1. Victoria Prince
  2. Professor and Dean for graduate affairs
  3. Reproducibility and rigor in quantitative biology: a hands-on approach
  4. https://biosciences.uchicago.edu/content/mbl-bootcamp
  5. University of Chicago
  1. Stefano Allesina
  2. https://allesinalab.uchicago.edu/
  3. Professor
  4. Reproducibility and rigor in quantitative biology: a hands-on approach
  5. https://biosciences.uchicago.edu/content/mbl-bootcamp
  6. University of Chicago
  1. Stephanie Palmer
  2. Associate Professor
  3. Reproducibility and rigor in quantitative biology: a hands-on approach
  4. https://biosciences.uchicago.edu/content/mbl-bootcamp
  5. University of Chicago
Public Discussion
  • Icon for: Victoria Prince

    Victoria Prince

    Lead Presenter
    May 12, 2019 | 07:42 p.m.

    Welcome to our video!  The University of Chicago QBio@MBL boot camp has now run a total of four times, twice as part of our funded NRT IGE award.  Our final funded session is scheduled for September 2019.  We follow up on our bootcamp with a Winter/Spring quarter "Responsible, Rigorous, and Reproducible Conduct of Research; R3CR" course, which includes refresher training in the open source language 'R' and workshops with a focus on reproducibility as well as content focused on responsible conduct of research (aka Ethics).  A major goal is to ensure students retain learning gains from boot camp. 

    We welcome discussion about boot camp formats in general, and how to capitalize on initial learning gains.  We also have a major focus on team building, and would love to hear from other groups interested in this topic.   

    We look forward to hearing from you, and we hope you enjoy our video!

    Vicky Prince, Stephanie Palmer & Stefano Allesina

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  • Icon for: Alex Rudolph

    Alex Rudolph

    Facilitator
    May 13, 2019 | 01:02 p.m.

    Very nice video and project addressing a clear need! I am particularly excited to see that this is happening at my own PhD institution (in Physics). You did a very nice job talking about the problem (lack of quantitative skills among biologists and the reproducibility crisis in science) and the approach you take to address it. I have a couple of questions:

    1) For outcomes, you mention that students who participate in the boot camp do retain their knowledge afterwards. Can you say a bit more about how you test that and how long after the end of the boot camp that occurs? Do you intend to follow boot camp participants longer to see if the experience informed their PhD thesis? What other outcomes can you measure?

    2) We have found in our own boot camps and cohort building experiences that social events allowing participants to get to know each other outside the formal part of the experience helps create a long-lasting impact on participants. Did the marine biology cruise you mentioned accomplish that? How do you know? Did you do anything else to promote peer interaction and learning?

    3) You mention that you take students to MBL. How do you plan to make the program sustainable after the grant funding ends? Will the University help?

    4) What are your plans for disseminating your work so other universities can replicate it? Do you have any plan to reach out to help underrepresented minority students benefit from your program?

     
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  • Icon for: Victoria Prince

    Victoria Prince

    Lead Presenter
    May 13, 2019 | 08:52 p.m.

    We have tested boot camp participants immediately after their experience and then again after another 1.5 years.  The tests are "quiz" based, with problems designed to evaluate boot camp concepts.  As might be expected, we find the biggest learning gains in those students who came in with the most limited knowledge.  Importantly, gains are retained in the long term (although this may additionally be related to subsequent instruction and experience).  It is a good idea to address impact on PhD theses - we will have to think about how to do that.  The other broad outcomes we measure are self-assessed confidence in, and familiarity with, quantitative approaches, and the extent of student interactions with other students outside their home program.

    Question 2: My last response above begins to respond to your second question.  We are very intentional about team building.  We engineer teams such that no two students are from the same graduate program.  We start the week with team building ice breaker games, and we ask the students to evaluate and discuss their "styles" as collaborators.  They also establish team compacts on he first evening. We use daily "challenges" is to encourage a fun rivalry and a team spirit, this is fostered further with team temporary "tattoos" (that students like to swap), course tea-shirts, and prizes for the team that does best in the daily challenges, but also for the team that shows the best team spirit.  We evaluate whether this works by asking the students about their network in their annual reports - we are still evaluating that data - and we have also had our consultant evaluator interview their program chairs.  The interviews have revealed that the student's programs are convinced that they have formed a supportive and cohesive network.

