22 October 2014

When a computational biologist yearns for the field/lab/greenhouse.

A darling little rose bush.
I'm a sucker for cute little plants on sale at the grocery store. I saw these delightful miniature rose bushes when I first started shopping, and waffled for the next 15 minutes as I circulated the store about whether to take one home with me. I ultimately relented, because I decided that it was a small price to pay to feel more connected to my new home city (Tyler has a thing for roses, including a pretty nice rose garden!).

My compulsion to surround myself with plants started during my undergraduate education after taking plant taxonomy and beginning to work in a molecular systematics of plants lab. I enjoyed working in the field, but realized during graduate school I was more suited to computational work. After three years as a NESCent postdoc, during which my work was exclusively computer-based, I found myself yearning to physically get my hands on some live organisms (hence the compulsive purchases of houseplants).

Happy Commelinaceae in the greenhouse.
The problem is that I've been hired as the resident bioinformatics/genomics person, which brings with it certain expectations about how I spend my time (mostly, analyzing data that other people collect). As a scientist, though, I think it's important to still maintain a connection to my study organisms. My plants a source of inspiration and wonder, as well as a resource for future research questions, and I'm loathe to permanently pigeonhole myself as a "computer person." How do I balance these opposing expectations?

My research mindset right now is one of nearly infinite possibility. I want (and need) to be productive as a scientist, but it's up to my discretion exactly how to make that happen. I work at a small, regional university, which means I may need to be creative (financially and with other resources) about how to set up research projects for my students in the future. I have some of my Commelinaceae living collection growing quite happily in the greenhouse here in town, and access to growth chambers on campus if I want to do hybridization or selection experiments.  Even though I don't have immediate research plans for my plant and DNA collections, I'll keep them as long as I can to keep my options open.

From a teaching perspective, I'm really excited about designing courses which capitalize on either computers or live organisms. I've already written about the bioinformatics course I'll be teaching next semester, and I'm considering offering a class on plants of Texas (taxonomy and systematics). I helped teach plant systematics as a graduate student, and find myself really excited at the prospect of getting back into the business of instructing students about the local flora.

Ultimately, I know trying to balance these opposing forces are making my life at least a little harder. It's more work to figure out effective pedagogy for classes based in the field and on computers. Oddly enough, my educational and work experience has set me up for precisely these tasks (see references to my experiences above), and there are quite a few other academics who successfully split responsibilities between different projects. What's the main reason that I remain committed to being a jack-of-(plant and computer)-trades? It makes me happy, of course.

21 October 2014

Student motivation, AKA Please take my class.

My current homework for Software Carpentry instructor training is to think about a time when I lost my motivation to learn. I posted my response to the SWC blog, where you can also poke around a see other folks' stories (click on the "Motivation" tag).

The other part of our homework is to work on a three-minute pitch to motivate students to learn a particular topic. The timing of this assignment is fortuitous, as I'm also promoting the bioinformatics class I'm teaching next spring as well as an undergraduate minor in bioinformatics and genomics. I took to twitter with my attempts at persuasion:

Disclaimer: I am not planning on physically harming students if they have a different shell preference than bash, and I don't particularly dislike perl. I'm really just rather fond of word games.

A few other folks chipped in with their own token words of wisdom:




It's not surprising that my motivation for getting students to take bioinformatics differs from their reasons for enrolling. I am personally passionate about teaching next semester because I think I can help students be better scientists and thinkers. I'm hoping to convince them that it will help them be more marketable (taking additional biology and computer science classes will certainly accomplish that). 

At times, these persuasive attempts seem like fighting a rather uphill battle. Convincing students to take extra classes that bridge boundaries between different types of knowledge is difficult, especially when students who might be interested are already quite overwhelmed by courses required for their major. I come across lots of folks who are intimidated by large datasets or using a command line interface. 

I spend a lot of time talking to folks about my experiences, and how I'm planning on teaching. 
Here are my talking points in encouraging folks to step up to the plate and learn some bioinformatics, from the perspective of a biology student who has little computation experience: 
  1. You can do this. Not too long ago, I was in your shoes. I didn't know a lot about computers, how they worked, or how I could use them to answer questions. I don't have a ton of formal training in computer science, and my degrees are all in biology. Writing computer scripts may seem really different from other things you've studied, but...
  2. Learning a little can be very powerful. Learning to work on the command line and write computer scripts will take work. You will be surprised, however, at how many tedious, mundane tasks you can accomplish much more quickly and efficiently with a little bit of shell scripting. Better yet...
  3. These skills are transferrable. You may not end up working in a job where you need to assemble genomes or build phylogenetic trees. It is possible, though, that you'll need to manage large numbers of files or answer questions about large data sets. You can apply these skills to lots of other practical tasks, but in addition...
  4. The topics are interesting. Technological advances are producing genomic and other large-scale biological datasets at an unprecedented rate. The applications of these data include empirical research, agriculture, and medicine. 
At the very least, I hope to convince students the first point is true. Nothing is more frustrating than hearing students declare, "I can't do that." A student saying "That's too hard" is a student who's hit a motivational brick wall, and can't even ask themselves whether it might be beneficial for them (or, heaven forbid, that they might enjoy it!). If they can do that, hopefully one of the last three points will be appealing.

