Bioinformatics

1
Bioinformatics

• The Application of Information Technology to
  Advance Biological Research
• April 14,2007
• Team 2 Members
• John Casarella
• Dave Fronckowiak
• Larry Immohr
• Sandy Westcott

2
Outline

• Introduction
• What is Bioinformatics
• Importance of Bioinformatics
• Current State of Affairs
• Aspects of Bioinformatics
• Currently Available Applications
• Conclusion

3
Introduction

• Infancy the 1953 milestone when James Watson
  and Francis Crick determined the structure of DNA
• Advanced even before named by Linus Paulings
  theory of molecular evolution (molecular biology)
• Advances in molecular biology, in genomic
  technologies, produced an explosive growth in the
  biological information
• This deluge of genomic information spurred the
  requirement for computerized databases to store,
  organize, and index the data and for specialized
  tools to view and analyze the data
• Molecular biology is discrete, a property it
  shares with computing
• Determined that AI approaches perform well in
  domains with an immense amount of data coupled
  with minimal theory

4
Introduction- continued

• Requirement of progress in combining the
  intelligent systems with the sheer volume of
  biomedical research
• Combining the knowledge of the tiny molecular
  mechanisms with knowledge of the biological
  systems as a whole
• Production of large, dissociated and distributed
  Biological Databases
• Lack of coordination and the knowledge of
  existence of critical biological data
• How to access all of this and more importantly,
  its application
• What is the role of computers in biology?

5
What Is Bioinformatics?

• Simply it is the application of computers to
  biology
• Formally -- Bioinformatics is the field of
  science in which biology, computer science, and
  information technology merge to form a single
  discipline
• Objectives
• Enable the discovery of new biological insights
• Create a global perspective do discern unifying
  principles in biology
• Create and maintain databases to store biological
  information, such as nucleotide and amino acid
  sequences
• Provide in-silico capabilities
• Allow for the integration of molecular biology /
  genetics to advance the understanding of complex
  structures with respect to living cells and the
  entire organism

6
Why Is Bioinformatics So Important

• Allows for a more global perspective in
  experimental design
• Provides the ability to mine data to generate
  testable hypotheses regarding the function or
  structure of a gene or protein
• Powerful tool in the battle against toxicity and
  last stage drug failures
• Ability to determine genetic variations and the
  incredible task of deciphering proteins
• Provides the mining the research literature to
  reveal hidden patterns or relationships between
  genes and processes that were unexpected
• Disease state analysis

7
Current State of Affairs

• Lack of data standardization for the construction
  of vocabularies and ontologies for both
  biologists and computer scientists
• Some major databases, such as NCBI, contain 26
  billion base pairs
• Protein databases contain catalogues of gt 45,000
  proteins specified by their 3D structures
• Data is increasingly become large scale, complex
  and unmanageable
• Biologists deal with essentially four types of
  data structures
• Strings - to represent DNA, RNA, and sequences of
  amino acids
• Trees - to represent the evolution of various
  organisms
• Sets of 3D points and their linkages - to
  represent protein structures
• Graphs - to represent metabolic and signaling
  pathways.

8
Aspects of Bioinformatics

• Availability of large public databases of
  biological data usually associated with
  computerized software designed to update, query,
  and retrieve components of the data stored within
  the system
• Many applications are available for MATLAB
• Vast majority of these applications are
  open-source and under the GNU, inclusive of
  documentation and user guides
• Hidden Markov model (HMM) is proving to be a
  statistical model well suited for many tasks in
  molecular biology
• Neural Network model has emerged as a promising
  AI technique in DNA sequence analysis
• Ability to design in-silico experiments which
  enable biologists to bypass costly and ethically
  sensitive in-vitro or in-vivo trials

9
Currently Available Applications

• Patikaweb interface for analyzing biological
  pathways using querying visualization
• K-Fold a tool for automatic prediction of the
  protein folding kinetic order and rate
• BioNetBuilder allows for the creation of
  biological networks via integration of databases
• Systems Biology Toolbox / MATLAB allows for the
  exploration of new ideas, prototyping and
  biological/biochemical stimulations.
• PySCeS an extensible research tool for the
  numeric analysis and investigation of cellular
  structures

10
Currently Available Applications

• COPASI (Complex Pathway Simulator) Biochemical
  simulator, uses optimization algorithms, GUI,
  model creation, native XML
• iPfam allows for the visualization of protein
  to protein interactions as stored in the protein
  databank
• BioIE a rule based system which allows for the
  extraction of information relating to proteins
  from the biomedical literature

11
Currently Available Applications

• BioLingua an interactive web based programming
  environment, allows for the analysis of
  biological systems
• CabosML an XML description of carbohydrate
  structures
• ChemDB a database of small molecules available
  across the web, using computational methods to
  form 3D structures, predict chemical properties

12
Importance and the Future

• The rapidly emerging field of bioinformatics
  promises to lead to advances in understanding
  basic biological processes and, in turn, advances
  in the diagnosis, treatment, and prevention of
  many genetic diseases.
• Bioinformatics has transformed the discipline of
  biology from a purely lab-based science to an
  information science as well.
• Increasingly, biological studies begin with a
  scientist conducting vast numbers of database and
  Web site searches to formulate specific
  hypotheses or to design large-scale experiments.
• Implications behind this change are staggering,
  for both science and medicine.

13
References

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• Chen, Jonathan, S. Joshua Swamidass, Yimeng Dou,
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14
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