02 October 2014

Developing a bioinformatics class as a part of a new bioinformatics/genomics minor.

Since I've been waxing philosophical about the small tasks I've been performing for students this semester, it seemed opportune to talk a bit more in depth about my big job for the semester: designing an undergraduate bioinformatics lecture and lab for next semester (spring 2015). This is actually something I'm really excited about, so I'm willing to expend quite a bit of time and energy being mindful and deliberate in how I set up the class schedule and assessments.

While I figure out particulars about hosting my own website, I've started a research webpage through Google Sites as a stand-in. This page includes resources related to a new undergraduate minor in Bioinformatics and Genomics created by my department chair, Srini Kambhampati. I'll eventually end up teaching genomics as well, but am mostly focused on developing the bioinformatics class material right now. I've got lots to say about the general premise of bioinformatics/computational biology education, but will save that for a later date.

I've talked to lots of folks about how they teach (or would like to teach) bioinformatics. Some are deeply rooted in a particular programming language (like perl), or focused on a particular type of bioinformatics (i.e., next generation sequencing analysis). I'm trying for a wider approach to capture a variety of student interests. Here's my first shot at explaining what my class will be like.


  1. Students will represent a mix of levels of computational and biological expertise, from folks who are rather computer-phobic but biologically savvy to computer science folks with relatively little biological knowledge. Lots of other biological research here at UTT is ecologically focused, and there's a lot of health professionals on campus and in the community
  2. I want to leverage extant and familiar educational technology (Blackboard, GUIs) while introducing students to more efficient and useful interfaces (Github, CLI, etc).
  3. I'm not expecting students to be expert programmers in any particular language at the end of the semester (with the exception of unix shell scripting, which is a necessary baseline for functionality).
Primary course objectives:
Students should be able to:
  1. Describe the scope of bioinformatics research and applications (including but not limited to next-generation sequencing, comparative genomics, ecological informatics, metagenomics, extensions to health informatics, etc)
  2. Design and implement bioinformatics pipelines to answer pre-defined questions from a variety of biological disciplines.
  3. Validate results from bioinformatics algorithms using hypothesis testing, correcting for multiple comparisons, etc.
  4. Characterize the limitations of data to answer questions of interests.
  5. Obtain resources to learn new languages and algorithms (i.e., be self-directed in learning more on their own).
How I'm doing it (which is mostly a list of questions I need to answer):
  1. In addition to the quick overview pages on my research website (which I'm hoping to transition over to the UTT Biology page when they are completed), I've set up a Github repository for the class that includes a modular syllabus (following the guidelines here) and will eventually include the materials used for in-class (lab) exercises. I'll still be posting grades on Blackboard, and haven't decided how to share lecture materials and assessments (Github, Blackboard, Slideshare, Wiki?).
  2. I'm not requiring students purchase a textbook. I will be relying on published scientific literature for objective 1, and (free to download!) OpenIntro Statistics for objectives 2-4 (in addition to examples from published literature). Of course, objective 5 teaches them to find and evaluate resources on their own.
  3. UTT Biology has a new building addition which will be completed by the end of this semester, and I've been put in charge of getting the computer lab set up. I'm hoping class sizes will be small enough that each student can work on their own machine. I'm still trying to decide if and how to include HPC/cluster usage, given that most analyses can run locally if the appropriate software is installed. There is the opportunity to get an instructional allocation from TACC, and I know other folks who have used Amazon Web Services Cloud Computing.
  4. I'm visiting classes taught by my colleagues this semester (both in computer science and biology) which may include students who are interested in taking my class next semester. I'm hoping to get a better idea of student desires and educational background to be able to craft materials that are both relevant and useful to them. I'm also considering cross-listing the class at the graduate level, as a few folks have asked me about that possibility (Sidenote: I'm brainstorming ideas for graduate level classes on my research page, too).
If you have ideas or experiences that you'd care to share, I'd be happy to hear them! Stayed tuned here, on my research webpage, and the Github repo over the next few months to see how the class develops.

