Schumer lab:Grad program

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Overview

Here is some information compiled to help make the degree progress process as smooth as possible!

  • A Stanford requirement is that you take 3 units with 4 faculty. One of those sets of units will be your first year seminar class with Marc, another will be units you take for research credit with Molly. Since you have to teach twice, it is super important that you make sure to record these units with **other** faculty that are not Marc or Molly
  • This is not an issue if you are also taking additional courses

Courses

Note: Taking the full version of a course is usually the best way to learn the material. But if the workload seems like too much, you can usually audit and be exposed to the material with much less effort.

Compiled here is a list of classes that members of the lab have taken and any relevant information:

  • BIO105A/B: Ecology and Natural History of Jasper Ridge Biological Preserve with Rodolfo Dirzo and Jorge Ramos
    • A two-quarter field-based course that takes place one afternoon per week at Jasper Ridge (transportation is provided)
    • Each week centers on a different aspect of Jasper Ridge: geology, soils, plants, trophic and community ecology, mammals, herpetofauna, fishes, plus research history and archaeology
    • Students propose and carry out a small independent research project in the Ridge, then present their findings at the end of the second quarter.
    • Completing both quarters certifies you as a Jasper Ridge docent, which gives you free access to the Ridge and the ability to bring others on hikes there.
    • Good for those looking for inspiration on local research projects, or who want to be more connected to Bay Area nature.
  • BIO 287A: Advanced Topics in Mathematical Evolutionary Biology with Noah Rosenberg
    • A mostly peer-taught seminar course: each lecture is given by a student and is based around an important paper in theoretical biology
    • Your responsibility in the course is to read one paper in enough depth to present it to the rest of the class, and to read the papers others choose in enough depth to follow along
    • The course ends with a final paper in the same style as the presentations: pick a paper and explain its main insights, plus what makes it important to the field.
    • Can be rough depending on the particular papers that people pick, but is in forcing you to go in-depth on the math that underlies the field, and that you would probably skim over if you were reading papers in another context.
  • BIO 296: Teaching and Learning in Biology with Jamie Imam
    • A weekly workshop class designed to help students be more effective teachers and TAs
    • Through in-class activities and light homework assignments, learn techniques for communicating clearly, keeping all students engaged, and continually improving your classroom.
    • Recommended to take at the same time as your first TAship, as many of the class activities are meant to be brought into the classroom where you're teaching.
  • BIO 302-304: Current Topics and Concepts in Population Biology, Ecology, and Evolution with Marc Feldman and Larry Bond
    • AKA Professor Parade AKA Pizza Party
    • A weekly seminar featuring a professor or an outside academic who happens to be visiting the department that day. Also featuring pizza.
    • Good socializing and free food, no responsibilities except skimming the paper that the speaker may or may not recommend.
  • BIO 313: Ethics in the Anthropocene with Liz Hadly
    • A weekly ethics seminar with a focus on topics relevant to ecology, evolution, and conservation biology
    • Subjects include different ways of deciding what has value, what is right and wrong, and who gets to set the standards for society
    • Students are only responsible for doing the readings and being ready to discuss them in class.
    • Seems to be slightly more of a time-commitment than the CMOB-oriented ethics class (since that one is only one day), but is more relevant to issues outside of research misconduct and lab animal welfare.
  • BIO 386: Conservation and Population Genomics with Liz Hadly and Stephen Palumbi
    • A weekly seminar centered discussing subjects relevant to conservation biology and genomics.
    • Students work in small groups to prepare a presentation about a topic of their choosing, choose papers relevant to the subject for everyone to read, then present for half the class before leading a discussion on the topic.
    • Relatively low-commitment and a good way to be exposed to a wide variety of subdisciplines related to conservation.
  • BIOS 221: Modern Statistics for Modern Biology with Susan Holmes (and sometimes Wolfgang Hüber)
    • A hands-on crash course in the methods commonly used in biology publications today.
    • Structured around Susan's awesome statistics textbook of the same name, which is available free online: https://web.stanford.edu/class/bios221/book/
    • Responsibilities include weekly lectures and R labs (no grades, just exercises), plus a self-directed final project in which you analyze a real biological dataset using one or more of the ideas discussed in class.
    • Highly recommended for an overview of differential expression analyses, mixed models, clustering, machine learning, etc. with the chance to say how they're implemented in R
  • BIOS 227: Mass Spectrometry and Proteomics: Opening the Black Box with Parag Mallick and Sharon Pitteri
    • A mini-course covering the fundamentals of proteomics and mass spectrometry
    • Subjects include mass spectrometry instruments and sample preparation, data processing, protein identification, quantitation, and other new applications
    • Responsibilities include lectures three days a week, plus (ungraded) labs, and a final presentation on a proteomics paper of your choosing
    • A nice proteomics crash course with two very effective instructors, but with big time commitments for the two weeks that it takes place
  • BIOS 267: Proteomics, Protein Interaction Maps, and Systems Biology with Peter Jackson
    • A mini-course centered on proteomics as it applies to the study of protein-protein interactions (PPI) and systems biology
    • Subjects include mass spectrometry techniques, molecular and computational tools for detecting and visualizing PPI, and applications to biomedicine
    • Only assignment was a very open-ended final project visualizing a PPI dataset in Cytoscape to form a hypothesis and devise a rough experiment to address it.
    • Lectures are pretty disorganized, but I did learn something about PPI and Cytoscape that has helped me since
    • Low commitment for a mini-course, but the fact that involves no work means you don't get much out of it
  • CME 193: Introduction to Scientific Python with Anjan Dwaraknath and Arun Jambulapati
    • A workshop course teaching basic Python in a STEM context
    • Subjects include a brief review of programming fundamentals (variables, control flow, etc.), object-oriented programming, data science in Pandas, plotting, and machine learning basics
    • Probably ideal for those with some programming experience but who want practice in Python; a steep learning curve for those with no programming experience, but doable; experienced Python programmers will probably be bored
  • GENE 211: Genomics with Gavin Sherlock and Michael Cherry (3 units)
    • A hands-on introduction to the field of genomics with lectures, paper discussions, and labs
    • Topics include the molecular biology and engineering of dominant sequencing platforms, assembly algorithms, genome browsers, and biological applications
    • Problem sets teach how to manipulate genomic data through Python (some prior experience recommended) and web interfaces


