Molecular
and Cell Biology
Bioprocessing
Technology Institute
Genome Institute
of Singapore
Schering Plough
Translational
Research
Eli Lilly
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Structure and Capabilities of ETC
Reagent development and production
Core
Technologies
- Protein production
- mAb production
Assay development and validation
HTS (siRNA, phenotypic)
Project
Management
Output
Target Validation
with collaborative partners
Validated targets, new exciting technologies,
novel therapeutics, quality reagents & diagnostics
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Building an Electronic Research
Habitat at ETC
• Integrated Informatics Environment
• A set of inter-related IT platforms that allows
data to be:
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Accessed
Queried
Integrated
Visualized
• Independently of equipment, data type, source,
originator, format and with a minimal of effort
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High Level View
Electronic
Lab
Notebook
Chemistry
Library
Results
Manager
Chemistry
Inventory
HTS
Manager
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Slightly More Informative View
eNovator eLN
Electronic
Lab
Notebook
Chemistry
Library
Results
Manager
jChem
Chemistry
Inventory
HTS
Manager
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Bespoke
in-house
Developed
Applications
Insanely Detailed View
A*STAR
ETC Scientific
Workflows
Other Academic
Institutions
Research
Institutions
Assay Protocol Definition
Companies
Draw Compound / Enter
Metadata / Specify Library
Rejected
Feedback
Definition of Assay
Results
Definition of Assay
Conditions
Check if all data is
provided
Result
Publication
Initial Review
HT
Submit for Approval
Legal /IP / SAB
Review
Rejected
Commencement
Feedback
Create Individual Plates
inheriting Layout
Check if structure is drawn
correctly
Email
Approver
Submit for Approval
Specify Lists / Library for
Assignation to Plates
Email
Approver
Review by Snr Investigator
Approved
Review by Data Steward
Email
User
Approved
Automated Data Type QC
Review by Snr Investigator
Approved
Rejected
Rejected
Upload experimental data
Review by Data Steward
Approved
Enter Experimental
Metadata
Specify Plate
mapping logic
Manually specify
well level data
Check for Similar Structures
Chemical Property Calculator
Registration of Assay
Researcher
Presentation
Select Assay / Protocol to
upload data into
Define Plate Layouts for
Assay
LT
Project Proposal
Data Upload & QC
Experimental Design
Compound / Library Registration
Assay Registration
ETC Scientific Project Initiation
Rejected
Rejected
Email
User
Email
User
Rejected
Email
User
Publication
Lock Plate Design
ChemLib
Plate Manager
Results
eLN
Supporting Services
Core Services
jChem System
PlateMan
ChemLib
Search Engine
jChem
Core
Cache
jChem
Streams
Cache
eLN Server
.net Application Server
Results
Upload
Manager
Integrated Knowledge
Applications
Business Data and
Process Integration
eLN
Tasklists
Library
Registration
Data
Steward
Plate
Actions
Registration
Workflow
Manager
Admin
Module
Well
Template
Workflow
Manager
Data
Steward
Program
Management
Workflows
Registration
Search
Engine
Admin
Module
Search
Engine
Admin
Module
Resource
Management
Email
Integration
Gb LAN
Fiber
Backbone
Exchange /
SMTP
LDAP / AD
DEV / TST Environment
TST .net
App Server
DEV .net
App Server
TST .net
jChem
Server
DEV .net
jChem
Server
TST
SVN
Server
DEV
Storage Area Network
Structured Data Sources
ChemLib
PlateManager
Results
Streams
Adapter
Chemistry
Indexes
Barcode
Server
Plate
Registry
Assay
Registry
jChem
Cartridge
Execution
Engine
Plate
Remapper
Plate
Formats
Data
Mining
Upload
Manager
eLN
Data
Visualization
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Livelink / eLN
ETC
N Tb SAN
ACRC
N Tb SAN
Backup / Archiving / DR
Document
Management
Knowledge
Management
eLN Archiving
Repository
ACRC
Tape Backup
Enterprise
Content
Workflow/
Forms
eLN DR
Server
DR
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Why jChem Cartridge?
