PUBLIC 1 2008 ChemAxon European UGM Building an Electronic Research Habitat at ETC Peter Condron
PUBLIC1 2008 ChemAxon European UGM Building an Electronic Research Habitat at ETC Peter Condron.
Mar 26, 2015
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2008 ChemAxon European UGM
Building an Electronic Research Habitat at
ETC
Peter Condron
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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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Institute of Bioengineering & Nanotechnology
Bioprocessing Technology Institute
Bioinformatics Institute
Institute of Molecular and Cell Biology
Genome Institute of Singapore
GSK
Health Sciences Authority (HSA)
Experimental Therapeutics Centre
Novartis (NITD)
Schering Plough Translational
Research
Eli Lilly
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Structure and Capabilities of ETC
Target Validationwith collaborative partners
Assay development and validation
Reagent development and production- Protein production
- mAb productionCore
Technologies
Project Management
HTS (siRNA, phenotypic)
Validated targets, new exciting technologies, novel therapeutics, quality reagents & diagnostics
Output
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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:– 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
Chemistry Library
Chemistry Inventory
HTS Manager
Results Manager
Electronic Lab
Notebook
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Slightly More Informative View
Chemistry Library
Chemistry Inventory
HTS Manager
Results Manager
Electronic Lab
Notebook
eNovator eLN
Bespokein-house
Developed Applications
jChem
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Insanely Detailed ViewETC Scientific Workflows
eLN
PlateManager
BarcodeServer
Plate Registry
Plate Formats
Plate Remapper
ChemLib
StreamsAdapter
jChemCartridge
ChemistryIndexes
ExecutionEngine
Livelink / eLNResults
AssayRegistry
DataVisualization
UploadManager
DataMining
jChemStreams
Search Engine
Cache
Cache
jChemCore
jChem System .net Application Server
WorkflowManager
WellTemplate
Registration
ChemLib PlateMan Results
PlateActions
AdminModule
AdminModule
DataSteward
UploadManager
WorkflowManager
SearchEngine
AdminModule
DataSteward
eLN Server
Structured Data Sources
Result Publication
Assay Registration
Assay Protocol Definition
Definition of AssayResults
Registration of Assay
Definition of AssayConditions
Submit for Approval Email Approver
Review by Data Steward
Approved RejectedEmail User
Result Publication
Assay Registration
Assay Protocol Definition
Definition of AssayResults
Registration of Assay
Definition of AssayConditions
Submit for Approval Email Approver
Review by Data Steward
Approved RejectedEmail User
Compound / Library Registration
Draw Compound / Enter Metadata / Specify Library
Check if all data is provided
Check for Similar StructuresChemical Property Calculator
Check if structure is drawn correctly
Submit for Approval Email Approver
Review by Data Steward
Approved RejectedEmail User
Compound / Library Registration
Draw Compound / Enter Metadata / Specify Library
Check if all data is provided
Check for Similar StructuresChemical Property Calculator
Check if structure is drawn correctly
Submit for Approval Email Approver
Review by Data Steward
Approved RejectedEmail User
Experimental Design
Define Plate Layouts for Assay
Create Individual Platesinheriting Layout
Specify Plate mapping logic
Specify Lists / Library forAssignation to Plates
Review by Snr Investigator
Approved RejectedEmail User
LT HT
Manually specify well level data
Lock Plate Design
Experimental Design
Define Plate Layouts for Assay
Create Individual Platesinheriting Layout
Specify Plate mapping logic
Specify Lists / Library forAssignation to Plates
Review by Snr Investigator
Approved RejectedEmail User
LT HT
Manually specify well level data
Lock Plate Design
SearchEngineRegistration
LibraryRegistration
ChemLib Supporting Services
Backup / Archiving / DR
Storage Area Network
DEV / TST Environment
Core Services
ETCN Tb SAN
ACRCN Tb SAN
ACRCTape Backup
eLN ArchivingRepository
eLN DRServer
TST .netApp Server
TST
TST .netjChem Server
DEV .netApp Server
DEV .netjChem Server
DEV
SVNServer
Gb LAN FiberBackbone
Exchange /SMTP
LDAP / AD
DR
Plate Manager Results eLN
Data Upload & QC
Select Assay / Protocol toupload data into
Upload experimental data
Review by Snr Investigator
Approved RejectedEmail User
Enter Experimental Metadata
Automated Data Type QC
Rejected
Publication
Business Data and Process Integration
Workflows
Tasklists
EmailIntegration
ProgramManagement
ResourceManagement
Integrated Knowledge Applications
eLN
DocumentManagement
KnowledgeManagement
EnterpriseContent
Workflow/ Forms
ETC Scientific Project Initiation
A*STAROther Academic
InstitutionsResearchInstitutions
Companies
Project Proposal
Initial ReviewRejected
Feedback ResearcherPresentation
Legal /IP / SABReview Rejected
FeedbackCommencement
ETC Scientific Project Initiation
A*STAROther Academic
InstitutionsResearchInstitutions
Companies
Project Proposal
Initial ReviewRejected
Feedback ResearcherPresentationResearcherPresentation
Legal /IP / SABReview Rejected
FeedbackCommencement
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Why jChem Cartridge?
