Bio/CS 251

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Bio/CS 251
Introduction to Bioinformatics
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• Class Web Site
• http//cs.gettysburg.edu/leinbach/Bio_CS251/
• This site will contain all important documents
  related to the class.
• Power points of all lectures
• Labs
• Exam Answer Keys (Posted after the exam)
• Homework Assignments and Answer Keys
• Note the updated syllabus contained at this
  site. It super cedes the one distributed on
  paper. Difference description of the final
  project. There are two options.

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My Definition of Bioinformatics A study of the
algorithms and programs that are used by
Molecular Biologists and others in the Biological
and Medical Sciences in their quest for
understanding protein structure and function in
living organisms.
This is just one of many definitions that may be
found in text books, scientific papers, and on
the web. The simplest definition is that it is
an interdisciplinary subject drawing on material
from Biology, Mathematics, and Computer Science.
To me this is like saying that e mc2 has
something to do with relativity theory.
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Some Implications of this Definition

• An individual studying Bioinformatics needs to
  have some understanding of the basic ideas of
  Molecular Biology research.
• They also need to have a familiarity with DNA
  sequences and how they contribute to 3D Protein
  Structure as well as gene identification and
  phylogenetics.
• They need to be familiar with the many in
  silico tools that are used and the parameters
  that control the output of the programs or
  algorithmically controlled devices.
• It is important for them to understand the
  objectives and limitations of both Computer
  Science and Molecular Biology.
• They need to have some experience with collecting
  biological data for analysis

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Computational Biology
Computational Biology
Micro Biology Medical Science
(Note the two way arrow)
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Some Timelines
Material taken from lecture given by Lucy
Skrabanek Institute of Computational Biology at
Weill Medical College of Cornell
University February 23, 2005
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Early Pre History
Computer Science
Micro Biology
Bioinformatics
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Late Pre History
Computer Science
Micro Biology
Bioinformatics
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Recent History
Computer Science
Micro Biology
Bioinformatics
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Two Scientists Who In 900 Words Reshaped the Way
In Which We View Life on Earth
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(No Transcript)
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With the power and storage capabilities of
computers biological databases began to
proliferate all around the world. By the mid
1980s users were demanding access to the latest,
up to date data. In 1988, a network was
established to link databases in European
Molecular Biology and Bioinformatics Labs. It
was called the European Molecular Biology
network, or EMBnet. At the turn of the century
it consisted of 34 national, specialist, and
associate nodes. In the United States the
National for Biological Information of the
National Laboratories of Medecine at the National
Institutes of Health became the repository for
sequence and protein information as well as a
link to other databases around the world. The
World Wide Web (a sophisticated internet tool)
has facilitated queries to these databases.
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The Net (no pun intended) Result is an
Asstounding Growth of Biological Information
Source Scrabanek op. cit.
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Protein Structure Data is Growing at a Slower Pace
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As a result, DNA sequencing and Proteomics have
had an increasing number of important
applications in the life, medical and social
sciences. Pickup any scientific journal that
deals with the life or medical sciences, any
popular scientific magazine, or, for that matter,
any daily newspaper and you will find an article
where DNA or related issues play an important
role Why, it even makes the comic section