30 September 2014

Pleasant surprises: teaching edition.

The first few weeks of my new professor life were absorbed by a long list of small tasks that, although unrelated to my main teaching and research duties, were still important and necessary for my work. You might remember my documentation of one such task, organizing my office. While plenty of these little tasks that are obnoxious to manage (learning how to order equipment, navigating Blackboard's abysmal interface, etc), I was pleasantly surprised to engage in a few satisfying duties. I'm going to take the opportunity right now to talk about two such additional tasks that are useful for students but also personally important to me.

My first obligation is to perform mid-semester teaching evaluations on a few graduate student teaching assistants. I've been thinking a lot about peer evaluations, in part because of its importance in the Software Carpentry Instructor Training in which I'm participating this semester, but also because the university is starting a peer-assessment teaching program. I wish I'd had the opportunity to have more structured assessments of my teaching during my graduate education.

My second obligation is to mentor and evaluate students as a part of our department's science communication class. Two semesters of the course are required for biology majors, during which students select a topic, work with a faculty mentor to shape empirical research into a 10-12 minute presentation, and formally present their ideas to a class of their peers. The faculty involvement is admittedly a bit time consuming. However, this seems like one of the best efforts I've encountered to embed in-depth scientific thinking and inquiry into a class project, so I consider it time well spent.

The two low-key responsibilities I mention here definitely serve students. On the other hand, though, they're also essential for me to develop a familiarity with a broad sampling of students and their educational backgrounds, especially as I continue developing new courses. I'm very fortunate that my department and college protects new professors from being overloaded with too many teaching and service obligations, allowing us to settle in and get our research programs started. I'm also lucky that the small tasks I have been assigned so far are helping me accomplish my other goals.

29 September 2014

Returning to my old stomping grounds.

I mentioned in my semester overview that I was doing a bit of traveling this fall. Last week I made the long drive from east Texas to Central Missouri to visit University of Missouri. My Ph.D. advisor, Chris Pires, was incredibly kind to store some research materials for me while I was working in North Carolina as a postdoc. Now that I'm starting my own lab, it seemed appropriate to resume custody of my plants and DNA stocks that were taking up valuable real estate in the greenhouse and freezer.

Lots of plants...the backseat was full, too!
Major life transitions (like moving halfway across the country and starting a new job) make me a bit nostalgic, so the drive back to Missouri was surprisingly emotional for me. I drove through the Ozarks several times as a graduate student as I collected plants from Arkansas, Texas, and Mexico for my dissertation research. This time, instead of returning to MU with a truck full of plants, I was leaving there with my Kia Soul packed with Commelinaceae goodness. Maintaining a living collection of plants takes a lot of time and energy, and I'm happy to see that so many of them survived. While my new university doesn't have a greenhouse on site, Tyler Junior College has a beautiful conservatory and have offered to house and maintain my collection. I'm looking forward to having my plants nearby again as I start thinking about developing them for research and/or teaching.

Perhaps more important than obtaining plants and DNA was the mental recharge I experienced by seeing some familiar faces and getting a much-needed pep talk from Chris. More pondering on reframing my mindset as a professor will assuredly occur over the next few weeks as I continue to develop my master plan (cue comically ominous chortling and cackling).

16 September 2014

Monocot sightings in Tyler Rose Garden

Evidence that there were, in fact, roses.

My mother visiting me for the first time here in Texas was a prime opportunity to indulge myself in some idle plant gazing. Tyler has the nickname of "Rose Capital of the World," due in part to Tyler Rose Garden. Despite being late in the season after a summer of odd weather (cooler than usual, and comparatively wet), there were still quite a few roses in bloom. I even managed to stop for a moment to smell one and snap a picture.

Rain lilies, or Zephyranthes

Leave it to me to go to a garden specializing in roses, which are eudicots, and pay the most attention to a few flowering monocots. Hence, the rest of my gratuitous plant pictures are a few exemplars of the diversity of late summer flowering monocots.

