Field Trip! Computational Biology on the Road

A few weeks ago I took my students to the Association Computing Machinery Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB) in Seattle, WA.  It was a fantastic experience for everyone involved – the organizers did an excellent job running the conference.  I asked my students to reflect on the conference, and I figured I should do the same.

With such a large cohort of undergraduates at a scientific conference, my role shifted to encompass one of an educator as well as a researcher.  I honed in on the accessibility of the material in talks, feeling a bit of pride when the speakers showed an image or mentioned a topic I have taught in class.  I also had some moments of “wow, should have taught them that” when a speaker presented a fundamental concept we have not yet covered.  Many of my students came out of sessions excited about what they had just learned – they talked with the speakers, asked for their papers, and are now delving into this new material.  Graduate student attendees became mentors, fielding questions about why they went to graduate school and how they picked their research topic.

ACM-BCB was an ideal size – the conference had compelling talks and tutorials while being small enough to chat with the keynote speakers and conference organizers.  I caught up with existing colleagues and met some potential collaborators in the Pacific Northwest.  I also found myself in discussions with  graduate students about my position in a liberal arts environment.  Reed had a research presence, since three Reed students submitted posters to the poster session.  My students had garnered enough research experience — either through their thesis, summer research, or independent projects in class — to have engaging conversations with other attendees.

Finally, the trip to ACM-BCB as a class taught everyone (including me) the importance of logistics.  Some gems:

  1. Make sure the taxi to the train station can fit the entire group.
  2. Remember who you gave the posters to in your mad dash to find parking before your train departs (see #1).
  3. Make sure your PCard credit limit is set so it’s not declined at the hotel.
  4. Tell your students the correct time of the first keynote.

And the question of the day: is a (very detailed) receipt for a can of soda written on a napkin by a bartender reimbursable?

Ready, Set, Year Two

I have returned from summer break to begin teaching a new course this fall.  My break  included a hiatus in blog posts; now that classes have started up, I’m back to writing them.  Other lessons from my first true “summer break:”

  1. Yep, I still love research. Summer was a refreshing change of pace, where I was able to chip away at existing research projects and establish new collaborations here in Portland.
  2. Pacific Northwest summer weather is great.  No humidity + few bugs. I didn’t think that was possible.
  3. Feelings of preparedness are relative.  Despite having a year under my belt, there are enough new tasks and responsibilities that I still feel like a newbie.

Happy back-to-school for those who live by the academic calendar, and welcome to the Reed Class of 2020.

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The Class of 2020 at Reed College’s Convocation.  Photo by Leah Nash.

 

Spotted in the Lab

This is the last week of classes.  Reed seniors are finalizing their theses — a culmination of their year-long projects — before sending them off to faculty readers.  As we near the end, my computational biology lab has a new round of students working night and day.  Don’t worry, though – Monty the Motivation Whale is there for you.

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Monty’s appearance might be due to the fact that one of the Reed seniors is a lead scientist at the Orca Behavior Institute, a non-profit he started in 2015.

Grants keep coming to Reed Biologists

As a new computational biologist at Reed College, I was excited about the prospect of continuing to do research while teaching innovative courses.  I’ve written about the research opportunities at Reed, and faculty across campus have received over two million dollars of grant funding in 2014/2015.

The Biology Department just secured two more research grants from the M.J. Murdock Charitable Trust to investigate neurogenesis in zebrafish (Dr. Kara Cerveny) and discover candidate driver genes in cancer (me!).

Small schools also have an opportunity to play a large role in undergraduate education programs.  Another NSF grant was recently awarded to Dr. Suzy Renn to organize a STEM workshop on undergraduate involvement in the NSF’s Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative.

All in all, 2016 seems like it will be another great research year.

My Dream Job, Part 4

As of August, I am an Assistant Professor of Biology at Reed College.  In this series of blog posts, I will explain why I chose this environment as my academic landing pad (or launching pad).

Part 4:  Being in a Biology Department changes my perspective.

