Projects for Scientific Computing Scholars – Murray Lab

While many pollutants are detrimental to wildlife health by poisoning individuals that are exposed, many
other compounds have cryptic deleterious effects at the population and community level. Anthropogenic
steroid hormone mimics, called endocrine-disrupting compounds (EDCs), bias the development of the
reproductive tract and can lead to sex ratio biases or reduce viability either by exerting estrogenic, anti-
androgenic, androgenic, or anti-estrogenic effects. This student would work with Dr. Chris Murray and Dr.
April Wright to generate a model that uses life history strategies, endogenous physiological traits, and
exposure risk assessment to predict population-level impacts of EDCs on crocodilian model populations
over time. The model will serve to predict sex ratio, population size, and genetic diversity over time and
will bet tested using real data from American crocodiles exposed to androgens and alligators exposed to

Direct questions to

Projects for Scientific Computing Scholars – Beachy Lab

But in the real world, there are distributions that have more than one group. We use this approach to help us think about the number of size groups in a population of an amphibian. In some cases, these distributions are really limited by the number of individual observations. For example, how many groups are in this distribution? We think that there might be three, but we do not have a statistical approach to this question.

Questions can be directed to

Projects for Scientific Computing Scholars – Kuhn Lab

Modeling and Control of Biologically – Inspired Flight with Dr. Lisa Kuhn

Recently there have been great advances in the development of flexible wing air vehicles. These vehicles are inspired by biology since biological flight (such as birds and bats) have better maneuverability and performance over fixed-wing drones. The focus of this project is to use computers to simulate flexible wing air vehicular models and control them. This project is of interest to us because it brings to light a number of interesting, unsolved scientific questions.

Participation in this project could involve any of the following:

  • Developing and coding algorithms to arrive at mathematical solutions that are not only accurate but can be achieved in a reasonable amount of time using a reasonable amount of computer memory and space.
  • Running computer simulations and analyzing results.
  • Deriving mathematical models.

Questions can be directed to Dr. Lisa Kuhn

Projects for Scientific Computing Scholars – Wright Lab

What do we know about evolution? Dr. Wright’s project concerns models of evolution for morphological characters. As seen on the figure below, we can collect many types of data about an organism’s form. These data may be quite complex. When we build a phylogeny, we assume we know something about how our data came to be. But what if we don’t? What if our assumptions about the way evolution has happened in our group are wrong? In this project, the student will work closely with other lab members to evaluate how well our models of evolution are actually capturing the process of evolution.

What do we know about time? Dr. Wright’s second project concerns how we can use fossils to tell how long ago a species diversified into multiple species. When paleontologists dig a fossil out of the ground, they might know something about what kind of species it is, or when it lived. How can we use this information to generate trees like the one below, which is dated to absolute time?

Building a CAREER

I was recently awarded an NSF CAREER proposal. I’m still in some amount of shock, but I wanted to share a little bit about how I approached writing the proposal at a primarily undergraduate institution. Writing proposals at PUIs is always a little fraught. We don’t have as many person hours devoted to research. We may or may not have grad students. Equipment may be old. But we have the best resource there is: awesome students, and a desire to use our science to help them learn and grow.

This blog post is going to be about how I approached writing my CAREER proposal. Everything in here might now be generalizable to other types of projects. My work is not equipment-intensive. I don’t do field work. Therefore, the majority of my budget is going to personnel costs. You can view the proposal here. A few job postings will appear soon.

Here are the three things I think were critical to all this working.

1. Have an idea you’re excited about

It goes without saying that you probably need a good idea to start writing your proposal. But everyone who submits one has a good idea. I’ve been on panels. Most proposals are good. You need to write a proposal that others will be excited by – and that starts with you being excited about it. The tricky thing about the CAREER is that you’re going to be judged on the research and the teaching components. But that’s what we’re good at at PUIs!

I started my proposal by taking it to lunch. I read the solicitation in my office, then took my notebook and pen to Tacos and Beer (this was in the Before Times), and wrote an outline. What did I see as major research problems that I was suited to address, and I wanted to address? For me, this was the fact that, depending on what exact phylogenetic model you choose, you can get basically any tree you want for a dataset I have. How can we trust anything when the answer is so dependent on methods? How can we know we’ve chosen the correct methods? And so my research question became how to perform model fitting for hierarchical Bayesian models, and developing some tools to make these analyses more tractable for biologists who may not be computer wizards. There’s some research in there. Some software. My CV supports that I am very capable of this work.

