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 Bioinformatics

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           

Sites we will use often in class

 

Syllabus J-Term 2013

Format:

2 Credits.  4-1/2  hours per day, Jan 4-15.  15 Wing            

Instructors:      

Unit 1-2        Bonnie Bratina (Microbiology)        bbratina@uwlax.edu                785-6994

Unit 3          Mike Abler (Biology)                       mabler@uwlax.edu                  785-6962

Unit 4          Anton Sanderfoot (Biology)             asanderfoot@uwlax.edu           785-8240

 

UNIT 1     Introduction to Databases and Alignments

Mon., Jan 7 Unit 1: Databases and Introduction to Alignment
Course overview; background in molecular biology, databases and
alignments  Lab 1A & 1B

UNIT 2     RNA

Tues., Jan 8

Quiz 1       Unit 2: Phylogenomics using ribosomal RNA as model molecule
Overview of phylogeny, identification of organisms using SSU rRNA.
Aligning multiple sequences and high throughput sequencing
Lab 2.1 & 2.2

Wed., Jan 9 Aligning multiple sequences and high throughput sequencing (cont.)
Creating and interpreting phylogenetic trees  Lab 2.2 (con't) & 2.3

UNIT 3     Genomes

Thurs., Jan. 10 Quiz 1                                                                                                                    
Unit 3: Genomics
Genomes, mapping and gene discovery  Lab 3.1
Fri., Jan. 11 Comparative genomics  Lab 3.2
Mon., Jan. 14 The transcriptome, mapping gene expression Lab 3.3
Take Home 1 due

 

UNIT 4     Protein Structure

Tues., Jan. 15

                   Quiz 2
Work Day

Wed., Jan. 16 Unit 4: Proteomics/Reactomics/Signal Transduction
Protein Structure and Domains
Homology and Paralogy  Lab 4.1
Thurs., Jan. 17 Take Home 2 due
Protein-protein Interactions and Signal Transduction Lab 4.2
Fri., Jan. 18 Quiz 3
Introduction to Docking and work day  Lab 4.3
Mon., Jan. 21 MLK Day No class
Tues., Jan. 22 Group project presentations for Unit 4 (50 pt)

             

 

Syllabus Spring 2013

Format:

2 Credits.  2:15- 5:20, Tuesday and Thursday, 15 Wing (7-week course)             

Instructors:        

Unit 1-2           Bonnie Jo Bratina (Microbiology)      bbratina@uwlax.edu               785-6994

Unit 3-4              Anton Sanderfoot (Biology)               asanderfoot@uwlax.edu         785-8240

Date:

Topic

Labs:

Jan. 29

Unit 1: Databases and Introduction to Alignment

Lecture: Course overview; background in molecular biology, databases and alignments

Lab: Using databases and aligning 2 sequences

Lab 1A & 1B

 31

Unit 2: Phylogenomics using ribosomal RNA as model molecule       

Lecture: Overview of phylogeny, identification of organisms using SSU rRNA.

Lab: Using the Ribosomal RNA Database Project (RDP)

Lab 2.1

 

Feb. 5

Lecture: Aligning multiple sequences and high throughput sequencing

Lab: Performing a MUSCLE alignment of rRNA sequences

 

Lab 2.2

7

Lecture: Creating and interpreting phylogenetic trees

Lab: Performing a Phylogenetic Analysis

Lab 2.3

12

Quiz on Unit 1&2 (35 points)

Lab: Open time to work on Take Home Project

Lab 2.3

14

Unit 3: Genomics

Lectures: Genomes, mapping and gene discovery

Lab: Using a genomic database

Lab 3.1

19

Lecture: Comparative genomics

Lab: Finding genes in genomes

Unit Project #1 due (50 pt)

Lab 3.2

21

Lecture: The transcriptome, mapping gene expression

Lab: Extracting expression data from microarray databases

Lab 3.3

26

Quiz on Unit 3 (25 points)

Unit 4: Proteomics/Signal Transduction

Lecture: Protein Structure and Domains

Lab: Searching for domains and motifs in proteins

Lab 4.1

28

Lecture: Homology and Paralogy

Lab: Introduction to 3D visualization and imaging protein structures

Lab 4.2

Mar. 5

Lecture: Protein-protein Interactions

Lab: Measuring distances in proteins, practice docking proteins

Unit Project #2 due (50 pt)

Lab 4.3

Lab 4.4

7

Signal Transduction

Lab: Work Time for Projects

 

12

Quiz on Unit 4 (35 points)

Lab: Work Time for Presentations

 

14

Presentations for Unit Project #3 (40 pt)

 

                                         

 

Grading:  Quizzes:                                        95                 92-100% = A         

                 Unit projects:                              140                 88-92%   = AB     

                 Lab exercises, cumulative points    20                  81-88%   = B  

                 Total:                                          255                 77-81%   = BC      

                                                                                           70-77%   = C        

                                                                                           60-69%   = D

Any student with a documented disability (e.g. physical, psychiatric, vision or hearing, etc.) who needs to arrange reasonable accommodations must contact the instructor and the Disability Resource Services Office (165 Murphy Library, 785-6900) at the beginning of the semester. 

                                        

           

   

 
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