Transcript GLS-Presentation

Proteomics Informatics:
Scientific Discovery or IT Development?
Clayton Stark
GenoLogics Life Sciences Software Inc
In this Presentation
 Who are these guys?
 Who’s doing Proteomics? Where do they see it headed?
 Research trend: build the “Proteomics Platform”
 Component parts of the Platforms we are seeing
 What parts are the bioinformatics people working on?
 Options to meet the challenges
©2003 GenoLogics Life Sciences Software Inc
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Who are these guys?
 GenoLogics Life Sciences Software Inc
 My name is Clayton, and I will be your presenter today
(my role at GenoLogics is VP Business Development)
 We are providers of proteomics-focused LIMS and SDMS
software and integration services
 Our main job is understanding the specific needs of the
investigators, the bioinformaticians and the laboratory
managers at proteomics facilities
 Our goal is to help investigators, bioinformaticians and
lab managers turn research – and the massive amounts
of proteomics data – into meaningful discovery, faster
and at lower cost
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Proteomics Today (what we are seeing)
 To date we have seen dozens of research proposals that
include proteomics and proteomics informatics
 There are 861 public universities, 1515 private
universities and 80 government institutions (US and
Canada) with established or new proteomics facilities
that we have seen so far
 About 20 pharma companies we have talked to
 Commercial R&D companies looking for applications
 Plus many Genomics researchers looking to augment
their research
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Proteomics Tomorrow
 Drastically reducing drug target discovery and drug
validation cycle time (by 66% …?)
 Clinical diagnostics, as far down as doctor’s offices having
diagnostic devices based on protein chip technologies
 More research initiatives looking to proteomics to promise
faster discovery – perhaps all major disease prevention
initiatives…?
“The use of proteomics technologies is the most
direct way to identify and study drug targets,
which is arguably the pharmaceutical industry’s
most important task.”
— Front Line Strategic Consulting
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Proteomics Platform – Common Theme
 Research proposals and grant applications describe each
organization's desired “Proteomics Platform”
 Collaboration sought from academia and industry
 Recurring concerns are data management, security,
ubiquity and investment magnitude – oh, and data
mining algorithm development, too
 What will these Proteomics Platforms look like?
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O T H E R D ATA
(e .g . G E N O M IC S )
GELS, LC/MS
MALDI-TOF, etc
EXCEL FILES
& ACCESS DBs
MASSAGE,
SEARCH, etc
MASSAGE,
SEARCH, etc
MASSAGE,
SEARCH, etc
PUBLIC
CONTENT
DBs
SUPER-SCHEMA
DATA MINING,
REPORTING
WEBIFYING
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What Part is IT?
 Are there tasks in the bioinformatics realm that can be
served by people with IT skills (i.e. without life sciences
backgrounds)?
 IT and DBA people are trained to:
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Create data transformation services
Design databases for content they do not fully comprehend
Automate the operation of software components
Build websites and populate them
Create report generation systems and build out reports
Keep it all running, and tweak it as it grows
 What is a bioinformatician’s job description?
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GELS, LC/MS
MALDI-TOF, etc
EXCEL FILES
& ACCESS DBs
OTHER DATA
(e.g. GENOMICS)
MASSAGE,
SEARCH, etc
MASSAGE,
SEARCH, etc
MASSAGE,
SEARCH, etc
PUBLIC
CONTENT
DBs
SUPER-SCHEMA
DATA MINING,
REPORTING
WEBIFYING
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Where do you want to be?
 Some bioinformatics people really want to facilitate
meaningful scientific discovery – that’s why they didn’t
go into IT
 Some bioinformatics groups report 50% to 90% of their
time is spent on tasks that fit the description of an IT
developer or DBA
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Options
 Standards, such as those proposed by HUPO, will get us
part of the way if we can get buy-in from the industry
gorillas
 Continued community development of best practices –
ground swell to force standards?
 Draw some lines separating IT/DBA and Bioinformatics
job functions – can we make both jobs more efficient
with clarity of scope and purpose?
 Take a look at your system’s plans from an IT expert’s
point of view, and see what can be taken out of your
way so you can proceed with science and discovery
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Thank You
Your comments are appreciated
[email protected]
www.genologics.com
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