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... |
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| Section A Monday |
Section B Tuesday |
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
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| 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 |
none |
| 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 |
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| Section A Monday |
Section B Tuesday |
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.) |
none |
| Section A Research Abstract 2 - Due Mon. Nov 5, 11 am Section B Research Abstract 2 - Due Tues. Nov 6, 11 am |
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| Nov 5 | Nov 6 | CONFERENCE 2: Oral presentations MAGIC Tool post-survey |
none |
Unit Three: Whole Systems Perspective - Constructing the big picture |
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| Section A Monday |
Section B Tuesday |
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 |
none |
| 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 |
| THANKSGIVING BREAK | none | ||
| 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 |
tba |
| Dec 10 | Dec 11 | CONFERENCE 3: Final Report web site presentation | none |
Davidson Academic Calendar - http://www3.davidson.edu/cms/x7693.xml