Transcript CS 177 Intro to Bioinformatics

CS 177
Intro to Bioinformatics
•Barry Zeeberg
–NIH/NCI/LMP/GBG
•email:
–Use only in “emergency”
–Subject line = “GW course”
–[email protected]
•downloads of ppt will be archived at
–http://discover.nci.nih.gov/~barry/CS177/CS1
77.html
Administrative Stuff
component
% of final grade
homework
25
quizzes
25
final exam
25
large team project
and presentation
25
Contact and Background Info
•Excel spreadsheet on my pc
–first column = names
–second column = email
–third column = major background area
–fourth thru n-th columns = other
background areas
Web Site
•http://discover.nci.nih.gov/~barry/CS177/CS17
7.html
•this will contain
–ppt for each week
–any additional materials
–Excel spreadsheet with names, emails,
backgrounds
–late-breaking announcements
•these might include corrections in
homework assignmentsetc.
•you are responsible to check this from
time to time
Expectations
• I will randomly spot-check selected parts of homework and
quizzes for grading
• You need to do all homework and quizzes and hand in to
me when due, unless you make a prior arrangement with
me in the event of emergency or hardship
• You will actually get a zero (0) otherwise
• All quizzes etc are open book; internet can be used
• Quizzes are to be done independently
• Homework can be done with some mutual consultation,
but what is handed in must reflect essentially your own
work
List of Major Topics
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transcription
translation
gene structure
genetic code
information and
entropy
• molecular biology
databases
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sequence homology
basic genomics
basic biotechnology
human genome project
microarrays
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statistics
disease genes
clustered image maps
automated literature
searches
Large Team Project
• “Start” right away
– consider how each topic we cover might relate to project
– organize teams (with my help) that are as diverse as possible
– dilemma: need to know stuff in course to do project, but can’t wait
too long to start
– “solution”: wait a couple weeks before getting too concrete; I will
try to do relevant stuff early; you might need to read-ahead
• In real world, project is driven by bio-medical question, in this course
opportunity to get experience with certain resources is also important
– automated batch processing
– accessing molecular biology databases
– parsing info retrieved from databases
• You can use Java, Perl, C, C++, Visual Basic
– Consult with me i f you need to use a different language
Large Team Project Meta Issues
• democracy versus benign dictatorship
– (“Singapore” model)
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prioritization and compromise
intra-group communication
specialization versus amortization
concrete milestones and evaluation
automated test suite
documentation
maintainability
abstraction
Molecular Biology and Genomics for
Bioinformatics
• major resources
– http://www.ncbi.nlm.nih.gov/Sitemap/index.html
– http://www.genome.gov/page.cfm?pageID=10002096
– http://www.ncbi.nlm.nih.gov:80/books/bv.fcgi?call=bv.
View..ShowTOC&rid=hmg.TOC&depth=1
• specific topics
• http://www.ncbi.nlm.nih.gov/About/primer/geneti
cs_genome.html
• http://www.genome.gov/glossary.cfm?key=gene
• http://www.genome.gov/Pages/Hyperion//DIR/VI
P/Glossary/Illustration/gene2.shtml
Example of UCSC Chromosome
Viewer
• find gene with suitable orientation using NCBI
genome viewer
– http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=45
06066&db=Nucleotide&dopt=GenBank
• copy and paste sequence into UCSC
– http://genome.ucsc.edu/cgibin/hgBlat?command=start&org=Human&db=hg16&h
gsid=28646227
– do this in 2 windows so you can have access to context
in “details” view while navigating in “browser” view
– check out start, stop, intron signals
Homework 1
•Large group project
–virtual or physical group meeting
– evaluate composition of group
–talk about possible project areas
–electronic notes of each weeks meetings
•BLAT
–look at one gene encoded on plus and one on minus strand
of genome
–one of the two will require thinking in terms of reverse
complement
–hint: start off by looking at initiator ATG
•Reading
–chapter 1 and 4 in Li and Graur
•beg, borrow, share, or xerox
–primer on NCBI site