BIO 309 - Genomics, Proteomics and Systems Biology
Dr. Haynes - Fall 2007

Lab Schedule

Watson Science Building, Room 247 (the "Big Head" room)

Section A meets every Monday, 1:30 - 4:20 PM
Section B meets every Tuesday, 1:00 - 3:45 PM

Unit One: Genome Sequences - Making sense of ATCG...

Section A
Section B
Research Objectives Pre-lab reading
Aug 27 Aug 29 No lab none
Sept 3 Sept 4 1. Introduction: brief lab guidelines overview
2. Exploring a human contig: summarizing features on your contig using the Ensembl browser
3. Pairwise BLAST: assessing sequence arrangement within your contig using bl2seq
4. Motif hunting: finding unannotated features using JASPAR (position weight matrices)
Web: Ensembl home page


Sept 10 Sept 11 1. Characterizing your favorite gene: general research; protein domain map (hydropathy plot, secondary structure, conserved domains)
2. Cross-species comparisons: finding orthologs; finding conservation across multiple species using ClustalW
Sept 17 Sept 18 1. SNP's: characterizing SNP's using Ensembl and NCBI
2. Oral presentations overview
3. Research wrap-up
Web: Assignment Help Guide (Lab Research Abstract, Lab Research Notes, Lab Research Oral Presentation)
Text: 186 - 187, 192 - 194
Research Abstract 1 - Due Fri. Sept 21, 5 pm
Sept 24 Sept 25 CONFERENCE 1: Oral presentations ----

Unit Two: Genome Expression - Microarrays & proteomics

Section A
Section B
Research Objectives Pre-lab Reading
Oct 1 Oct 2 1. MAGIC Tool pre-survey
2. Using MAGIC Tool: intro. and practice with gridding, data extraction, etc.
Text: Math Minute 6.1, 6.2, 6.3
Web: DeRisi et. al. paper
Web: About MAGIC Tool
Oct 8 Oct 9 1. Choose your experiment: select microarray tiff's
2. Data extraction: gridding, flagging, segmentation, expression profiles
3. Clustering expression profiles: exploring, calculating dissimilarity, clustering
Web: BIO309 Microarray Experiment Resource Page
Oct 15 Oct 16 FALL BREAK, No lab (or work on your own) none
Oct 22 Oct 23 1. Continue work: real data
2. Data mining: answering more questions about your favorite gene using public data
Web: SGD Expression Connection
Oct 29 Oct 30 1. Oral presentations overview
2. Research wrap-up (finalize figures, etc.)
Section A Research Abstract 2 - Due Mon. Nov 5, 11 am
Section B Research Abstract 2 - Due Tues. Nov 6, 11 am
Nov 5 Nov 6 CONFERENCE 2: Oral presentations
MAGIC Tool post-survey

Unit Three: Whole Systems Perspective - Constructing the big picture

Section A
Section B

Research Objectives Pre-lab Reading
Nov 12 Nov 13 1. Building the disease model: review lessons learned from previous Units
2. Human disease gene: review your favorite gene's structure; find 3-D protein structure
3. Protein interactions: explore DIP
Nov 19 Nov 20 1. HiMAP: incorporating other players into your model
2. Cell Designer: building your wild type model
Web: The Human Interactome Map (register before lab!)
Web: Cell Designer
Nov 26 Nov 27 1. Finish your wild type model: Cell Designer
2 . Building the disease model: create a disease model based on the wild type model
3. Final Report web page: Overview
Web: Assignment Help Guide - Lab Research Final Report
Dec 3 Dec 4 1. Filling in the gaps: use your diagram to propose future research
2. Medical challenge: use your diagram to propose a treatment for the disease
3. Research wrap-up
Dec 10 Dec 11 CONFERENCE 3: Final Report web site presentation none

Davidson Academic Calendar -