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Ability to handle ~10 Million Compounds
Easy to Register / Search
Easy to Integrate with other Systems
Easy to Customize
Building on existing skills (Oracle)
Rapid Implementation
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Approach
Portfolio Management
• Iterative
methodology
• Time-box
development
• Phase – Gate
Process control
mechanism
Project Execution
Prioritization
Identification
Survey of actual /
potential projects w/
6 month sliding
advance window
Monthly
Prioritization of
projects based on
Business needs ,
technical
requirements and
capabilities
Project Initiation
Creation of code and user
documentation. Updating of
design documents.
Integrated into all tasks.
Project Planning
PF Artifact
Candidate projects
with stakeholders,
business case, high
level scope, risks
and resources
Development
Documentation
Project Charter.
Definition of release,
iteration, and overall
project timeline.
Resource allocation
Gate 1
Gathering of
detailed users
stories to
describe
functionality
required.
Internal Testing
Review
Internal Unit and
integration
testing of codebase
Review of
delivered
functionality by
business lead and
key stakeholders
Database Design
Design Spike to
define initial data
model for
application
Testing
Review of code
base by
development team
to ensure fitness
for purpose
Project Artifact
Documentation of
planning documents
such as Charter /
WBS / Gantt Chart /
User Stories and
Technical Tasks
Requirements
Peer Code Review
Usability
Unscripted /
Open usability
testing of
application by
users w/ dev
team
Scripted Test
Testing using
predefined UAT
scripts covering
all implemented
user stories
< 1 Day
Gate 2
Architecture
1 Month
Coding
Design Spike to
define
application
architecture and
compatibility with
existing systems
Design Artifact
Documentation of
system architecture,
system design,
database design
Creation of
application code
implementing
technical tasks
Testing Artifact
Test Review
Bug Fixing
Identify, prioritize
and fix all problems
before starting
development on
new functionality.
Prototyping
Creation of a simple
prototype based on
initial user stories to
drive requirements /
identify technical issues
Summary of all test
results – Issues /
Enhancements
from both scripted
and unscripted
testing
Review of all test
results by
development and
user teams
Prototype
Gate 3
Deployment Planning
Agreement of
deployment details and
procedures for
deployment and
transition to support
Prototype to
demonstrate
aspects of UI /
BL / Data Model
Prototyping
Deployment Plan
Document outlining
deployment timelines
and methodology for
handover from DEV
team to deployment
team
Deployment &
Testing
Execution of
deployment plan
and testing of
deployed
application
Training
Deployment
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Instructor led
group training
sessions and 1:1
follow up
sessions.
Gate 4
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Results
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Results
• Complete enterprise Chemical Registry
System
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Centralized Oracle Database to store all compound information Completed
ETC registry number system for all compounds (The ETC number) Completed
Ability to add newly synthesized compounds to the database Completed
New compound QC: Duplicates, Similarity matches, Chemical properties
Completed
Review and Approval workflow for new compounds Completed
Bulk / Library upload request and approval mechanism Completed
eLN link for synthesis protocols, project information Completed
Substructure, Superstructure, Similarity Searches Completed
Chemical property / Metadata Searches Completed
Marvin View / Sketch Integration Completed
Chemical Calculator Integration Completed
User / Group Management
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Results
• Designed / Developed / Tested / Deployed
to Production in 1.5 Months with 1.5 FTE !!
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Thoughts so far
• Really well thought out / efficient core
functionality
• Cartridge allows access to majority of
functionality
• Simple to integrate with .net
• Rapidly deployable
• Jchem Manager application a bit clunky
• .net documentation / examples a bit lacking
• License files for calculators a bit problematic
• Knowledgeable / Responsive Support (Thanks)
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Next
• Looking forward to creating v2.0
(Sometime Q4 this year)
– Migrate to version 5.0
– Improved UI
– Improved integration model (Services)
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[email protected]
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www.etc.a-star.edu.sg