I did the same thing for the education component. What are the big problems that I can address? I’m a computational evolutionary biologist, at an institution without PhD students. I need to train up undergrads, and fast! But how do we get more computation into the curriculum? What class we cut? Perhaps … nothing. Perhaps we integrate computation into existing courses via code-to-learn exercises. I do this in my classes, but a lot of faculty are skeptical. Will we need to cut content to do this? Designing an experiment to assess this is the core of my educational component. This cannot be business as usual: anyone who isn’t a straight white dude gets penalized by teaching evaluations, and that hurts tenure cases. Moreso when active learning and quantitative thinking are involved. To support this aim, in the broader impacts, we’re doing a faculty mentoring network where faculty can workshop code-to-learn biology modules, and upon completion, get a letter for promotion and tenure explaining how the instructor has used best teaching practices. The hope is this might help insulate instructors teaching these topics from a dip in teaching evaluations.

Once I had my good idea, I outlined it, then put it away for a week. Then I read over the outline alongside the solicitation. Seemed good, so I wrote the project summary and sent it to the PO and requested a short meeting to discuss if it was appropriate. This was about 5 months before it was due.

2. Stand in the place where you are

I don’t have PhD students. But my project is a lot of work. I need to train up undergraduates. I need to train MS students. How can I get reliable labor if I’m always training? Southeastern is situated in Southeastern Louisiana, a historically low-income region. It’s a region with entrenched inequality. I reached out to our local TRiO and Upward Bound folks. I requested undergrad salary lines that would be specifically earmarked for these students to come and do lab work. I can recruit on this. Come to Southeastern, we have 4 years of undergrad research funding for you! You want to stay and do an MS? We can do that, too. Early on, I knew I wanted this component to help improve our retention with historically excluded students, and to create a pipeline to our MS program.

This was actually the first piece of the proposal I wrote in earnest because I wanted to get feedback from our wonderful TRiO program administrators. They know how to recruit students. They need our involvement as faculty to retain them. Their feedback helped me spend money I was always going to spend more equitably. Not more money – the same money, but better. I started this four months before the due date so I could get plenty of feedback.

I know a lot of PUI folks worry about not getting as much research done as R1 folks, or that they’ll be dinged for not having all the newest equipment. I wrote in to have my postdoc also get desk space at a local R1 so they have more community, access to seminars, etc. One thing I’ll say is I was on a panel once, and some questions were raised about if the PUI PI had access to certain facilities. I know we all have a little tendency to reuse the facilities and equipment documents, but really do make sure everything you need to be successful is accounted for. That includes things like private office space, if you’re dealing with student assessment data. Can your lab space grow to meet your labor needs? This should be in your proposal and the department chair letter.

3. Start Early

I had the whole thing written two months out, and spent the other two months focusing on getting out a couple pubs that would support my qualifications to do the work. I was writing between trying to keep my undergraduate research projects running. Teaching a 3/3. Buying a house. Two kids under 5 home in a pandemic. An hour here, an hour there. Memorizing a clunky paragraph and trying to work it out over a run with my dog. Printing the proposal and reading it out loud late at night in my living room.

I asked for feedback early from my Dean, who is a physicist. Physics has a long history of doing intensive research on education and retention, so he was able to help. I asked for feedback about two months out from my department head to make sure everything was feasible. I reached out to a few people with CAREER awards at similar institutions or similar projects. Something that is tricky about the CAREER is that you have your education, research, and broader impacts. You might have more collaborators and experts to get letters from than normal. And these are all valued collaborators! They need plenty of time to read your proposal, assess it, give feedback, and determine if they can assist in the way you’ve asked. I asked for letters of collaboration to arrive by two months from submission. That way, there was lots of time to discuss.


Have a project you dig, think carefully about how to do it where you are, and then give yourself time to write the proposal.

Edit 2/23/20

A lot of you read this post! I’m going to use that as an opportunity to plug the PUI Science Slack community. We have a #CAREER channel, and a lot of us used it to support each other while writing. If you’re a PUI faculty member, please feel free to join. We’ll have to make some decisions on the #CAREER channel, like if we want this year’s awardees to remain on the channel (I guess that’s me – am I “we” anymore?), or if there should be a separate channel to bounce off awardees, etc. If you want to be part of a supportive, awesome group of faculty at similar institutions, please join!

What I did for my summer vacation

Been a while since I wrote on here. I’ve been meaning to, but I’ve also been home with my entire family on months of quarantine. Such is life.

This summer, I only put two things on my docket: finish my NSF CAREER submission, and finish a preprint. I’ve managed to do both, and then some. Let’s take a peek at some new stuff in the lab.

Graeme Lloyd and I have a new paper on interpreting the posterior sample in Bayesian paleo phylogenetics. The code and data are here, along with some talk slides where I discuss the manuscript. We used treespace visualizations in RWTY to look at the distribution of treespace metrics across the posterior sample. In the paper we make the argument, hopefully convincingly, that the posterior sample has more information than a mean or median of the distribution might capture. We also provide some comparisons with the most parsimonious set of trees and discuss how and why summary trees of parsimony sets can be misleading.

