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Some notes for a Ph.D.

Notes written by Malin Pinsky, 2013-2024

Skills to develop

My goal is to help you understand and succeed in our discipline as it is now, while also empowering you with the agency to reshape it in the image of all of us.

  • project design
  • data analysis and interpretation
  • oral presentation: see Scientific presentation tips (to add)
  • grant-writing
  • manuscript writing
  • collaborating and networking in academia
  • teaching
  • peer reviewing

(see our onboarding guide for resources)

Expectations/Milestones

  • Throughout
    • Participate in the community and build your professional network
      • attend all seminars, meet most or all speakers, come to lab meetings, work from CBB
        • Contribute to the community: clean up after yourself, do maintenance, do chores, etc.
      • Reproducibility for collaboration with future self, with others in lab, with others outside lab (see the Data Management Guide)
      • Practice any talks and present any posters to the lab, before you take them to a conference
    • This is will be substantially more work than a 9-5 job or taking classes as an undergraduate or MS student
  • First year
    • First meeting topics
      • Expectations for me from you
      • Expectations for you from me
      • Your expectations for the PhD experience
        • What you want to learn from the PhD
      • Where your are tentatively heading
      • First year project?
      • If you have fears, concerns, questions, or just want to talk, please come find me. If you’re upset with me, please tell me.
    • Apply to fellowships (fall)
    • First year talk (lab meeting or other venue)
    • Start and perhaps finish a first year project that is publishable (begin and perhaps finish writing)
    • Attend a conference, present a poster or tal
    • Comprehensive exam on the first-year courses
  • Second year
    • Write draft dissertation proposal by January
    • First year paper submitted
    • Attend a conference, present
    • Write dissertation proposal and defend it, “Qualifying exam"
  • Third year
    • If not done, finish dissertation proposal and defend it, “Qualifying exam"
    • Continue research
    • Attend a conference and present
  • Fourth year
    • Continue research
    • Submit papers
    • Attend a conference and present
  • Fifth year
    • Finish research
    • Submit remaining papers
    • Defend dissertation
      • At least 6 weeks in advance of defense: last draft of dissertation chapter to Malin. Others must already be done.
      • Defense date is tentative until
        • Full dissertation written
        • At least 2 chapters submitted for publication
        • All chapters comply with our Data Management Plan
    • Attend a conference and present
    • Apply for postdoc fellowships (fall) and contact potential mentors, or network and do informational interviews for non-academic opportunities

6-Month Check-ins

At the end of the fall and spring, we take a meeting to step back from the details and think about big picture career trajectories. It’s a good chance to go back the goals you wrote for yourself, think about your progress, and think about whether they’re still the right goals for you. Please start a running document of your goals in our Google Drive (how_we_work/Group_member_goals/, make a copy of the template and add your name to the title) and share it with Malin.

This is your meeting to use as you want, but I often find it useful to loosely structure the meeting like this:

  • First 1/3: Highlights from the semester/last six months:
    • What have you done?
    • What have you learned?
    • What connections have you made?
  • Last 2/3: Plans for the next six months:
    • What do you want to do?
    • What do you want to learn?
    • What connections do you want to make?
    • How can I support you in that?
  • Also let me know if you want me to think about answers to any questions.
  • Funding plan during each end-of-year checkin

Training resources

Course ideas

  • At UCSC
    • Stats and applied math
      • STATS 206 Applied Bayesian Stats (with David Draper) (can get permission to skip prereqs)
      • STATS 203 Introduction to Probability Theory
      • STATS 204 Introduction to Statistical Data Analysis (includes some R)
      • STATS 206B Intermediate Bayesian Stats
        • EART125 - Statistics and Data Analysis in the Geosciences (Matthew Clapham)
        • OCEA 267 Applied Environmental Time Series Analysis (Claudie Beaulieu)
  • Off campus
    • Stats
      • https://www.statstree.org/
      • Tyre, ecological statistics in R, online, University Nebraska Lincoln
      • Biostats suggestions from Ecology
      • Two recommended stats books from economics
        • Pindyck, R.S., Rubinfeld, D.L., 1998. Econometric Models and Economic Forecasts, 4th ed. McGraw-Hill New York, NY
        • Cameron, A.C., Trivedi, P.K., 2005. Microeconometrics methods and applications. Cambridge University Press, NY
      • Coursera
        • Brian Caffo, Mathematical biostatistics boot camp 1 and 2
          • 7 weeks, taught several times per year
          • Recommended by: Columbia Univ PhD student: The teacher and format are very good. But it is pretty elementary; covers what you would learn in a rigorous basic stats course (comment on boot camp 1)
        • Roger Peng, Computing for data analysis
          • in R, generally taught Sept, 4 weeks
          • Recommended by: Tia-Lynn Ashman lab member says excellent, pretty hard, 10-15 hrs per week, covers both data management and stats
        • Jeff Leek, Data analysis
        • John McGready, Statistical Reasoning
          • seems to be not available every time I check. aimed at public health
          • Recommended by: Brian Caffo, fantastic course
        • Note: Peng and Leek are collaborators, both at Johns Hopkins. They additionally teach the below but Rae Winfree has not found out more on these courses:
          • R programming
          • Getting and cleaning data

Funding ideas

Conference ideas

  • American Society of Naturalist (January)
  • Species on the Move
  • International Biogeography Society Meeting
  • Gordon Conference in Marine Global Change (July)
  • Ecological Society of America (August)
  • Evolution (June)
  • Effects of Climate Change on the World's Oceans (ECCWO) (ICES/PICES): next to be in 2027 or 2028
  • American Genetics Association
  • American Fisheries Society
  • Western Society of Naturalists
  • Benthics
  • specialized
    • Western Indian Ocean Marine Science Assoc (WIOMSA)
    • Asian Pacific Coral Reef Society (APCRS)

Awards

  • ASN Jasper Loftus-Hills, <3yrs from PhD, Jan 31
  • ESA Early Career Fellow
  • ICRS Awards (Feb. 15)

Postdoc funding

  • Life Sciences Research Foundation: open to non-US citizens, 3 years, network-building
  • NSF
  • David H. Smith
  • Liber Ero
  • Fulbright
  • iDiv fellowships
  • HIFMB (Helmut Hillebrand center in Germany)
  • SESYNC postdocs
  • Institutional fellowships
    • UT Austin integration biology
    • U Michigan
    • UC Berkeley
    • Harvard sustainability
    • UVM Voss Postdoctoral Fellows
      • others...
  • Policy
    • AAAS Science-Policy Fellowship
    • Knauss Marine Policy Fellowship
  • https://asntech.github.io/postdoc-funding-schemes/

Training suggestions

  • Leadership
    • USFWS National Conservation Training Center
  • Communication
    • COMPASS
  • TULIP summer school on interdisciplinary ecology
  • SIIECS: early career society of ICES
  • Michigan State University Kellogg Biological Station - Jennifer Hoey enjoyed them. Not offered every year? - Part of CIC (Committee on Institutional Cooperation), so Rutgers students get an "in"
  • Santa Fe Institute's Complex Systems Summer School

Jobs