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Bioinformatics
BIO/MIC 440/540 The term bioinformatics is often used as a synonym for "biocomputing" or "computational biology". This field uses computers to study living systems and applies computer science and information technology to biological problems. Much of the data analyzed in bioinformatics is molecular in nature, i.e. the sequence of nucleotides in DNA or RNA, or the amino acids in a protein. Being able to manipulate and study this information is the basis for the current revolution in Biotechnology. Students with a strong background in bioinformatics will have many job opportunities in both corporate and academic settings. This course also gives students an opportunity to see the relationships between biology, microbiology, chemistry and computer science. J-term Syllabus Spring Syllabus Grading J-Term Grades
Sites we will use often in class
Format: 2 Credits.
4-1/2 hours per day, Jan 4-15.
150 Murphy
Instructors: Unit 1
Mike Abler (Biology)
abler.mich@uwlax.edu
785-696 Unit 2
Mike Abler (Biology)
abler.mich@uwlax.edu
785-69 Unit 3
Mike Abler (Biology)
abler.mich@uwlax.edu
785- Unit 4
UNIT 1 Introduction to Databases and Alignments
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Format: 2 Credits.
2:15- 5:20, Tuesday and Thursday, 150 Murphy Library (7-week
course)
Instructors:
Unit 1-2
Bonnie Jo Bratina (Microbiology)
bbratina@uwlax.edu
785-6994
Unit 3
Nicholas Downey (Biology)
ndowney@uwlax.edu
785-6975
Unit 4
Anton Sanderfoot
(Biology)
asanderfoot@uwlax.edu
785-8240
Date
Topic
Unit 1: Databases and Introduction to Alignments
Jan. 24
Course overview; background in molecular biology, databases and
alignments
Unit 2: Phylogenomics using ribosomal RNA as model molecule
Jan. 26
Overview of phylogeny,
identification of organisms using SSU rRNA.
Jan. 31
Aligning multiple sequences and high throughput sequencing
Feb.
2
Creating and interpreting phylogenetic trees
Unit 3: Genomics
Feb.
7
Quiz 1
(25 pt, Unit 1 & 2)
Genomes, mapping and gene discovery
Feb.
9
Comparative genomics; Take home
project for Unit 2 due (50 pt)
Feb. 14
The transcriptome, mapping gene expression
Feb. 16
Introduction to the methylome
Unit 4: Proteomics/Reactomics/Metabolomics
Feb. 21
Quiz 2
(25 pt, Unit 3)
Introduction, signal transduction, protein structure and domains
Feb. 23
Protein interactions and docking of structures;
Take home project for Unit 3 due (50 pt)
Feb. 28
Examples of docking and comparisons to known structures
Mar.
1
Introduction to the “reactome” and building pathways
Mar.
6
Quiz 2
(25 pt, Unit 4)
Group work day to prepare for project presentations
Mar.
8
Group project presentations for
Unit 4 (50 pt)
Grading:
Quizzes 25 points each (x3) Unit projects 50 points each (x3) Lab exercises, cumulative points 20 points Total 245 points
A 92-100%
AB 88-92%
B 81-88%
BC 77-81%
C 70-77%
D 60-70% |
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