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Proprietary and Confidential
24th September, 2013
Instant JChem as a Cloud Hosted LIMS
A Platform for Delivering Chemical, Biological, Sensorial,
and Inventory Data to the Team
Adam Idone
Information Systems Manager
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Proprietary and Confidential
OVERVIEW
“Data! Data! Data! I can’t make bricks without
clay!” – Sir Arthur Conan Doyle
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Why?
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Proprietary and Confidential
INDEX
Overview of Chromocell
Implementation
Data Views and Entities
Compound Registration/Informatics
Other Uses of IJC
Closing Thoughts
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Proprietary and Confidential
OVERVIEW
• Small business started in 2002 based on Chromovert®
Technology
• Based in North Brunswick, NJ with a team consisting of about
100 full time scientists, management and support staff.
• Growth
• Originally outsourced all chemistry support on projects to CRO’s
and collaborations.
• Moved into new building in 2009
• With new partnerships, Chromocell expanded into Natural and
Synthetic Chemistry in Q4-2010
• Informatics grown out in 2011.
• Numerous flavor and flavor enhancement projects for Sweet,
Salty and Bitter profiles
• Multiple projects in Therapeutics area with a focus on analgesics
and respiratory disorders
• Sister company, Gustatec, handles sensory testing for Flavors
projects
RECEPTOR BASED
DISCOVERY
Chromocell: Background, Challenges and Goals
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Proprietary and Confidential
OVERVIEW
• 2010: All data tracked in Microsoft Excel, collaboration occurred though SharePoint and
e-mail. Chemistry viewing support was limited to 3 licenses of non-enterprise Instant
JChem(IJC).
• Q1-2011: Natural and Synthetic chemistry teams brought on board. ChemDraw was
purchased for reaction and chemical drawing support.
• Q3-2011: Off-the-shelf software purchased with limited modules and # of users to keep
costs down.
• Q3-2012: Licenses purchased for IJC Enterprise to phase out software due to cost and
functionality with set of modules available to the informatics group
• Q3-2013: Overwhelming support for IJC. Customizable, configurable, in-house support,
extensible, powerful, and fast!
Chromocell: Timeline
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Proprietary and Confidential
OVERVIEW
• Molecular Biology
• Core Tech
• Cell Culture
• Assay Development
• Sensory Lab
• Natural Products
• Medicinal Chemistry
• Legal & IP
Chromocell: Departments and Scope
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Requirements
• Serve as a chemical registration service within our organization for
screening libraries, building blocks, reagent chemicals, and other
purchased inventories.
• Track analytical, solubility, toxicity, and descriptive data on chemical
structures.
• Keep all inventory information up to date for vials, plates, and neat
stock with respect to quantity, location, vendor information, etc.
• Relationally link all cell data and sensory data at the experiment
level with ability to drill down.
• Serve as a collaboration platform for idea sharing within Medicinal
Chemistry.
• Provide access to chemistry informatics support to Legal and IP
team for associated work.
• Support Natural Products in data and workflow management via
Biomass>Extract>Fraction>Deconvolution workflows.
• Serve to automate numerous workflows within the organization.
• Provide an easily searchable and secure data store for all the above
listed
• Keep costs low!
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Proprietary and Confidential
INDEX
Overview of Chromocell
Implementation
Data Views and Entities
Compound Registration/Informatics
Other Uses of IJC
Closing Thoughts
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Proprietary and Confidential
OVERVIEW
• Hosted on Amazon Web Services(AWS)
• Utilizes Relational Database Service(RDS) to host
IJC schemas in addition to others. Uses Oracle
11g Database
• Amazon EC2 Web Servers used for:
• Hosting of Oracle APEX application server
• Hosting of IJC project configuration/shared
URL server
• Application Server to host toxicity
calculators in addition to other custom
applications
• Soon to be IJC Application Server for Web
Client
• All wrapped behind Amazon Virtual Private Cloud
with VPN gateway
Implementation: Architecture
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Proprietary and Confidential
OVERVIEW
• Project driven company turns into project driven
data schemas
• All information is stored in 4 data schemas:
• Compounds: Structures, Lots, Analytical,
Descriptors, Solubility, Toxicity, etc.
