Bioinformatics

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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

Sites we will use often in class

BIOLOGY WORKBENCH

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

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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