    Question 3: How we will sustain the program? This is still a work in progress.  We hope to obtain University and Divisional support, but are also interested in philanthropy and industry sponsorship.  The number of our graduates going into data science careers is now quite significant (11% of graduates in the last 5 years) suggesting that we are developing a useful pipeline to industry that may be considered worthy of support.

    Question 4: I have talked about the program at the AAMC Graduate Education and Teaching (GREAT) Annual Meeting, and have been invited to speak at the upcoming “Transforming the Learning Environment in Biomedical Education” symposium at the University of Nebraska Medical Center (UNMC).  We also plan to publish our findings next year, once the funding comes to a close.  All our students attend the boot camp, and we are pleased to have a diverse class that this year includes 16 students from under represented backgrounds.  We have also developed a new mechanism to ensure underrepresented students are encouraged to return to the MBL for educational courses, and that they have access to funds to help support such training.

    Thanks for the great questions!

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    Alex Rudolph
  • Icon for: Molly Phillips

    Molly Phillips

    iDigBio Education, Outreach and Diversity Coordinator
    May 13, 2019 | 03:16 p.m.

    This is a really exciting program! We (iDigBio) are involved in workforce development throughout the data pipeline for natural history collections professionals and biodiversity data scientists. We are also working with BLUE (Biodiversity Literacy in Undergraduate Education) to incorporate more biodiversity data skills in the undergraduate curricula, but we do not normally reach people transitioning from undergrad to a graduate program. I would think this would be a really great time to reach emerging professionals though and we would love to learn more.

    I am interested in your answers to 3, and 4 of Alex's questions above because it would clarify some paths that we could potentially work with you, and/or build off of your programs. Have you connected their marine collecting experience in the beginning of the boot camps back to natural history collections data in the workshops? Our program is really interested in these types of "field to database" trainings.

     
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  • Icon for: Victoria Prince

    Victoria Prince

    Lead Presenter
    May 13, 2019 | 08:58 p.m.

    Our 18 graduate programs are extremely broad (see https://biosciences.uchicago.edu/programs).  They span from immunology to computational neuroscience, from ecology to molecular biophysics, from developmental biology to public health sciences.  Because of this incredible breadth we insist that all boot campers are just "biologists" for a week, and we usually analyze 3 diverse data sets, one of which may be field based.  Our emphasis is on the commonalities of analysis problems, not on the details of the data itself.   While it would be fun to work with data we collect at MBL there is just not time to make that happen for nearly 100 students in a one week period, so instead we use previously collected dat sets from our workshop instructors who are UChicago faculty, so the precise datasets follow the individual's research interests.  Let me know if this addresses your questions adequately.

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  • Icon for: Erin Kraal

    Erin Kraal

    Higher Ed Faculty
    May 13, 2019 | 03:55 p.m.

    This is an interesting approach!  Do you have an insights into how it might translate into the undergraduate environment?  Do you think it is important to have it START the program - as in be one of the first experiences they have?  Versus have it occur later in the program.

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  • Icon for: Victoria Prince

    Victoria Prince

    Lead Presenter
    May 13, 2019 | 04:39 p.m.

    We have felt that having the boot camp as the students' first experience is helpful in that it immediately establishes valuable relationships across our broad cohort, seeds a certain way of thinking about data analysis, and also shows our doctoral students that they are now in a different environment (with—at least for some—more intense expectations of hard and focused work). 

    I do think many aspects of the boot camp would translate to the undergraduate arena, but perhaps the importance of starting the program with a boot camp experience would be reduced.  I would of course be interested to hear from any groups that have applied boot camp approaches to undergraduates. 

     

     
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  • Icon for: Alex Rudolph

    Alex Rudolph

    Facilitator
    May 13, 2019 | 05:30 p.m.

    We have used a boot camp as part of one of our summer research programs for students working as part of a large multi-university consortium to build a radio telescope in South Africa. The students work on different aspects of the project in the summer at different universities, so we start the summer with one week boot camp. At the camp, they basic skills in programming specific to the projects they will be working on, as well as basic information about the science (cosmology) and the observational technique the telescope employs (interferometry). There are also social events to further build the sense of cohort the students have before leaving to their respective research sites for the summer.