• 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
• Iterative methodology
• Time-box development
• Phase – Gate Process control mechanism
Portfolio Management
Project Initiation
Project Execution
Deployment
Identification
Survey of actual / potential projects w/ 6 month sliding advance window
Identification
Survey of actual / potential projects w/ 6 month sliding advance window
Prioritization
Prioritization of projects based on Business needs , technical requirements and capabilities
Prioritization
Prioritization of projects based on Business needs , technical requirements and capabilities
PF Artifact
Candidate projects with stakeholders, business case, high level scope, risks and resources
PF Artifact
Candidate projects with stakeholders, business case, high level scope, risks and resources
Requirements
Gathering of detailed users stories to describe functionality required.
Requirements
Gathering of detailed users stories to describe functionality required.
Project Planning
Project Charter. Definition of release, iteration, and overall project timeline. Resource allocation
Project Planning
Project Charter. Definition of release, iteration, and overall project timeline. Resource allocation
Project Artifact
Documentation of planning documents such as Charter / WBS / Gantt Chart / User Stories and Technical Tasks
Project Artifact
Documentation of planning documents such as Charter / WBS / Gantt Chart / User Stories and Technical Tasks
Prototyping
Prototyping
Creation of a simple prototype based on initial user stories to drive requirements / identify technical issues
Prototyping
Creation of a simple prototype based on initial user stories to drive requirements / identify technical issues
Prototype
Prototype to demonstrate aspects of UI / BL / Data Model
Prototype
Prototype to demonstrate aspects of UI / BL / Data Model
Development
Testing
Coding
Creation of application code implementing technical tasks
Coding
Creation of application code implementing technical tasks
Internal Testing
Internal Unit and integration testing of code-base
Internal Testing
Internal Unit and integration testing of code-base
Usability
Unscripted / Open usability testing of application by users w/ dev team
Usability
Unscripted / Open usability testing of application by users w/ dev team
Scripted Test
Testing using predefined UAT scripts covering all implemented user stories
Scripted Test
Testing using predefined UAT scripts covering all implemented user stories
Review
Review of delivered functionality by business lead and key stakeholders
Review
Review of delivered functionality by business lead and key stakeholders
Bug Fixing
Identify, prioritize and fix all problems before starting development on new functionality.
Bug Fixing
Identify, prioritize and fix all problems before starting development on new functionality.
Documentation
Creation of code and user documentation. Updating of design documents. Integrated into all tasks.
Documentation
Creation of code and user documentation. Updating of design documents. Integrated into all tasks.
Deployment Planning
Agreement of deployment details and procedures for deployment and transition to support
Deployment Planning
Agreement of deployment details and procedures for deployment and transition to support
Training
Instructor led group training sessions and 1:1 follow up sessions.
Training
Instructor led group training sessions and 1:1 follow up sessions.
Test Review
Review of all test results by development and user teams
Test Review
Review of all test results by development and user teams
Testing Artifact
Summary of all test results – Issues / Enhancements from both scripted and unscripted testing
Testing Artifact
Summary of all test results – Issues / Enhancements from both scripted and unscripted testing
Deployment & Testing
Execution of deployment plan and testing of deployed application
Deployment & Testing
Execution of deployment plan and testing of deployed application
Architecture
Design Spike to define application architecture and compatibility with existing systems
Architecture
Design Spike to define application architecture and compatibility with existing systems
Gate 1
Database Design
Design Spike to define initial data model for application
Database Design
Design Spike to define initial data model for application
Design Artifact
Documentation of system architecture, system design, database design
Design Artifact
Documentation of system architecture, system design, database design
Gate 2Gate 2
Monthly
Peer Code Review
Review of code base by development team to ensure fitness for purpose
Peer Code Review
Review of code base by development team to ensure fitness for purpose
1 Month
< 1 Day
Gate 3Gate 3
Deployment Plan
Document outlining deployment timelines and methodology for handover from DEV team to deployment team
Deployment Plan
Document outlining deployment timelines and methodology for handover from DEV team to deployment team
Gate 4Gate 4
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Results
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Results• Complete enterprise Chemical Registry
System– 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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