Courses that lab members have not taken but have heard good things about:

  • BIO 202: Ecological Statistics with Leslie Decker and Tad Fukami
  • BIO 208: Spanish in Science/Science in Spanish with Rodolfo Dirzo
  • BIO 305: Managing your PhD with Fio Micheli and Jose Dinneny

Yearly requirements

  • Make sure to complete your IDP with Molly each year and submit it on GST
  • Make sure you are signing up for research credits as needed to accumulate 135 units by your fourth year. Talk to Student Services about your plan for this

First year

  • First year committee meeting
  • First year paper
  • First year talk

Quals

For EcoEvo you are expected to prepare the following:

  • 40-50 minute presentation of your dissertation plan and preliminary results. Be prepared to be stopped for questions, the whole presentation with questions will take about two hours.

Schedule at least one practice with Molly and at least one practice with the lab

  • A written document describing your plan for each chapter. This should include 3-4 chapters, each expected to result in a publication.

Plan to have this written document completed >1 month before your qualifying exam. Molly will give you multiple rounds of comments. You should also schedule one-on-one meetings with each member of your committee ~2 weeks before your qualifying exam and send them this document a few days before. This way you will be able to incorporate their feedback before your exam.


There are example qualifying exam proposals and presentations in Box, check them out:

/Box/Schumer_lab_resources/Shared_lab_resources/Example_quals_proposals

Other important info

  • One you advance to candidacy you have a 6 year window to graduate
  • This can include up to 8 quarters on leave

Reading committee & Defense

  • Your reading committee must include four faculty (including Molly)
  • You can have external people (non-University) on your reading committee, but you need to fill out a form that you can get from the Student Services office and send in the external member's CV
  • For your actual defense you will need a 5th person outside of the department. This is often difficult to arrange so start thinking about and asking people it early!
  • People in Biology frequently ask faculty in Genetics but it can be any non-Biology department