Category Archives: Education

Conferences, Conferences, Conferences

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Thanksgiving break is quickly approaching, and it’s amazing how time flies — that goal of writing a blog post once a week?  Try once a semester!

Luckily, there has been one major theme since I’ve started teaching again – conference travel.  Undergraduate travel to conferences are a major part of my NSF grant, and I’ve also been making rounds on the conference circuit presenting work students and I conducted during my sabbatical last year.

ISMB/ECCB in Basel, Switzerland.  I’ve already talked about the heat wave & the wickelfisch, and I mentioned Ananthan Nambiar’s poster on NLP-based methods for protein family classification.  I also presented a poster on pathway connectivity with hypergraphs that has since been published in PLOS Computational Biology.   Ananthan was also featured in Reed Magazine’s annual “What is a Reedie?” 

Pacific Northwest Quantitative Biology (PacNoW QB) Symposium at OHSU in Portland, OR.  This one-day symposium focuses on quantitative and computational biology efforts in Oregon and Washington, encompassing different types of institutions and programs. Tunc Kose and Jiarong Li presented a poster on pathway reconstruction. (They also presented at the Pre-Inauguration Showcase at Reed College in honor of our new president Audrey Bilger).
 

ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (BCB) in Niagara Falls, NY.  I was excited to meet the eight undergraduates from the New York area who received travel funds to attend ACM-BCB as part of my NSF grant.    The students came from institutions large and small, and got to learn a bit about computational biology.  My student Amy Rose Lazarte, who now works at Puppet, also presented a poster on her senior thesis research.

Murdock College Science Research Conference, Vancouver, WA. Tayla Isensee, who was co-advised by Kara Cerveny, presented a poster at the annual conference organized by the Murdock Charitable Trust that celebrates undergraduate research.  She also presented at the Pre-Inauguration Showcase earlier in the semester.

IEEE Conference on Bioinformatics and BioMedicine (BIBM) in San Diego, CA.  Finally, my upper-level Computational Systems Biology course just returned from sunny San Diego after attending part of BIBM.  I presented a workshop paper based on Alex King’s thesis and post-bac work, which should be out soon as an IEEE proceedings.  Remarkably, all ten students and I managed the travel with no large holdups!

Many of my summer students also presented posters at the Reed College Poster Session early in the semester (including Karl Young, Jiarong Li, Tunc Kose, and Tayla Isensee), which highlighted computational biology at Reed.  I’m looking forward to continuing the tradition of conference attendance and presentations of Reed student work!

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Sabbatical Part 8

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It’s summer, and faculty have submitted their grades, attended their last faculty meeting, and have gleefully moved on to full-time summer research.  Faculty on sabbatical have a few more precious months to wrap up the year’s worth of research projects before returning to teaching.  Sabbatical is not over, but the end is in sight.

The last few weeks were a whirlwind of meetings – first to Memphis, TN to the NCWIT Summit, where I received an Undergraduate Research Mentoring award.  I ate some hot chicken, saw the Grand Ole Opry, and did some novice line dancing.

summitemail_messagingsmcard

I then flew to Madison, WI for the Great Lakes Bioinformatics conference.  It was a great meeting – the talks presented new and innovative ideas in bioinformatics and computational biology.  I gave two talks — a research talk on hypergraph connectivity measures for signaling pathway analysis and an education talk on undergraduate engagement in computational biology through conference attendance.  Materials related to these talks will be posted on my website in the next few weeks.

Madison and the University’s campus has changed a lot since I was a kid, but I was excited to introduce the Great Dane Pub to some folks.  I also probably talked about cheese curds more than I should have.  I also caught up with other liberal arts computational biology faculty: Layla Oesper from Carleton, Catie Welsh from Rhodes, and Getiria Onsongo from Macalester.  Undergraduate institutions in the midwest are certainly stepping up their computational biology game!

Summer research is now in full swing, with three students and two post-bacs working on a bunch of different projects.  I’ve also taken advantage of the outstanding (dry!) Portland weather to get back into playing ultimate frisbee – my last sabbatical goal is to not get (too) injured.

 

Sabbatical Part 4

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This fall has has been filled with meetings of all types:

Meeting 1: Pacific Northwest Quantitative Biology (PacNow QB) Meeting
Who: Organized by yours truly and Derek Applewhite.
What: Regional meeting for faculty, researchers, and students interest in quantitative, data-driven biology.
Where: Hosted at Lewis & Clark College (thanks Clarkies!).
When: September 22
Interested? The meeting has been held annually, and includes a student poster session and faculty/researcher invited talks.

Meeting 2: Computational Biology Workshop
Who: Organized by kick-ass computer scientist Layla Oesper.
What: Undergraduate workshop that brought together faculty from five liberal arts institutions to introduce computer science students to applications in biology.
Where: Hosted at Carleton College in Northfield, Minnesota (proudly known as the city of “Cows, Colleges, and Contentment”).
When: September 29-30
Interested? No immediate plans for a future workshop of this type, but all the materials are freely available online.

Meeting 3: Consortium for Computing Sciences in Colleges (CCSC-NW) Regional Meeting
Who: Organized by Kelvin Sung and others, including pretty fantastic women in CS: Tammy VanDeGrift, Haiyan Cheng, and Shereen Khoja.
What: Regional meeting for computer science educators at colleges in the Pacific Northwest, with a focus on CS education.
Where: Hosted at University of Washington, Bothell.
When: October 12-13
Interested? This was my first time and I loved meeting new colleagues.  CCSC-NW is usually held in early October every year, and will be held in the Portland area next year.