With one semester under my belt, I took some time this break to reflect on my position at Reed.*  As I begin teaching another round of Introduction to Computational Biology, I will try to articulate why I find my position so exciting.

The students who are taking my classes have had a mixture of backgrounds, but most of them major in the natural sciences.  Up to this point, I have been surrounded by people with strong backgrounds in math and computer science.  As a result, students ask questions that have a completely different underlying motivation than the questions I’ve received in talks and research meetings.  I walk a fine line between oversimplifying the biology in order to describe a problem in computational terms and oversimplifying an algorithm in order to describe how it is applied to a biological concept.  In some ways, this makes teaching class hard.  Talk about inviting the imposter syndrome to step in when you have to answer “I don’t know” in class more than once.  Yet it also makes class engaging, unexpected, and fun.  Add to that an occasional power pose, and teaching is very satisfying.

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Screenshot from Amy Cuddy’s TED Talk (provided from a blog post by Amy Neuzil)

I am currently one of two tenure-track computer scientists at Reed.  We are at the cusp of establishing a computer science program: students are excited, funds have been acquired, and an active search is underway. I feel like much of the incredibly hard work has been done, and I get to show up for the fun part.**  This momentum has trickled over to the Biology Department through the students I advise and teach.

The other computer scientists at Reed are affiliated with the Math Department.  One might think that being in a different department from the faculty who are “most like me” may make my research life isolating.  Instead, I may just have the best of both worlds.  I get to sit in the same department as my biological collaborators, while networking with faculty in the Math Department to establish computational research collaborations.  Put simply, I love being interdisciplinary.  I deeply appreciate the flexibility that Reed offers in designing my courses to be hybrids of two fields.

My professional identity is quickly becoming steeped in teaching interdisciplinary courses and conducting research across departments.  Over the next few years, my research will undoubtedly become more applications-focused as I co-advise more student projects with Biology faculty. Yet there is enough interest at Reed, from both faculty and students, for me to continue algorithmic research.

*It’s been a while since I posted. Consider it a Spring semester resolution to start posting more.

**This might be naive, but hey, I’m an optimist.

My dream job, part 3

As of August, I am an Assistant Professor of Biology at Reed College.  In this series of blog posts, I will explain why I chose this environment as my academic landing pad (or launching pad).

Part 3: Reed is designed for conducting research in a liberal arts environment.

A friend and Reed alumnus once described her experience at Reed as “mini grad school.”  One of the main reasons for this is the long-standing tradition of the senior thesis.  The thesis, which must be approved by a committee of readers, is part of the requirements for graduation.  It is also engrained in the student culture — the end of thesis writing is celebrated by ritualistically burning of a copy of the document. All theses are placed in the Library’s “thesis tower” for perusal by the public, becoming a permanent item in the Reed community.

Thesis Parade [photo posted by Reed College on Facebook]

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Library thesis tower, 1992. Image from the Reed College Hauser Library Special Collections and Archives, Reed College Library.

As Reed faculty, we advise students on this year-long thesis writing endeavor.  Part of our responsibility, as educators, is to think about new problems in our field that become thesis topics.  In some departments, providing students with research experiences and opportunities goes hand-in-hand with academic scholarship.  For example, in the Biology Department, student theses may fit into the professor’s larger vision of their research.  I think this is echoed in the success of faculty all over campus at securing external funding – over $2.2 million in 2014/2015, a ten year historical record.

Conducting high-quality research is not an anomaly at liberal arts schools.  Granted, it may take more time than at larger institutions, since training and teaching undergraduates is a much larger piece of the work.  But the quality does not have to diminish.  Recently, Biology professor Todd Schlenke published a paper in Science with Shelly Skolfield (class of 2014) and others.  The work was a continuation of the senior thesis Shelly did with Todd in 2014.

I intend to continue my research projects with the help of Reed students – in fact, it is one of the reasons why I took the job.  Advising senior theses will be a great way to kick off my research program.