Screening plates, Vials, Amounts, Neat
Stocks, Ordering Information, etc.
• Experiment Data: Cell Data, Sensory Data,
etc.
• Natural Products: Biomass, Extracts,
Fractions, LC/MS data, etc.
• Legal & IP
• External Vendors
• Bottom four schemas represent virtual IJC
schemas, no actual data stored here, mainly used
to compartmentalize access to information.
Implementation: Data Model
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• All Schemas have custom roles and row-level
security
Legal & IP
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Proprietary and Confidential
OVERVIEW
• Security Policy for all schemas is, ‘Username/password using IJC database’ with
required encryption
• 1 Admin to maintain all Schemas
• 2 Users per Project with Role Edit Schema
• Roles implemented to filter entities and columns from certain users
• Row-Level Security implemented on a project basis for a handful of tables
• ‘Delete Rows’ not enabled on any table in IJC (Active column is changed to 0 and
filtered out)
• IJC logging performed on certain schemas for informational and security
purposes.
Implementation: Users/Security
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Proprietary and Confidential
INDEX
Overview of Chromocell
Implementation
Data Views and Entities
Compound Registration/Informatics
Other Uses of IJC
Closing Thoughts
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Proprietary and Confidential
OVERVIEW
• Project Schema copied for the purposes of this presentation and stripped of all
data, replaced with Acetaminophen or structure omitted
• All compounds are registered and assigned corporate ID. This corporate ID is the
basis for all primary/foreign keys in the database/IJC Schemas
• Relationships are defined – data trees built – indexes set
Schemas, Entities, Views Galore
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Project Navigator
Data Tree Navigator
Entities Navigator
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Proprietary and Confidential
OVERVIEW
Schemas, Entities, Views Galore
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Proprietary and Confidential
OVERVIEW
Schemas, Entities, Views Galore
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• Solubility and Tox data to the right.
Currently Tox predictions are
computed automatically via database
triggers signaling external
softwares/KNIME workflows/Java.
• Solubility is based off experimental
data, though we are excited for
ChemAxon’s LogS predictor
• Many files which are viewed through
IJC are stored on Chromocell’s intranet
and linked to via a URL path.
• Below is an image of an analytical
spectra (replaced with link from Google
Images for purposes of this
presentation)
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Proprietary and Confidential
OVERVIEW
Schemas, Entities, Views Galore
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• All screening inventory is tracked via
IJC and updated on a nightly basis
through automated data pulls from our
robotics department. This process is
assisted by database scripts.
• An extremely simple view, which had
great feedback from the scientists, was
to include a ‘Search’ view in the larger
data trees to filter out values based on
Corporate ID’s/Projects
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Proprietary and Confidential
OVERVIEW
Schemas, Entities, Views Galore
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• One of many cell data
views with structures,
corporate ID’s, and
headers replaced.
• Conditional formatting
applied to Mol Matrix.
• Big utilization of IJC’s built
in plotting capabilities.
• When ChemAxon releases
the 5.5 OData Connector
for IJC-Spotfire Bridge we
will begin utilizing this
workflow again..
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Proprietary and Confidential
OVERVIEW
Schemas, Entities, Views Galore
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• Structures and data
replaced for purposes of
this demonstration (graph
grabbed from Google
Images)
• For advanced graphing
functionality we have
developed automated
methods to analyze and
upload data to an intranet-
based repository.
• When data is formatted to
IJC upload template, using
the same automated
function, it’s URL is
appended for IJC viewing
purposes
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Proprietary and Confidential
INDEX
Overview of Chromocell
Implementation
Data Views and Entities
Compound Registration/Informatics
Other Uses of IJC
Closing Thoughts
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Proprietary and Confidential
OVERVIEW
Compound Registration – ChemAxon Collaboration
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• Contracted ChemAxon to work with us on
generating a Groovy script to perform
compound registration.
• Handles registration of unique structures,
assignment of Corporate ID, lot/batch tracking,
initial inventory registration and salt handling.