And then there’s the crazy beautiful weather here in Portland – fantastic view of St. John’s Bridge in North Portland during a hike in Forest Park:

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Changing Demographics of the Biomedical Workforce

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Thanks to Mike the Mad Biologist’s blog, this article (from January 2017) resurfaced:

The new face of US science : Nature News & Comment

This study looks at census data to determine the demographics of PhD recipients in the biological or medical sciences.  The authors characterize a biomedical workforce that is fundamentally different from previous generations.  Their infographic contains the main trends:

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Heggeness et al, The new face of US science. Nature Comment, 2017

 

 

 

My dream job, part 2

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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 2: The teaching opportunities are tremendous.

I have always wanted to teach.  Ironically, very few Ph.D. programs incentivize learning how to teach.*  In 2013, Derek Bok, former president of Harvard, wrote a great commentary in the Chronicle of Higher Education about how technology necessitates a change in preparing Ph.D. graduates to teach.

In graduate school, I explicitly sought out a teaching experience.  I helped students develop computational tools to solve questions relevant to their own majors (English, History, Political Science, Gender Studies) and interests (NASCAR, music, food).  Forget about me inspiring the students – I was inspired by them!

I have joined a college that encourages faculty to teach what they believe are the most important and relevant aspects of their field.  The classes I will teach at Reed, which focus on learning computer programming to solve biological problems, are completely new additions to the existing courses in the Biology Department.  Some may scoff at the “course load release” I and other assistant faculty have obtained in the first year, but the point is to teach at these types of schools.  Engaging with students, educating them, and inspiring them is one of my major career goals.

I will end with hefty dose of reality, one that everyone in education is well-aware of.  Teaching is hard.  Teaching well is harder.  Add to that teaching on my own for the first time and creating course content from scratch, and this year will be a daunting rollercoaster ride.  But I am more excited about the teaching opportunities three weeks into a hectic first semester than I was when I first took the job.

*I personally don’t know of any computer science Ph.D. programs that incentivize learning how to teach.  Perhaps in other fields it is more commonplace.

My dream job, part 1

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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 1: I went to a liberal arts college, and it completely changed my career path.

This comment is not about Reed in particular, but about small liberal arts colleges.  I went to one of these colleges as an undergrad, determined to be an English major.  I took English classes, studied abroad in London with the English Department, and was well on my way to completing the required courses.

But something happened.  I was encouraged to try out new disciplines.  Like many other schools,* my alma mater offers an option to take a limited number classes pass/fail (“scrunch” them) and not have them count towards the students’ GPA.   So I took introductory courses in religion (didn’t like it), psychology (fun, but didn’t want to take more of it), and, finally, computer science.

I don’t know why I chose CS. Despite the small class size and the fantastic professor, I was intimidated.  After the first day I figured I would fail the class.  After a few weeks, I was hooked.  By that summer I was doing undergraduate research.  And now I have a Ph.D. in Computer Science.

Without the encouragement to use scrunch classes in a small class setting, I would not be a computer scientist.  I am surprised by my certainty about that statement.  I knew that I liked solving puzzles and finding creative solutions, but I didn’t connect that to computer science.  I hadn’t even connected that to science.

I am not necessarily on a mission to turn students towards computer science or computational fields.  Instead, I hope to show students a new field of study that they hadn’t considered before.  Students will be armed with new information to help them discover their academic interests.  I think this is will be easier to accomplish in a liberal arts environment.  Maybe this is unfair, since I didn’t attend a large school for undergrad, but it seems so easy to get “lost” at a large university if a student tries to venture out beyond their comfort zone.

*Some large public schools probably encourage this pass/fail option for select classes as well.  It would be interesting to know how many students use it as a mechanism to try out different career paths.

Tenure

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A couple articles came across my news feed in the past week a few months ago related to tenure.  While they are not directly related to each other, I thought I’d mention them in the same post.

First, how many faculty in the United States are actually tenured?  I was surprised to find that, according to the American Association of University Professors (AAUP), over 50% of faculty hold adjunct (non tenure-track) positions.  AAUP calls these positions “contingent faculty” because, regardless of their full-time or part-time status, their school makes little to no long-term commitment in terms of job security.  The increasing reliance of institutions on adjunct faculty has an impact not only on the faculty but also on the students and the research at the institution.  An article from The Atlantic summarizes many of these points:

The Cost of an Adjunct | The Atlantic

Now, tenure itself may be a controversial topic – some say that the system encourages faculty to slack off after getting tenure, or to keep teaching outdated material long after they should have retired.  The tenure process is incredibly stressful, sometimes unclear, and notoriously unfair – and this is just scratching the surface.  But once tenure is obtained, faculty may end up doing more out-of-the-box, high-risk research and teaching that they wouldn’t have attempted otherwise.

Trying to Kill Tenure | Inside Higher Ed

Funding models for Ph.D. programs

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UC-Irvine is adopting a new funding model for Ph.D. programs in some departments.  The idea is to provide increased funding for five years, and then offer a two year postdoc teaching position.

This article, from Slate, is written about Ph.D. programs in the humanities, where it is generally much harder to secure a job than in the computational sciences.  Still, an interesting perspective.

UC–Irvine’s 5+2 program: A good idea, but the worst job title in academia..

If you go to UCLA, you can be a Big Bang Theory scholar

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Jim Parsons and Mayim Bialik are two of the `The Big Bang Theory’ people funding the scholarship. Image from http://newsroom.ucla.edu/releases/the-big-bang-theory-creates-scholarship-fund-for-stem-students-at-ucla

STEM funding for undergraduates is cropping up from many unusual places, including Cards Against Humanity.  People from the show `The Big Bang Theory’ have done it for UCLA, raising over $4 million to endow a scholarship for students in STEM majors.

`The Big Bang Theory’ creates scholarship fund for STEM students at UCLA