Bio343: Laboratory Methods In Genomics
Spring, 2016
A. Malcolm Campbell

Tentative Syllabus

Class meets 1:40 - 2:55 pm in Chambers 3146 (GAMCo)
Office Hours: M&T 3 - 4 pm; or most anytime by appointment

Learning Goals

Learning Objectives

  1. Define terms used in RNA sequencing and assembly. (knowledge)
  2. Describe a gene based on in-depth analysis of a genome. (comprehension)
  3. Report your findings to the class verbally and to a wider audience in writing. (comprehension)
  4. Explain how transcriptomes reveal which parts of the genome are activated. (comprehension)
  5. Demonstrate computer skills used in modern genomics. (application)
  6. Examine different signaling pathways that lead to cell and tissue growth. (analysis)
  7. Test whether a known pathway is activated in experimental tissue compared to control. (analysis)
  8. Collect and integrate published data with RNAseq data to describe tissue growth. (synthesis)
  9. Evaluate data quality and completeness of signaling pathway activation. (evaluation)
  10. Assess the objectivity and subjectivity used in genomic research. (evaluation)
Bio343 is a lab-only course that is primarily data analysis by computer - everyone must use the Mac OS. Furthermore, every student will have to use computer command line in Unix and R languages. I am very excited about this course. Very few students in the world get to answer an interesting biological question using RNAseq data. It will be a lot of fun to do real genomics research on an invasive species. The Burmese python is decimating the wildlife of the Everglades where it has established itself permanently.

Because this is a research course, we will all have to be flexible in the material we learn. It is impossible to know where this course will take us exactly. I have a rough plan, but nothing firm yet until we see how these projects unfold. If you need a highly structured course, this will not be a good fit for you. Each student will need to learn how to edit a wiki site used for this research project.


Student Collaborators

Required Readings

1) Online web sites

2) Research publications on genomes (PDFs gathered during semester)

3) Course wiki site


Tentative Weekly Schedule

Week of Semester
Subject Matter and Assignments Due
Week 1:
Jan 12 & 14

Week 2:
Jan 19 & 21

Week 3:
Jan 26 & 28
  • Each person outlines his/her project based on literature
  • Word file emailed to Dr. C by start of class
    (graded by Dr. C.)
  • Fixed Gene Names from Todd
Week 4:
Feb 2 &4		 Start working with RNAseq data
What questions to ask? How to answer them?
Correlation Exercise download
Week 5:
Feb 9 & 11

Continue Correlation, Discuss Clustering (Dr. Heyer's PPTx)
Online Clustering Tool
Clustering Self-Test
Can we use BLAST2Go?
Can we assign GO terms to our genes?
What can DESeq do for us?
Would DAVID be helpful?
Week 6:
Feb 16 & 18

Continue working on RNAseq data 

Continue working on RNAseq data
Drs. C and H results from Tuesday
Week 7:
Feb 23 & 25

Continue working on RNAseq data

Continue working on RNAseq data 

null Week
Mar 1 & 3

Spring Break

Spring Break

Week 8:
Mar 8 & 10

Continue working on RNAseq data
Connecting gene names with GO terms (excel file)

Continue working on RNAseq data - finalize plans
Week 9:
Mar 15 & 17

Group oral Presentation #1 with peer review

  • peer feedback is graded by Dr. C.
  • presentation is graded by Dr. C.
Individual status report on RNAseq projects
graded by Dr. C.
Week 10:
Mar 22 & 24

Continue working on RNAseq data
Continue working on RNAseq data
Week 11:
Mar 29 & 31

Easter Break

Continue working on RNAseq data
Week 12:
Apr 5 & 7

Field Trip to Dorcas lab to feed pythons

Assess Status and Agree on Endgame

start working on term research paper (solo author)

Week 13:
Apr 12 & 14

Group oral Presentation #2 with peer review
(first 3 presentations)

  • peer feedback is graded by Dr. C.
  • presentation is graded by Dr. C.

Group oral Presentation #2 with peer review
(second 3 presentations)

  • peer feedback is graded by Dr. C.
  • presentation is graded by Dr. C.
Week 14:
Apr 19 & 21

Keep working on term paper
First draft of final paper due; I will be giving a talk in CA.
Bring Hard Copy to collect comments form peers
submit to Dr. C. for grading of comments (due by 5 pm Friday)
Week 15:
Apr 26 & 28
May 3

Keep working on term paper

fellowships presentation
Dr. C. says thanks for a great class
course evaluations
Final paper due (as Word file) emailed by noon on Reading Day

No Class Optional Tuesday
Final paper due (as Word file) emailed by noon on Reading Day

Grading
Grades will be based on:

The exact nature of the presentations and papers cannot be determined at this point. You will use the course wiki page as an online lab notebook to track your daily progress. Keep in mind that your work will be the foundation that investigators will use for subsequent research so it is important to keep good notes online.

Grading Scale:

Conversion of Percentage to Letter Grade

A = 100 - 94 A- = 93 - 90
B+ = 89 - 87 B = 86 - 83 B- = 82 - 80
C+ = 79 - 77 C = 76 - 73 C - = 72 - 70
D+ = 69 - 66 D = 65 - 60

F = < 59

 

Genomics Lecture Course

Genomics Minor

Biology Department

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Send comments, questions, and suggestions to: macampbell@davidson.edu