New Reed CompBio Blog

As part of a recently-funded collaborative REU (generously supported by the CRA-W), my colleague Derek Applewhite and I are working with undergraduates to study machine learning methods to predict genes that regulate cell movement patterns in schizophrenia.  The team will post their work on new a Reed College blog, The Pathway Not Taken, and I may re-post selected pieces here.  The first post gives a general idea of the problem we will work on, and how biology and computer science are intertwined in the project.

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Congratulations Seniors

It’s been a long while since I posted, so I figured it’s appropriate to resume this blog by congratulating all the seniors at Reed who have labored over their theses throughout the year.  Now, they will ceremoniously burn all their drafts this afternoon at the bonfire.  Happy Renn Fayre!

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Spotted outside my office door in the Biology building.

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.