Onions, glorious blooming onions!

I found all of these plants in the IDEA garden, sponsored and maintained by Smith County master gardeners, so they certainly accomplished their mission of inspiring visitors.

Side-by side comparison of monkey grass varieties.

As an ardent admirer of plant diversity, I was delighted to find no fewer than four varieties of Liriope (monkey grass) growing in close proximity. Here you can see variation in leaf color (green, variegated, dark purple), leaf morphology (long, leggy vs short, compact leaves), and growth habit (clumping vs spreading).
Several varieties of agave

Given all the rose bushes in sight, it was a pleasant surprise to come across a xeric rock garden with several interesting varieties of agave. I'm working on a computational project with agave right now, so it's nice to be inspired by seeing the plants growing. I know there are lots of other resources in Texas for these and related species!

11 September 2014

In which I admit new depth to my dorkiness: knitting and teaching.

Greg Wilson did a great job during Software Carpentry instructor training this afternoon of using interesting examples and analogies to explain the psychology of learning. Long time readers of this blog might remember my use of analogies to explain research and teaching (sandwiches and DDR?). This is a habit I picked up from my first class on college science teaching, during my first year as a graduate student. My professor was the incomparable Sandi Abell, without whom I likely would not have achieved my career aspirations. Although she is no longer with us, I think often of her and the time I spent in her classes. One of our course requirements was to write a teaching philosophy using an analogy for teaching. I didn't do very well on the assignment. I tried to compare teaching to the scientific process or ecosystems or something similarly silly, given that the point of the assignment was to make our views on teaching more accessible to a layperson.

When I started applying for jobs a year ago, I pulled that teaching philosophy out of my file archives, blew off the metaphorical dust, and wrapped it in fluffy, wooly goodness. Indeed, I spent a good-sized paragraph describing how teaching and learning are like knitting. I know you're dying to hear how I made that work, so here you go:
Much of my leisure time is spent knitting. I'm not surprised anymore to meet other scientists and educators who play with sticks and string. In fact, knitting possesses many parallels to the process of teaching science in particular. Yarn represents content knowledge like vocabulary that forms the foundation of learning. Knitting needles are like questions offered to students to assist in connecting together loops of yarn to form fabric. A student's misconception is like dropping a stitch in knitting; the instructor must backtrack, correct the mistake, and then pick back up with the previous pattern or lesson. The knitted product represents the goal of learning: a cohesive object which unites together different aspects of knowledge and imparts functionality. In my opinion, science learning is a multidisciplinary, dynamic process that requires flexibility, and instructors who approach science teaching actively and inquisitively are most effective. In the same way, some of the most entertaining knitting projects include many different types of yarn, use interesting stitch patterns, and produce objects which are both functional and beautiful. Both teaching and knitting are skills which require time, effort and continual assessment to yield successful outcomes.
I probably could've written another five pages! Of course, that was just the introductory paragraph to my two-page statement, which was tied up nicely at the end with this hum-dinger of a line:
I hope to continue helping students “knit” scientific concepts together in an interesting, engaging manner.
See what I did there? I'm SO (or maybe just mildly) PUNNY. I'd totally take a class from me.

Gratuitous wool picture, spun and knit by me!
I was halfway through the application season, having submitted at least a dozen applications, before I started to wonder if that was really the best way to present myself as a serious, authoritative scholar. I chalked it up to job-season jitters, though, and persevered. Apart from the analogy method being Sandi-approved, I sincerely believe the analogy to be about as accurate as I could devise. And as I learn more about pedagogy through new faculty orientation and the SC instructor course, I'm finding that things which seem silly to me in the moment are actually an effective way of communicating about science.

I sally forth with my renewed commitment to knitting + teaching. I consider fiber arts and science to be sometimes contradictory but more often complimentary parts of my life. I'm comfortable with that, and I'm extremely grateful to have found a new group of colleagues who can appreciate it as well (I couldn't help it...I knit during my first faculty meeting last week).

