instant jchem as a cloud hosted lims...page 1 proprietary and confidential 24th september, 2013...

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


OVERVIEW

“Data! Data! Data! I can’t make bricks without

clay!” – Sir Arthur Conan Doyle

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Why?


INDEX

Overview of Chromocell

Implementation

Data Views and Entities

Compound Registration/Informatics

Other Uses of IJC

Closing Thoughts


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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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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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!


INDEX


Implementation



Other Uses of IJC

Closing Thoughts


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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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


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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INDEX


Implementation



Other Uses of IJC

Closing Thoughts


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


OVERVIEW


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OVERVIEW


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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)


OVERVIEW


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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


OVERVIEW


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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..


OVERVIEW


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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


INDEX


Implementation



Other Uses of IJC

Closing Thoughts


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)


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.


INDEX


Implementation



Other Uses of IJC

Closing Thoughts


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


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


INDEX


Implementation



Other Uses of IJC

Closing Thoughts


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


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


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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Chromocell Corporation

685 U.S. Highway One

North Brunswick, NJ 08902

Tel 732-565-1113

Fax 732-565-1183

[email protected]

www.chromocell.com

Thank you for your attention!!

instant jchem as a cloud hosted lims...page 1 proprietary and confidential 24th september, 2013...

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