The Role of Computer Science in the Biomedical Research

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The Role of Computer Science in the Biomedical
Research

• Stephen Kwek
• Department of Computer Science
• kwek_at_cs.utsa.edu

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S.A Texas Research Park

• Institute of Drug Discovery
• San Antonio Institute of Biotechnology
• Sam and Ann Barshop Institute of Aging.
• San Antonio Oncology Group

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S.A. Southwest Biomedical Research Foundation
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S.A. UTHSCSA
Children Cancer Research Institute
PhD in Bioinformatics (UTHSCSA), PhD in
Bioinformatics (UTSA-UTHSCSA)
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Other Research Organization (relevant to
Bioinformatics) in S.A.

• Cancer Therapy and Research Center
• San Antonio Cancer Institute
• San Antonio Life Science Institute
• Conversion of Lackland Air force Base to
  (Bio)technology Park

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Private/State Biomedical Research Foundation

• Howard Huge Medical Institute
• Celebrities Elton John, Bill Gates, etc.
• Stem Cell Research George Bush restrict federal
  stem cell research funding. California raised
  3billion bond. New Jersey followed 0.5billion,
  .. Etc.
• Stanford University all out for biotech.
• Palo Alto Research Center Heavily involved in
  Bioinformatics

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Federal Funding
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Biotech Century

• Bioinformatics / Computational Biology aspect
• Human Genome Project (HGP)
• High Throughput devices

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Consequence

• Change the entire way we look at biology (system
  biology, molecular medicine, integrative biology,
  etc)
• Generate huge amount of data
• The cell is MANY times more complex than a
  computer system, need CS people to organize and
  make sense of these data.

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The Role of CS

• Bioinformatics Resaerch, development, or
  application of computational tools and approaches
  for expanding the use of biological, medical,
  behavioral or health data, including those to
  acquire, store, organize, archive, analyze, or
  visualize such data. Database, visualization,
  algorithms and machine learning/data mining
• Computational Biology Development and
  application of data-analytical and theoretical
  methods, mathematical modeling and computational
  simulation techniques to the study of biological,
  behavioral and social systems. Machine
  learning/Data mining and visualization

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Job Prospect

• Typical CS Ph.D.
• Academic
• Some Government Research Organization
• Bioinformatics/Computational Biologists from CS.
• Academic
• Industrial
• Government Research Organization NIH, FDA
• Private Research Organization SWBR, and many
  others around the country.
• http//www.bioplanet.com/index.php
• There is still a lack of people who can do
  computation and understand (a bit of) molecular
  biology.

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The Course Objective

• Survey computational techniques essential to
  biomedical research
• Sequence analysis
• Functional elements finder
• Pathway constructions
• Comparative Genomics
• etc.
• In depth project to get experience working with
  biomedical researchers

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Pre-requisite

• CS graduate students, CS senior undergraduate
  (with A in CS 3343), other students consent of
  instructor.
• Have programming background.
• Some knowledge of probability and statistics.

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Textbooks

• Required text book
• CGA Computational Genome Analysis (1st edition,
  Corr. 2nd Printing 2006). Deonier, Tavare and
  Waterman. Springer
• References
• HMB Human Molecular Biology (Chapter 1 Only)
  2nd edition. Available free from NCBI bookshelf,
  http//www.ncbi.nlm.nih.gov/entrez/query.fcgi?dbB
  ooks
• BCBS Bioinformatics and Computational Biology
  Solutions using R and Bioconductor.
• DGPB Discovering Genomics, Proteomics, and
  Bioinformatics  (2nd edition)

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Structure of the Course

• 4 lectures overview of molecular biology for CS
• Biomedical Researchers talk about appolications
  (3-5 lectures)
• Survey of bioinformatics problems and
  computational techniques to solve them.

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Grading

• (5) Quiz on the 1st Feb on molecular biology
  basic. Students will given be given a second
  chance to take the quiz if the first attempt
  failed.
• (25) final TBA
• (20) 4 assignments
• (50) 1 individual/group project
• Project Proposal (15) Due 1st March
• Final Project Report (35) Due 11th May