lecture 10 computers in biology

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Online bioscience course for grades 6-12

Fall 2009

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Class mechanics…

• Attend the online Office Hour on Tuesdays at 3 PM via tokbox-Discuss previous week’s video lecture• Online video lecture e-mailed every Wednesday-view lecture and prepare to discuss the following Tuesday• Comment on video lecture using website discussion board• Online Final Exam given 12/18/2009

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Final Exam:

• Online form• Link will be e-mailed by 12 noon 12/18/2009• One hour to complete-finish no later than 12 noon 12/19/2009• Will cover all 10 lectures…• “Honor System”…

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Lecture 10: Computers and biology

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Ultra-realistic simulation:

Viral DNA packing process…

http://www.dnatube.com/video/1232/Viral-DNA-Packaging--Part-I

Viral DNA Packaging - Part II

http://www.dnatube.com/video/1233/Viral-DNA-Packaging--Part-II

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Take Homes:

I. Computational biology and bioinformaticsII. Biological databasesIII. ProgrammingIV. Modeling and simulationV. Synthetic biology

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http://en.wikipedia.org/wiki/Computational_biology

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http://en.wikipedia.org/wiki/Bioinformatics

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Sequencing of the human genome was made possible by computing:

Human genome sequencing-Animated tutorial

http://www.youtube.com/watch?v=-gVh3z6MwdU

Shotgun sequencing

http://www.youtube.com/watch?v=vg7Y5EeZsjk

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Take Home IComputational biology and bioinformatics

The application of Information Technology to studying biological systems has led to the development of two new areas of research-Computational biology and bioinformatics…

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Biological databases:

BLAST

Text CentricENTREZ

Sequence Centric

Literature Databases

Molecular Databases

Genome Databases

External NIH

External non-NIH

NCBI BioDataSpacehttp://www.ncbi.nlm.nih.gov/

BioDataSpace

• ENTREZ Genome• ENTREZ Genome Project• Map Viewer• Cancer Chromosomes• SKY/M-FISH & CGH

• Nucleotide Sequences• Protein Sequences• Structures• Genes• Gene Expression• Taxonomy

• PubMed• PubMed Central• OMIM• Books

• CGAP

• UCSC• e!• GDB• MGC

BLink

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National Center for Biological Information (NCBI)-an overview:

http://www.youtube.com/watch?v=X7s1zewqeLI

Tutorial: Overview of the NCBI Bioinformatics Website

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National Center for Biological Information (NCBI)-a protein:

http://www.youtube.com/watch?v=gnc2qUcmhWE

Tutorial: Examining the 3D Structure of Rhodopsin at NCBI

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The Kyoto Encyclopedia of Genes and Genomes (KEGG):

Tutorial: Overview of KEGG Bioinformatics Website

http://www.youtube.com/watch?v=mGS0n8aJu5o

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University of California Santa Cruze (UCSC) Genome Browser:

BIT 1.1 UCSC Genome Browser: Getting DNA Sequence

http://www.youtube.com/watch?v=ehIH-rpQoQ4

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Take Home II

Data ranging from DNA sequences of bacterial, viral, animal and plant DNA to protein structural data to imaging data are all stored on Web based databases…

Biological databases

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Programming languages for biology-Practical Extraction and Reporting Language (PERL):

http://en.wikipedia.org/wiki/Perl

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Get PERL:

http://www.perl.org/

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BioPERL:

http://en.wikipedia.org/wiki/BioPerl

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Take Home III

Programming has become a required skill in biology, and the scripting language PERL (Practical Extraction and Reporting Language ) is currently the most commonly used tool…

Programming

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Biological animation:

http://www.youtube.com/watch?v=2fHuJMnDUPI

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Swine Flu - Pandemic Flu Simulation Model:

http://www.youtube.com/watch?v=htnh7pBBtrM

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Biology and video games:

http://www.youtube.com/watch?v=KTRV4FKDNvo

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Take Home IV

Computers have revolutionized our understanding of biology through animations and simulations modeling biological processes…

Modeling and simulation

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Synthetic biology video:

http://www.youtube.com/watch?v=PCxSa6vGEFY

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International Genetically Engineered Machines (iGEM):

http://en.wikipedia.org/wiki/Igem

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2009 iGEM competition:

Edinburgh iGEM 2009 - MINEBUSTERS

http://www.youtube.com/watch?v=QLsmjL3RIKw

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UW iGEM:

BioBrick-A-Bot Model C V 1.1

http://www.youtube.com/watch?v=FRijFX0BpGI

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Take Home V

Synthetic biology involves applying the concepts of computer hardware and software design and implementation to biology…the annual iGEM competition involves students from many nations developing “bio-gadgets”…

Synthetic biology

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Thanks!

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instructorMark E Minie PhD

mark@meminie.com