• Stage table handles initial upload of structures
and data, button script then registers values into
respective tables with a Status, Error, and ID
column output
• Very satisfied with work done (Thanks Erin,
Dennis, Tim)
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Proprietary and Confidential
OVERVIEW
Informatics
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• Use of R-Group Decomposition function has been a big hit
with chemists in the company. It has become a standard part
of their workflows when dealing with structure activity
relationships.
• The overlap analysis feature has proven to be an extremely
useful function within IJC. It allows us to compare large
datasets with relative ease and analyze the results using
macros in Microsoft Excel. These extracted values, from the
macro, are reformatted with appropriate information and their
corporate ID’s are used to pull structures from JC4XL.
• Overall, IJC’s role in Informatics at Chromocell lay mainly
with handling, viewing, and modifying large data sets as they
are transported and used by different software's with results
being transferred back into IJC. These range from MatLab,
R, network graphing software, GraphPad Prism, custom
softwares which utilize IDBS’ XLFit, and others.
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Proprietary and Confidential
INDEX
Overview of Chromocell
Implementation
Data Views and Entities
Compound Registration/Informatics
Other Uses of IJC
Closing Thoughts
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Proprietary and Confidential
OVERVIEW
Other Uses
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• IJC hosts a database schema of external vendor compounds. Every month database
files from numerous large synthetic and natural chemical suppliers are uploaded
• Additional rows for new compounds
• Update of existing record for quantity/lot updates
• This external chemical database serves to aid the Chemists in new analog selection,
chemical sourcing, training models, etc
• Legal & IP Schema for use of checking IP space, pursuing new scaffold ideas, and
filing.
• Check for drugs/hazardous chemicals
• Flavors-olfaction database
• One aspect of IJC we did not cover in this presentation is the Natural Products
integration in IJC.
• This schema serves to track Biomass in relation to:
• Extracts
• Extraction experiments
• Fractions
• HPLC runs
• Deconvolution data
• Analytical files (LC/MS, UV/ELSD, NMR)
• Exact mass, proposed formulas, adducts, etc.
• Cell and sensory data in relation to fractions
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Proprietary and Confidential
OVERVIEW
Oracle APEX
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• Web interface for
all non-chemistry
related activities
can be used to
register, search,
and query entities
• New instance to
be deployed Q4-
2013
• Has access to IJC
data schemas in
addition to it’s own
Oracle Schema
• Hosted via Apache
Application Server
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Proprietary and Confidential
INDEX
Overview of Chromocell
Implementation
Data Views and Entities
Compound Registration/Informatics
Other Uses of IJC
Closing Thoughts
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Proprietary and Confidential
OVERVIEW
What’s to come…
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• We currently hold licenses for JC4XL, JKlustor, a few descriptors, and Document to
Structure.
• Automation of JKlustor via scripting and command line functionality for all scientists to
use as opposed to IT super users
• In the coming months:
• Reactor as a replacement for our existing solution
• Screen Suite for virtual screening of large datasets and proposed compound
purchases
• Markush Search and Enumeration for enhanced IP searches. Currently IP
functionality in the system is limited to tracking known patent numbers and
pulling there associated info from the web. A lot of room for growth here.
• Standardizer for all chemical registration within Chromocell
• JChem Cartridge backend for IJC hookup
• KNIME plugins for IJC to automate from this level as opposed to database level
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Proprietary and Confidential
OVERVIEW
Nice to have…
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• Drop down lists from static or dynamic lists
• Auto-push of IJC updates via shared projects/configuration
• List boxes with multi-select enabled for querying
• Sliders in forms for filtering
• AND/OR functionality within queries
• Be able to change order of Entities in Data Tree by dragging them or setting a
sequence number
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Proprietary and Confidential
OVERVIEW
ChemAxon
• Jon Patterson
• Erin Bolstad
• Dennis Sprous
• Tim Dudgeon
• Entire ChemAxon team!!
Informatics Collaborations
• Dennis Moccia
• Amr Ragab
Thank You!
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Proprietary and Confidential
Chromocell Corporation
685 U.S. Highway One
North Brunswick, NJ 08902
Tel 732-565-1113
Fax 732-565-1183
www.chromocell.com
Thank you for your attention!!