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@discover.nci.nih.gov downloads of ppt will be archived at http://discover.nci.nih.gov/~barry/CS177/CS177.html

2. Administrative Stuff

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.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

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. 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 List of Major Topics

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 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

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?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/genetics_genome.html • http://www.genome.gov/glossary.cfm?key=gene • http://www.genome.gov/Pages/Hyperion//DIR/VIP/Glossary/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=4506066&db=Nucleotide&dopt=GenBank • copy and paste sequence into UCSC • http://genome.ucsc.edu/cgi-bin/hgBlat?command=start&org=Human&db=hg16&hgsid=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

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