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BIO520-Syllabus

(Note, I will try to provide printer-friendly files of ducments that you may wish to print in .doc or .pdf format)

Chuck Staben/257-2161/312 Morgan/ staben@pop.uky.edu Lecture:  M,W 1-2, 312 Whitehall
Tom Badgett/257-2120/312 Morgan/ tcbadg00@pop.uky.edu Lab: F 1-3, Whitehall Computer Microlab (319)

Office hours are by appointment, but we are happy to see you.

This syllabus gives specific times for BIO520-001. BIO520-201 students may proceed at a slightly different rate, although assignments will be due at the same times. If section 001 students miss class, they should plan to watch the broadcast or videotaped lectures.

Minimum computer configuration for a distance learning student is:

Internet capable computer (Intel486 or comparable Mac)
Internet accessibility (computer microlabs or internet service provider)
Netscape Navigator 4.0 or Internet Explorer 4.0 or later
Telnet client (EWAN or Win95 Telnet)/FTP client (WinFTP minimun, CuteFTP or similar recommended)
Additional downloadable software will be needed as described

Each student is expected to have and to monitor an e-mail account. Students will be provided with SeqWeb and seqanal.mi.uky.edu UNIX accounts as needed. Each student is expected to subscribe to the class listserv: BIO520@lsv.uky.edu and/or to monitor the corresponding. newsgroup. Students should bring a 1.4 Mb diskette to each lab session.

Grading: Grades will be based upon performance on assignments submitted on time. Each student will be expected to participate in the class project. Failure to participate fully in this project will result in a reduction in grade AND will prevent credit in the event of publication.

Attendance during lecture is not mandatory, but participation in lab sessions is mandatory for section 001 students. Net-discussion is mandatory for section 201 students. Students may collaborate on assignments in general terms, but they should individually complete each assignment. Exams are to be done individually.

You will have a simple assignment almost every week, except for exam and project weeks. This assignment will be the primary subject of that Friday’s lab meeting. The results are due at the beginning of the following class (Monday). You will lose 10 points each day late.

Each assignment is worth 10 points. The take-home exam is worth 30 points. The final exam is worth 40 points. The final project is worth 50 points. Grades will be no worse than the standard 90/80/70/60 scale, but I reserve the right to liberalize grades to achieve a distribution more typical of a graduate/undergraduate class.

Text: At this time, there is no text recommended for this class. Indicated readings will be put on reserve as indicated on the syllabus and in class. The biology in this class is covered best by:

Genes IV, Lewin
Introduction to Protein Structure, Branden & Tooze

DATE

TOPIC

READING

August 26 Bioinformatics-Intro  
August 28 Computer Skill Session  
August 31 Biological Principles  
September 2 Genes and Genomes  
September 4 DNA Sequences: Access/Formats  
September 7

LABOR DAY

September 9 DNA sequence manipulation  
September 11 DNA sequence manipulation  
September 14 Gene Finding  
September 16 Gene finding/Consensus Sequences  
September 18 Gene Identification  
September 21 Protein Structure  
September 23 Protein Structure and Characterization  
September 25 Protein viewing/interpretation  
September 28 Protein sequence alignment  
September 30 Database/Multiple alignment  
October 2 Protein sequence alignment  
October 5 Alignment interpretation  
October 7 Protein sequence analyses  
October 9 Protein sequence analyses  
October 12

FALL BREAK

October 14 RNA structure prediction  
October 16 EXAM1  
October 19 Protein structure prediction  
October 21 Protein structure prediction  
October 23 Structure prediction: RNA and protein  
October 26 Evolutionary Biology  
October 28 Evolutionary Biology  
October 30 Evolutionary Inference  
November 2 Genome Sequencing  
November 4 Physical Mapping  
November 6 DNA sequence acquisition  
November 9 Trait mapping  
November 11 Candidate genes/QTLs  
November 13 Relational databases/Entrez  
November 16 Transcriptomes  
November 18 Proteomes  
November 20 Genome Projects/WWW resources  
November 23 Knockouts/Assorted genome projects  
November 25 Genome-wide analyses  
November 27

THANKSGIVING HOLIDAY

November 30 Medical informatics  
December 2 Applications of bioinformatics  
December 4 Scripting/database usage  
December 7 Project discussions  
December 9 Project Discussion  
December 11 Project Discussion  
December 18

FINAL EXAM, 1-3 PM

 

University of KentuckyMorgan School of Biological SciencesNSF-CCD Support wpe1.jpg (5798 bytes)Chuck Staben, copyright reserved || 09/21/98