Bio-Instrument Signal Processing : A Prospective GRID-Based Application to Enhance Drug Discovery Shen Haige, Liu Fang and Ke Youan BISP Unit, Laboratory BioInformatics Programme, BioInformatics Centre, National University of Singapore E-mail:

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Bio-Instrument Signal Processing A Prospective
GRID-Based Application to Enhance Drug
DiscoveryShen Haige, Liu Fang and Ke
YouanBISP Unit, Laboratory BioInformatics
Programme,BioInformatics Centre, National
University of SingaporeE-mail
haige_at_bic.nus.edu.sg Tel [phone] Fax [phone]
BioGrid Computing Symposium 2001, National
University of Singapore, 26 Oct. 2001
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Overview

• Bio-Instrument signal processing (BISP) in drug
  discovery for natural products
• Problems in BISP-aided drug discover for natural
  products
• BISP based on GRID technology

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The applications of signal processing methods to
data generated by bio-instruments provide
efficient soft-solutions to some problems in drug
discovery.
BISP in drug discovery
B I o S A M P L E S
User
Sig Pro
LC/MS
F u s I o n
LC/UV
Sig Pro
User
Sig Pro
NMR
User
Sig Pro
MALDI
Sig Pro
QTOF
User
Signal Processing
Data Acquisition
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Our problem-solving algorithms
BISP in drug discovery

• Data format translation
• Denoising
• Visualization
• Crude extract dereplication
• Compound purity measure
• Mixture main component estimation
• Bio-active compound detection
• Compound structure analysis (under development)
• Protein sequence analysis (under development)

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Problems in BISP-aided drug discovery for nature
products
Problems in BISP-aided drug discovery

• Tremendous amount of samples large-scale
  databases
• Diverse instruments control data accessing
• Data processing and re-allocation
• Integration of analysis results from different
  data sources
• The calculation burden brought by increasing size
  of single bio-instrument data and some
  sophisticated algorithms
• Geographically distributed databases
• Data and results exchange between different work
  groups.

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Once bio-instrument data are digitized and the
traditional industry turns to seek much higher
efficiency and profits from the aid of
information technology, it will no longer be
satisfied with the single pipeline and close
operation mode. Good technology needs to be made
full use in an environment with great-scale
resources.GRID is the right technology in such
a context.
Problems in BISP-aided drug discovery
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BISP based on GRID technology
Resources coordinating system monitoring
Internet protocols authentication
Bio-Instruments (LCMS, LCUV, NMR, MALDI, QTOF
), Networks computers
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BISP based on GRID Technology
New Sample Database
Crude Extract Database
New Sample
Save in Database
Group A Crude Extract Dereplication
Bio-Instruments
Data Translation Denoising Feature Extraction
for Further Processing
New Extracts
Replicate Extracts
Bio-Active Compounds
(Isolation)
Potential Components Database
Group D Chemical Analysis
Group B Bio-active Compound Dereplication
Group C BioAssay
Chemistry Knowledge Database
Bio-Active Compound Database
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Grids are expected to drive the economy of the
21st century in a similar fashion to how
electrical power grids drove the economy in the
20th century. ------ From GRID2000 The first
IEEE/ACM International Workshop on Grid
Computing Bangalore, India, 17 Dec 2000