02 September 2014

Fall 2014 semester preview

As of yesterday, I'm officially an employee and noob professor at UTT. As a way of previewing my plans for the semester, I decided to outline my plans for the semester. The bonus side effect is a feeling of accountability for me to report back about said plans as they come to fruition!

I'm fortunate as a new professor to have a semester reprieve from teaching. However, I'll be teaching bioinformatics (a lecture and lab) next semester, so I'm doing some professional development homework to give myself the best start possible to developing the course. I'll definitely be doing a lot of writing over the next few months about my preparations for teaching this course and related professional development workshops.
I'll be traveling a bit this semester, too. I've tried to limit myself to one work trip a month, and the resulting schedule reads like "Kate Visits Places She Used to Work":
  • September: Visiting U of Missouri, where I did my graduate work.
  • October: Departmental seminar at Western Kentucky University, where I did my Bachelor's.
  • November: Catalysis meeting (long term experimental evolution) at NESCent, which occurs right before a meeting to celebrate accomplishments of sponsored scientists and projects.
Of course, this is all in addition to the plethora of other routine tasks that I'm learning are a part of the professor job package: writing manuscripts, analyzing data, consulting with students and colleagues on projects, applying for grants, attending meetings, etc. My goal here is to have a decent balance between development of my educational and research job responsibilities. Will I manage it? Stay tuned to find out!

29 August 2014

Greetings from Texas, and my new office!

It's been quiet around here lately. My excuse this time was moving halfway across the country. I announced a few months back that I'm starting as an assistant professor at the University of Texas at Tyler, and I'm happy to report that I've arrived and am adjusting to this new role. Five days of orientation and other meetings last week was followed by a week of getting settled in to my office here on campus.

Getting an office of my own was high on my list of things to gleefully anticipate after moving. I'm very invested in having a working space that is comfortable with my commonly used materials readily accessible. That seems common sense, but it's a bit more unpredictable in practice. To be frank, my sense of aesthetics is somewhat...weird. I was assigned an office that formerly belonged to a group of graduate students, complete with a wealth of academic detritus to sort and clean. Rather than being disgruntled at the extra work, I was delighted! I enlisted the help of my kind partner, Matt, to rearrange furniture and bring in my books. What treasures did we unearth?

Hiding behind a bookcase was an old-school bulletin board. My office it near a main entrance for the building, so a campus map is handy for directing brand-new students to their classes (most of them are looking for another building, of course). I'm also adding some obligatory cat cartoons and geeky science pictures (top right is a sticker from Craig McClain's wood fall project).

Dum Dums....
of the chewy variety
Lurking in desk drawers were various electronics. I'm the proud new owner of a Dell desktop, three scanners, a printer, and too many other peripherals to count! I'll be setting them up in my lab next spring for students to use.

I've also learned that Chewy Dum Dums are a thing. I have a 2 lb bag, although I only keep a portion of them "on display" in this lovely fall-themed container (there's a This Is Public Health sticker on the other side). In the interest of public health, I'll probably eat the entire bag of candy myself...who knows how long they've been there!

The blood II
The pièce de résistance of my new office finds is a poster aptly titled "The blood II," made in Soviet Occupied Germany. It suits my pseudo-vampiric aesthetic quite nicely. On the wall opposite that masterpiece is one of my most prized possessions...a microbiology lab report in quilt form, made and gifted to me by my dear friend Katy. I have a few other posters and pieces of art to hang in here, and am planning on adding at least one wall hanging of my own (which has yet to be created...I'm thinking something knitted with needle felted elements, with nature motifs?). 

Katy's quilted microbiology lab report
So far, I'm satisfied with the setup of my space for now. I don't have any windows, so I might add a desk lamp (see my post about headaches and the importance of lighting). I also want to add some plants, and I have a few cricket "pets" hiding beneath my desk right now. Regardless, I'm very much looking forward to finally getting back to science after too many weeks of moving and administrative work.