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  • Icon for: Victoria Prince

    Victoria Prince

    Lead Presenter
    May 13, 2019 | 08:59 p.m.

    This sounds like a great experience for your students - thank you for sharing that information.

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  • Icon for: Patricia Marsteller

    Patricia Marsteller

    Facilitator
    May 14, 2019 | 12:23 p.m.

    Great program for new grad students.  have you all considered extending this to UG faculty?  and what one might do to extend this to UG students?

    Can the materials be adapted by other faculty?  I'd really love to see such programs made available to undergraduates and undergraduate educators.  Would you all consider presenting at a BioQUEST/QUBES workshop? https://bioquest.org/

    BTW Emory has a Quant. Science UG program.  I bet they'd love to use your materials.

    http://quantitative.emory.edu/for-undergraduate...

     

     
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    Rebecca Roberts
  • Icon for: Victoria Prince

    Victoria Prince

    Lead Presenter
    May 14, 2019 | 10:47 p.m.

    We would love for our material to benefit others and are very happy to share it.  However, my co-presenters are better equipped to respond to this question than me, so I will let them tackle this one,

     
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  • Icon for: Stefano Allesina

    Stefano Allesina

    Co-Presenter
    May 15, 2019 | 09:47 a.m.

    Dear Patricia,
    the materials we prepared are actually well-suited for junior or senior undergraduates. We have collected the latest rendition of all of our materials in this GitHub repository. For example, here you can find a pdf collating all of the lecture notes, while here you can find self-contained short tutorials introducing programming in R. I think that the "basic" and "advanced" tutorials would be especially useful for undergraduates who want to start analyze their data in R. All the materials are open source: we welcome anybody who wants to adapt them to their own needs. I have also prepared similar notes for my undergraduate teaching, and I would be happy to share them.

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    Rebecca Roberts
  • Icon for: Stephen Alkins

    Stephen Alkins

    Facilitator
    May 14, 2019 | 02:39 p.m.

    This is a great initiative and the concern with data reproducibility cannot be overstated.  I, myself, am a cellular neuroscientist by training, and at Brandeis we had a Quantitative Biology concentration and there has been some talk about making one or two of the courses mandatory across the life sciences, so this boot camp is excellent way to build cohort and faculty rapport and confidence as students begin rotations.

    1) As a way to continue building those skills, similar to what MBL does in Cold Spring Harbor or Woods Hole do you incorporate peer instructors. This always gives an opportunity to bridge mentoring from more experienced graduate students

    2) I wonder if programs like this would increase likelihood of publishing earlier in graduate careers.  That may be another factor to measure.

     

     
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  • Icon for: Victoria Prince

    Victoria Prince

    Lead Presenter
    May 14, 2019 | 10:43 p.m.

    Thanks for your comments and questions.   We take 8 teaching assistants with us to MBL each year, who are more senior graduate students. They play a key role in the instruction and the students often feel more comfortable asking them naive questions than they might of the faculty.  

    Regarding publication, we do track all papers across the division, however I know that there is significant variation discipline by discipline, and even lab by lab. While we could quantify number of papers and time of first publication, we do not have any 'control' students who did not attend the boot camp.  So the only comparison we can do is between the last 4 'boot camp' cohorts versus the preceding 4 years—unfortunately not a very well controlled experiment given the temporal offset.  

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  • May 16, 2019 | 05:37 p.m.

    Great program (and as a Cape Cod native it was nice to see Woodshole!). I would imagine that your boot camp would be very popular for undergraduate biology faculty both as a way for us to learn the more quantitative aspects of the field and to generate a community to discuss how best to incorporate quantitative learning for our students.

     
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  • Icon for: Victoria Prince

    Victoria Prince

    Lead Presenter
    May 16, 2019 | 09:27 p.m.

    We had not previously considered the utility of our program or one like it for undergraduate faculty, but the questions and comments are showing us that there could be a lot of interest in such a program. I will also share these comments with MBL leadership.  Thank you for the suggestion.

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