It was my privilege to be involved in this collaboration on active learning and inclusive teaching online. Ecology and evolution are among the least diverse fields of study. In this manuscript, we intend to provide some basic definitions for common terms and concepts around active learning and inclusive teaching. This is very much a baby steps manuscript, and I hope everyone who looks at it will find a couple things they can do to make their classroom a more equitable and engaging place this coming semester.

Rachel Warnock and I had this paper accepted. We were both in a position of beginning to teach MS students about the work that we do, particularly with the fossilized birth-death model. We both found ourselves in need of a good, strong, explanation of the model and its underprinnings that could be read by a student who is new to this research. So we wrote one. We’re hoping this is a nice jumping off point for new students, but also a good catch-up review for people who might be more familiar with the concepts, but missed bits about how they fit together for analysis.

A nice companion is this published tutorial with Tracy Heath & co. In this tutorial, we provide a clear and simplified FBD analysis that pretty much anyone should be able to follow along with. Something that is very cool is that this tutorial appeared in a book that is entirely free and open source. It’s an incredible effort!

And lastly, this preprint with Davey Wright and Pete Wagner. Something that is very tricky about the FBD is that there are some parameters for which you might have little intuition. Speciation or extinction in your group, for example. It’s also a complex model, with submodels for parts of the data. We show some tractable ways to engage in finding the best model and rigorously testing for fit.

For my summer vacation, I got a lot done. But here’s the thing: I had my kids home. My husband was working from home. It was chaos. I worked with people who are kind. I worked with people who listen and exercise patience. I exercised more patience. I wasn’t perfect. I said “No” pretty much constantly to anything that didn’t make me feel genuinely excited and charged up. Things are about to kick off again for the semester, but that’s my mindset: do what you love and the rest follows


I had a little bit of a rough women in science day Thursday. I turned to Twitter for some support:

It turns out quite a few people, and not just people who identify as women, do want to chat about being faculty at PUIs. So I created PUIScienceSlack.

Edit March 12: Thanks to our new members for noticing our invite link had expired. I’ve regenerated an invite link that does not expire.

Who is it for: Anyone teaching science at a primarily undergraduate institution. I’ve left science broadly defined – social scientists and applied sciences welcome. If you would call yourself scientist, please, come aboard!

I’ve also left “PUI” slightly nebulously defined. Different organizations define this differently, often capping the ratio of graduate students to undergraduate students at something like 1:10. I don’t feel as strictly – some R2s straddle that boundary, and some departments at more research-intensive institutions don’t have well-supported graduate programs and mostly work with undergrads. If you feel like you belong in this group, you probably do.

Edit: I think it would be fine if trainees who want to have PUI jobs in the sciences joined, too! The types of discussions we have might really benefit you!

What is it for: Discussions of teaching and research in the sciences. To start, I made several public channels, #women (since that’s what prompted this), #grants, #general, #research, and #quantitativeskills. These are public – they can be viewed by anyone who clicks the link. There is also one private channel, #confidential, that members who want to discuss a sensitive issue can request to join. Direct messages are private between members. This is a free-tier plan, which means messages over the 10k line get purged in send order.

A note on “private”: private refers to the fact that you need a log-in to access this info. Like most digital communication, this information can be requisitioned in a court case.

Some of us are starting to work on CAREER proposals – perhaps this can be a jumping off point for writing groups. Many of us are solving the same challenges about curricula – let’s solve them together. At many institutions, there is a unique isolation. You might be the only person who works on any topic even remotely related to yours. But maybe we can all make some new friends! Or maybe this is all a big bust and goes no where. No big deal. Slack is pretty low-stakes;)

Other info: My lab’s code of conduct applies to this space. I consider that code of conduct expansive – if you are afraid to participate in the space because of prior harassment from another member, please get in touch.

Addition, 2/10/2020 on rules: We took two votes last week. Here are the results:

  • Real names: Unless you get in touch and have an exceptional circumstance, please use your real name and sign up with an email that can be verified as belonging to you
  • Confidential: Conversations on the Slack channel should not be shared outside the Slack channel without explicit permission from those involved.

Wright Lab @LBRN

This week, the Wright Lab is at LSU for the LBRN annual meeting. Here are the talks and posters for the lab:

My talk:
Christina’s Talk:

Christina’s Poster:

Basanta and Courtney’s poster:

RevBayes & the universe

One of the interesting things about having a blog is that you can see what people are interested in, and when. This week, I can see a lot of traffic going to a couple of blog posts, Teaching Phylogenetics in the Cloud and Plan C. This is pretty common around the start of the semester – people are interested in trying new things in their teaching, and particularly using cloud technologies to improve access to compute resources.

