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 Pauling’s 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 > 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.

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