Transcript Bio-Instruments Signal Processing : A Prospective GRID

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: [email protected]
Tel: 871-9705
Fax: 779-0724
BioGrid Computing Symposium 2001, National University of Singapore, 26 Oct. 2001
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
BISP in drug discovery
The applications of signal processing methods to data
generated by bio-instruments provide efficient soft-solutions
to some problems in drug discovery.
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LC/MS
Sig Pro
LC/UV
Sig Pro
NMR
Sig Pro
MALDI
Sig Pro
User
QTOF
Sig Pro
User
Data Acquisition
Signal Processing
User
User
BISP in drug discovery
Our problem-solving algorithms
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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)
Problems in BISP-aided drug discovery
Problems in BISP-aided drug discovery
for nature products
• 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.
Problems in BISP-aided drug discovery
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.
Applications of BISP
BISP based on GRID technology
Resources coordinating
& system monitoring
Access to computation, databases (sample, old extract,
bio-active compound, chemistry knowledge databases)
& information about system
Internet protocols & authentication
Bio-Instruments (LCMS, LCUV, NMR, MALDI, QTOF ……),
Networks & computers
BISP based on GRID Technology
New Sample
Database
Crude Extract
Database
New Sample
Bio-Instruments
Data Translation;
Denoising;
Feature Extraction
Save in Database
Group A:
Crude Extract
Dereplication
for Further
Processing
New Extracts
Replicate Extracts
Bio-Active
Compounds
Potential
Components
Database
Group D:
Chemical
Analysis
Chemistry
Knowledge
Database
(Isolation)
Group C:
BioAssay
Group B:
Bio-active Compound
Dereplication
Bio-Active
Compound Database
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 GRID’2000 The first IEEE/ACM
International Workshop on Grid Computing
Bangalore, India, 17 Dec 2000