BIO 384C, Fall 2015

This is the home page for class BIO 384C, Subjects and Skills for Graduate Students in the Biological Sciences.

Syllabus and schedule: BIO384C_syllabus_fall2015.pdf

Lectures

1. Aug. 27, 2015 – Overview of course goals and materials
(Ochman, Wilke)

Readings:

• Gu and Bourne, 10 Rules for graduate students
• Watson, Succeeding in science

2. Sep. 1, 2015 – Becoming a better writer: Avoiding the official style
(Wilke)

• Reading assignment: Blog post on official style
• In-class worksheets:
  • Exercise 1
  • Solutions to Exercise 1
  • Exercise 2

3. Sep. 3, 2015 – What makes for good writing and a good abstract?
(Ochman)

Readings:

• Bargmann, Decisions
• Brenner, Graduate student

4. Sep. 8, 2015 – Becoming a better writer: Topic and stress position
(Wilke)

• Reading assignment: Blog post on topic and stress position
• Lecture slides
• In-class worksheets:
  • Exercises and solutions

5. Sep. 10, 2015 – How to prepare a grant application or research proposal
(Ochman)

Readings:

• Pinker, Why academic writing stinks
• King and Wilson, Evolution at two levels

6. Sep. 15, 2015 – Copy-editing text
(Wilke)

• Lecture slides
• In-class worksheets:
  • Exercises and solutions

7. Sep. 17, 2015 – The Hook: Setting up the problem
(Ochman)

Readings:

• Alon, How to choose a good scientific problem
• Schwartz, The importance of stupidity

8. Sep. 22, 2015 – Outline for a Specific Aims page
(Wilke)

• Reading assignment: Blog post on critical need
• Additional materials:
  • Proposal writing handout
  • Example grant application

9. Sep. 24, 2015 – Punctuation
(Ochman)

Readings:

• Zimmer, Inuit Study Adds Twist to Omega-3 Fatty Acids’ Health Story

10. Sep. 29, 2015 – Outline for a Specific Aims page, Part II
(Wilke)

• Lecture slides
• In-class worksheets:
  • Exercises and solutions

11. Oct. 1, 2015 – Combining writing style with writing contents: Thinking about the Specific Aims
(Ochman)

Readings:

• Brenner, On Publications
• Bourne, Ten simple rules for getting published

12. Oct. 6, 2015 – Writing a scientific paper
(Wilke)

• Reading assignments:
  • Blog post on when to start writing a scientific paper
  • Blog post on how to write a scientific paper
• In-class exercises:
  • Universal paper outline
  • Parmley et al., PLOS Biol 2007
  • Musacchia et al., PNAS 2007

13. Oct. 8, 2015 – Evaluating scientific productivity
(Ochman)

Readings:

• Hirsch, Index to quantify scientific research output
• Claus Wilke blog post on h index

14. Oct. 13, 2015 – Factors to consider when making figures
(Ochman)

• Lecture slides

15. Oct. 15, 2015
(Ochman)

16. Oct. 20, 2015 – Making figures with R
(Wilke)

• Download R from here: http://cran.r-project.org/
• Download RStudio from here: http://www.rstudio.com/products/rstudio/download/
• General R tutorial (read Sections 1-3): http://www.cyclismo.org/tutorial/R/index.html
• Lecture slides
• In-class worksheet:
  • html version
  • R Markdown version
  • solutions

17. Oct. 22, 2015
(Ochman)

18. Oct. 27, 2015 – Making figures with R, Part 2
(Wilke)

• Lecture slides
• In-class worksheet:
  • html version
  • R Markdown version

19. Oct. 29, 2015 – Giving presentations
(Ochman)

Readings:

• Alon, How to give a good talk
• Roty, Giving a talk

20. Nov. 3, 2015 – Giving presentations
(Wilke)

• Lecture slides

21. Nov. 5, 2015 – Student presentations
(Ochman)

22. Nov. 10, 2015 – Student presentations
(Ochman)

23. Nov. 12, 2015 – Student presentations
(Ochman)

24. Nov. 17, 2015 – Student presentations, parallel structure
(Wilke)

• Lecture slides
• In-class worksheet & solutions

25. Nov. 19, 2015 – Avoiding Jargon
(Ochman)

Readings:

• Baker, The ‘Omes Puzzle
• Young, Rant against Jargon
• Petsko, No place like Ome

26. Nov. 24, 2015 – Significance & Innovation, figure captions
(Wilke)

• Lecture slides

Readings:

• NIH criteria for significance and innovation

Assignments (please read carefully!):

• 2-page research proposal (due Dec. 1)
• Proposal review form (will be used to rank your proposal)

27. Dec. 1, 2015 – Proposal review
(Wilke)

• Review assignments

28. Dec. 3, 2015 – Mock review panels
(Ochman, Wilke)