I want to emphasize some new developments on this front. Jeremy Brown and I taught a workshop at the SSB2020 meetings on developing a hands-on classroom using RevBayes. Slides are here.

We covered three main things: Graphical models, and why they’re cool; how to build a graphical model; and some of the graphical interfaces that you might use to deliver RevBayes to your students. That last point is important – systematics isn’t a science isolation. To use phylogenetic methods, students need to understand statistics, they need to understand where their data come from, and what the biases in those data may be. Common tools like R and RStudio, or Python and the Jupyter notebook are often used for “data science.” Given the integrative nature of systematics as a discipline, doesn’t it make sense to make our tools interoperate more smoothly with a broader universe of tools for working with data?

We have some tools to help RevBayes play nicer with tools like RStudio and Jupyter. Michael Landis and Sebastian Frost developed a Jupyter Kernel for using Rev inside of Jupyter notebooks. Lately, David Bapst and I have been working on an RStudio interface. If you’re interested in any of these tools, please do see the install page for them, and give us feedback. A manuscript describing the classroom contexts for these tools is forthcoming; in the mean time, you might find interesting tidbits related in the paper described here.

If you were at the workshop, you ought to have received an email inviting you to take a survey on it, and inviting you to comment on the issue tracker for the RevKnitr repository. I’d like to extend that invite more widely – if you are teaching with RevBayes and would like to join the conversation with other educators, do feel free to open an issue on the RevKnitr issue tracker. It would be wonderful to have an active discussion on how to teach systematics expansively and inclusively.

Nantucket DevelopR 2019

This past week, we (Drs. Liam Revell, Klaus Schliep, Josef Uyeda, Claudia Solis-Lemus, and myself) hosted the Nantucket DevelopR Phylogenetics workshop again.

This is a really interesting course because it’s aimed at intermediate learners. Intermediate is slippery to define. I often think of it as the point where questions stop having clear answers – i.e., when you google for an answer, you don’t just get back “How to initialize a list.” You have to start thinking about optimization, or making code clean to read for other contributors.

Basically, an intermediate learner is someone who might not have a clear path forward. And at many universities, they might not have someone more advanced to go to for help. For intermediates, we don’t just need skills/information transfer, we need network-building.

So our goal with this workshop was a few things:

  • Get everyone a base of some basic intermediate skills: functional programming, efficient use of Git and GitHub, packaging R code, and phylogenetics in R. Materials here
  • Get motivated folks who might be on different ends of the “intermediate” spectrum together to work together productively on R phylogenetics packages
  • Create a diverse network of people who now all know each other and are connected by work on packages. Build a community of R-phylo developers

What worked

Bear in mind, these are personal reflections; we’ve not yet done our surveys.

  • Diverse leadership. Diverse teams are known to produce better results. And it’s known that diverse faculty can assist in establishing and maintaining diverse communities. I think that is reflected in the make-up of our course, which is more gender-balanced than the previous offering. We also took other steps, like a more verbose course advert, since literature suggests minoritized students don’t apply for things unless they meet more of the criteria than white male students. Making it easier to see how you fit means you see how you fit.
  • More coordination on the front end. Last time we offered this, Klaus and I were really unsure what the students would already know and need to know. This time, we had a little more blueprint, so we decided a few topics we would cover in advance.
  • Larger leadership team. Last time we did this, it was Klaus and I doing everything (+ my husband doing the cooking). This time, there were four of us with a more distributed knowledge base. This meant better lectures, and a wider array of things to accomplish.
  • Balance of work & lecture time. We only had four real days on the island. Two were mostly spent lecturing, two mostly working. The students got a lot done on the various projects.

What we could improve

  • More organization on the lead end. We had some last-minute upsets to infrastructure, which meant we did some last minute scrambling. This probably won’t happen next time, but we could do a bit more polling on interests for lecture topics, and organize food purchases somewhat better.
  • Scalability. This workshop was great, and there was far more interest than we could accommodate. Many great applicants we just couldn’t make room for. And for sustaining something, funders often want to see through-put. It would be great to keep the feel of everyone in one lodging, coding in the shared spaces, eating in the shared spaces. But we have little room to grow in the current location.
  • Something else will come up in evals, I’m sure.

In conclusion

What a wonderful week. I hope we can do it again. On a personal note, as much as I adore being PUI faculty, we do have fewer research active faculty. It was really nice to go somewhere and be in the company of other researchers and new PIs for a week. I feel very much refreshed going into the last month of classes.

Our next steps are to put together a post-workshop survey + check-in schedule to keep people motivated to finish projects.