Slide 1 : 7/13/2010 Lecture 10: COMPUTERS AND BIOLOGY 1 Online Bioscience Course for IT Professionals
Spring 2010
Slide 2 : 7/13/2010 Lecture 10: COMPUTERS AND BIOLOGY 2 Class mechanics… Last of 10 lectures delivered Monday 7/12/2010 (1-2 hour)
Comment on video lecture using website discussion
board
Last online Office Hour on Wednesday (7/14/2010)
at 12 NOON online using WizIQ.com and webcam
Online Final Exam delivered 7/12/2010 and discussed
during last online Office Hour
Slide 3 : 7/13/2010 Lecture 10: COMPUTERS AND BIOLOGY 3 Lecture 10: Computers and biology
Slide 4 : 7/13/2010 Lecture 10: COMPUTERS AND BIOLOGY 4 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
Slide 5 : 7/13/2010 Lecture 10: COMPUTERS AND BIOLOGY 5 Take Homes: Computational biology and bioinformatics
II. Biological databases
III. Programming
IV. Modeling and simulation
V. Synthetic biology
Slide 6 : 7/13/2010 Lecture 10: COMPUTERS AND BIOLOGY 6 http://en.wikipedia.org/wiki/Computational_biology
Slide 7 : 7/13/2010 Lecture 10: COMPUTERS AND BIOLOGY 7 http://en.wikipedia.org/wiki/Bioinformatics
Slide 8 : 7/13/2010 Lecture 10: COMPUTERS AND BIOLOGY 8 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
Slide 9 : 7/13/2010 Lecture 10: COMPUTERS AND BIOLOGY 9 Take Home I Computational 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…
Slide 10 : 7/13/2010 Lecture 10: COMPUTERS AND BIOLOGY 10 Biological databases:
Slide 11 : 7/13/2010 Lecture 10: COMPUTERS AND BIOLOGY 11 National Center for Biological
Information (NCBI)-an overview: http://www.youtube.com/watch?v=X7s1zewqeLI Tutorial: Overview of the NCBI Bioinformatics Website
Slide 12 : 7/13/2010 Lecture 10: COMPUTERS AND BIOLOGY 12 National Center for Biological
Information (NCBI)-a protein: http://www.youtube.com/watch?v=gnc2qUcmhWE Tutorial: Examining the 3D Structure of Rhodopsin at NCBI
Slide 13 : 7/13/2010 Lecture 10: COMPUTERS AND BIOLOGY 13 The Kyoto Encyclopedia of Genes
and Genomes (KEGG): Tutorial: Overview of KEGG Bioinformatics Website http://www.youtube.com/watch?v=mGS0n8aJu5o
Slide 14 : 7/13/2010 Lecture 10: COMPUTERS AND BIOLOGY 14 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
Slide 15 : 7/13/2010 Lecture 10: COMPUTERS AND BIOLOGY 15 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
Slide 16 : 7/13/2010 Lecture 10: COMPUTERS AND BIOLOGY 16 Programming languages for biology-
Practical Extraction and Reporting
Language (PERL): http://en.wikipedia.org/wiki/Perl
Slide 17 : 7/13/2010 Lecture 10: COMPUTERS AND BIOLOGY 17 Get PERL: http://www.perl.org/
Slide 18 : 7/13/2010 Lecture 10: COMPUTERS AND BIOLOGY 18 BioPERL: http://en.wikipedia.org/wiki/BioPerl
Slide 19 : 7/13/2010 Lecture 10: COMPUTERS AND BIOLOGY 19 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
Slide 20 : 7/13/2010 Lecture 10: COMPUTERS AND BIOLOGY 20 Biological animation: http://www.youtube.com/watch?v=2fHuJMnDUPI
Slide 21 : 7/13/2010 Lecture 10: COMPUTERS AND BIOLOGY 21 Swine Flu - Pandemic Flu
Simulation Model: http://www.youtube.com/watch?v=htnh7pBBtrM
Slide 22 : 7/13/2010 Lecture 10: COMPUTERS AND BIOLOGY 22 Biology and video games: http://www.youtube.com/watch?v=KTRV4FKDNvo
Slide 23 : 7/13/2010 Lecture 10: COMPUTERS AND BIOLOGY 23 Take Home IV Computers have revolutionized our understanding of biology through animations and simulations modeling biological processes… Modeling and simulation
Slide 24 : 7/13/2010 Lecture 10: COMPUTERS AND BIOLOGY 24 Synthetic biology video: http://www.youtube.com/watch?v=PCxSa6vGEFY
Slide 25 : 7/13/2010 Lecture 10: COMPUTERS AND BIOLOGY 25 International Genetically
Engineered Machines (iGEM): http://en.wikipedia.org/wiki/Igem
Slide 26 : 7/13/2010 Lecture 10: COMPUTERS AND BIOLOGY 26 2009 iGEM competition: Edinburgh iGEM 2009 - MINEBUSTERS http://www.youtube.com/watch?v=QLsmjL3RIKw
Slide 27 : 7/13/2010 Lecture 10: COMPUTERS AND BIOLOGY 27 UW iGEM: BioBrick-A-Bot Model C V 1.1 http://www.youtube.com/watch?v=FRijFX0BpGI
Slide 28 : 7/13/2010 Lecture 10: COMPUTERS AND BIOLOGY 28 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
Slide 29 : 7/13/2010 Lecture 10: COMPUTERS AND BIOLOGY 29 Thanks!
Slide 30 : 7/13/2010 Lecture 10: COMPUTERS AND BIOLOGY 30 instructor
Mark E Minie PhD
mark@meminie.com