CS 177 Intro to Bioinformatics

1
CS 177Intro to Bioinformatics

• Barry Zeeberg
• NIH/NCI/LMP/GBG
• email
• Use only in emergency
• Subject line GW course
• barry_at_discover.nci.nih.gov
• downloads of ppt will be archived at
• http//discover.nci.nih.gov/barry/CS177/CS177.htm
  l

2
Administrative Stuff
component of final grade
homework 25
quizzes 25
final exam 25
large team project and presentation 25
3
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

4
Web Site

• http//discover.nci.nih.gov/barry/CS177/CS177.htm
  l
• 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

5
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

6
List of Major Topics

• transcription
• translation
• gene structure
• genetic code
• information and entropy
• molecular biology databases

• sequence homology
• basic genomics
• basic biotechnology
• human genome project
• microarrays
• statistics
• disease genes
• clustered image maps
• automated literature searches

7
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 cant 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

8
Large Team Project Meta Issues

• democracy versus benign dictatorship
• (Singapore model)
• prioritization and compromise
• intra-group communication
• specialization versus amortization
• concrete milestones and evaluation
• automated test suite
• documentation
• maintainability
• abstraction

9
Molecular Biology and Genomics for Bioinformatics

• major resources
• http//www.ncbi.nlm.nih.gov/Sitemap/index.html
• http//www.genome.gov/page.cfm?pageID10002096
• http//www.ncbi.nlm.nih.gov80/books/bv.fcgi?call
  bv.View..ShowTOCridhmg.TOCdepth1
• specific topics
• http//www.ncbi.nlm.nih.gov/About/primer/genetics_
  genome.html
• http//www.genome.gov/glossary.cfm?keygene
• http//www.genome.gov/Pages/Hyperion//DIR/VIP/Glos
  sary/Illustration/gene2.shtml

10
Example of UCSC Chromosome Viewer

• find gene with suitable orientation using NCBI
  genome viewer
• http//www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val
  4506066dbNucleotidedoptGenBank
• copy and paste sequence into UCSC
• http//genome.ucsc.edu/cgi-bin/hgBlat?commandstar
  torgHumandbhg16hgsid28646227
• 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

11
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