Welcome To: Computers In Biological Research ZOO 49705970

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Welcome ToComputers In Biological ResearchZOO
4970/5970

• 3 hour, letter gradedMW 1100 - 1215 NH122
• (Nielsen Hall computer lab)

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New Fields and Paradigms

• Today there are entirely new fields of science
  emerging,
• and there are new paradigms in existing
  disciplines
• "chaos", "nonlinear studies", "sciences of
  complexity", "artificial life", etc.

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The Computational Engine

• The common engine that is driving these new
  developments is the computer

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Languages of Description

• Some have suggested that the historical reliance
  of science on calculus may have been due not just
  to its merits,
• but also to the fact that before the computer,
  alternative languages of description were not
  practical (Toffoli, 1984)

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Third Domain

• Others have suggested that computational science
  will eventually grow into a third domain of
  science,
• coequal with the traditional domains of theory
  and experimentation (Pool, 1989 Kelly, 1998).

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Doing Something New

• To participate in these fields, it is not enough
  to have a computer.
• One must be able to use the computer to do
  something that has never been done before.
• This is facilitated by programming skills, while
  software packages provide limited potential.

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Programming Skills

• The new course, Computers in Biological
  Research'', is designed to provide the
  programming skills that will allow participation
  in these emerging new fields of science.

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Course Project

• Apart from these goals, students enrolled in ZOO
  4970/5970 will develop software to solve a
  specific research problem of their choice.
• The course will provide down-to-earth computer
  skills and apply them to real problems in
  biological research.

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Required Work

• The material to be taught in this course can not
  be learned by attending lectures or reading
  books.
• The only way to learn it is by working on a
  computer.
• Each student must complete small weekly
  programming assignments, and one larger
  programming project.

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Required Effort

• This will require a substantial and sustained
  effort throughout the semester.
• Students should be prepared to spend about eight
  hours per week on class work, in addition to
  scheduled class time (2.5 hours).

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Grading

• Weekly assignments will not be graded
• final grade will be based on the term project
• one letter grade will be earned for each
  element included in the term project, up to
  five
• ...

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TentativeTerm project elementsone letter
grade per element

• Classes
• functions
• pointers
• file input/output
• Windows controls, mouse/keyboard, dialog boxes

• Windows graphics functions
• Windows data bases
• Windows multitasking
• Windows network communications
• list may change ...

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Syllabus
Jan 13 Compiling C programs Jan 20 Guest
Lecture David Certain - GIS A tool for
natural resource analysis through space and
time Jan 25 Variables and Constants Jan 27
Expressions and Statements Feb 1 Functions Feb
3 Basic Classes Feb 8 Pointers and
References Feb 10 Advanced Functions Feb 15
Arrays Feb 17 Inheritance Feb 22 Polymorphism Feb
24 Streams Mar 1 Object-Oriented Analysis and
Design Mar 3 Templates Mar 8 Exceptions and
Error Handling
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Syllabus
Mar 10 Windows Programming Mar 22 Windows -
Controls Mar 24 Windows - Mouse and Keyboard Mar
29 Windows - Dialog Boxes Mar 31 Windows -
Graphics Functions Apr 5 Windows - Data
Bases Apr 7 Windows - Multitasking Apr 12
Windows - Network Communications Apr 14
Portability in C Apr 19 Guest Lecture Joe
Bastian - Computers in
Neuroscience Apr 21 Individual Project
Demonstrations Apr 26 Individual Project
Demonstrations Apr 28 Individual Project
Demonstrations
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Zoo Language Requirement

• ZOO 5970 has been approved by the Zoology faculty
  to meet the Foreign Language and Research Skill
  Option requirement
• Earning a B or better in ZOO 5970 will
  demonstrate proficiency in a computer language

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Floppy Disks

• The computers in the laboratory are not a safe
  place to store your work
• You will need a couple of floppy disks to keep
  your work
• At the end of the semester, you must submit your
  project on a floppy disk

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Former TextbookThe C Programming Language,
Brian W. Kernighan, Dennis M. Ritchie, 1988,
Prentice Hall
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Recommended C TextThe C Programming
Language, Third Edition, Bjarne Stroustrup, 1997,
Addison Wesley
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Required C TextSAMS Teach Yourself C in 21
Days, Second Edition, Jesse Liberty, 1997, SAMS
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Required Visual C 6.0 TextSAMS Teach Yourself
Visual C 6 in 21 Days, Davis Chapman, 1998, SAMS
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Recommended Visual C 6.0 Text Microsoft
Visual C 6.0 Programmer's Guide, Beck Zaratian,
1998, Microsoft Press
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What is a Computer?
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What is a Computer?

• A word processor
• a spread sheet
• a data base
• an electronic mailbox
• a web browser
• a CD player
• a presentation system
• ...

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What is a Computer?

• A paintbrush
• a musical instrument
• a telephone
• a videophone
• a fax machine
• an accountant
• a phone book
• ...

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What is a Computer?

• A calendar
• an encyclopedia
• a video arcade game
• an educational game
• a training course
• a medical diagnostician
• an industrial control system
• ...

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What is a Computer?

• A simulation of the economy
• a simulation of weather
• a simulation of colliding galaxies
• a simulation of an ecosystem
• of a newly designed computer
• an environment inhabited by digital life
• ...

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What is a Computer?

• A simulation of the economy
• a simulation of weather
• a simulation of colliding galaxies
• a simulation of an ecosystem
• of a newly designed computer
• an environment inhabited by digital life
• anything that you can imagine ...

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What is a Computer?

• A chameleon machine - waiting for your next
  imagination ...

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The First Computer Revolution

• The first computer revolution can be considered
  the advent of the personal computer

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The Second Computer Revolution

• The second computer revolution can be seen as the
  spread of computational skills beyond the
  computer sciences.

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The Computational Artist

• We are moving beyond the day when the
  artist/scientist with no computational
  understanding tries to explain their ideas to the
  computer programmer with no artistic/scientific
  understanding

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One Individual

• Today the full understanding can be found in one
  individual
• the artist/scientist can master the computer
• Thus the artist or astronomer can directly
  implement their ideas in their most profound
  form, with no understanding lost in translation

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Revealing the Potential

• The spread of computational technology and skills
  into every walk of life is revealing more of the
  potential of the computer

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Embracing the Machine

• It is difficult to imagine the forms that our
  chameleon machine will take-on a hundred or a
  thousand years in the future
• when the technology is fully matured through
  people who directly and deeply embrace the machine

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This Course

• The purpose of this course is to empower you to
  shape this chameleon machine to your imaginations

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References

• Gleick, James. 1987. Chaos, making of a new
  science. Penguin Books.
• Kelly, Kevin. 1998. Essay on Science and
  Society The Third Culture. Science 279 992 -
  993 (Feb. 13)
• Langton, Christopher G. ed.. 1989. Artificial
  life proceedings of an interdisciplinary
  workshop on the synthesis and simulation of
  living systems. Vol. 6 in the series Santa Fe
  Institute studies in the sciences of complexity.
  Addison-Wesley.
• Pool, Robert. 1989. Is it real, or is it Cray?
  Science 244 1438-1440.
• Sun, Marjorie. 1989. Supercomputer market needs
  supersalesmen. Science 245 596-597.
• Toffoli, Tommaso. 1984. Cellular automata as an
  alternative to (rather than an approximation of)
  differential equations in modeling physics.
  Physica 10D 117-127.
• Wolfram, Stephen. 1984. Computer software in
  science and mathematics. Scientific American
  251(3) 188-203.
• Wolfram, S. 1984. Cellular automata as models
  of complexity. Nature 311 419-424.