On the other hand, I'm still trying to figure out effective ways to appeal to computer science students. The fourth point above definitely still applies, and they can arguably improve (or at least broaden) their job prospects by gaining some understanding of biology. More importantly, they can learn to answer hypothesis-driven questions, which seems to be less of a focus in their curriculum than in biology. 

As always, this is a work in progress. What am I missing? I'm planning a few mini-workshops on for students (graduate and undergraduate) on campus, which will certainly allow me more opportunity to pinpoint more effective pitches. These students are not motivated by the same factors that convinced me to pursue higher education, and bioinformatics for research. I need to find out what they need. However, I struggle with how much I should cater to student interests. That, however, is part of a broader discussion about the purview of higher education, and is perhaps left to another post.

15 October 2014

My office is a pit fall trap.

A real conversation starter.
If you couldn't tell from the entire post I wrote dedicated to my new office, I'm very committed to the space where I do the majority of my professional work. The items I choose to display in my office are used by students and colleagues, both consciously and subconsciously, to assess me as a person and scientist. Given that I'm trying to recruit students for research but also depend on other people for data, I'm invested in making sure visitors see my office as comfortable and welcoming (despite the dulcet tones of the toilet flushing next door, which are very audible at times).

To foster a sense of openness, I prefer to leave my office door open. I knew from the start that it would invite random visitors to drop in. What I didn't realize is how many such requests I would receive. I started keeping track of them: 


Most of the requests are innocuous (students looking for a particular classroom or office). I get pretty annoyed when students stop and ask for things like staplers, or for someplace ambiguous ("Advising?" For what department, pray tell?) as it's obviously a lack of foresight on their part. I was amused when a guy offered me a turtle that he found in the mechanical room (because OF COURSE a biologist would want a turtle, even if I don't actually have a lab yet or do wet lab work? I told him to take it outside to lake where DOZENS of other turtles live). 

While in the process of writing this post, a student stopped by and we had the following conversation:
Her: I know I don't have you for any classes, but you're a biologist, so can I ask you a question about inductive and deductive reasoning?
Me: Why me? It's just because I'm here? You have an exam today, don't you?
Her: Well, yeah... 
I've asked my colleagues, and I know they get far fewer questions like this. I sometimes wonder if students would interrupt my work so frequently if I were male, or 30 years older. But then I thought about how my office looks if you're walking down the hall:


That door is admittedly awkward, sticking out into the hallway. Then I realized how much my office looks like a pit fall trap, a commonly used method for capturing animals in the field:


As animals are wandering around, they hit the fence and walk along it until falling in the trap....just like what happens when someone is walking down the hallway, lost and confused. The location of my office is also partly to blame; I'm the first room inside the door to a confusing connection between buildings.

There aren't any easy solutions to alleviate my periodic irritation at having to answer random questions from strangers. I can open my door all the way to prevent the "drift fence" effect. I'm talking with campus facilities about putting up some signs to help direct folks to the appropriate building/department. I can remind students each time they interrupt me that they have the capacity to think ahead (i.e., look at the syllabus to find an instructor's office). 

Every once in awhile, though, I assist a student who is legitimately frustrated and I feel better for having alleviated their anxiety a little. Our university has a lots of first generation college students, and I empathize with folks who have little experience on which to base their interactions with folks working in higher education. As a result, there are a number of programs set up to help alleviate these issues and promote better students learning. It's easy for those of us from privileged backgrounds to view these efforts as hand-holding, but there is plenty of evidence on the efficacy of such programs in student retention and success.

If I challenge myself, I too admit the impact of a few individuals on my academic success, and how getting a simple question answered quickly makes a huge difference when juggling work, school, and family responsibilities. Besides...I wanted to work in academia because I like interacting with students! Ultimately, a handful of interruptions to my workday each week are a small price to pay for helping a student succeed.

14 October 2014

A trip back to my ol' Kentucky (and Indiana) home.

Historic buildings on Franklin Street are framed by neon
lights for one week a year.
As promised in my semester preview, and as a follow up to my Missouri trip a few weeks back, I had the opportunity to head back home to southern Indiana and central Kentucky last week. The timing of my trip was fortuitous, as my hometown of Evansville, Indiana was celebrating a momentous yearly event: the West Side Nut Club Fall Festival. More than a street fair, the Fall Festival marked the official start of autumn during my childhood. It's been probably ten years since I last partook of the food and frivolities. However, I was born and bred on the west side of town (my high school is less than a mile from the festival's location), so I fell back into old celebratory patterns without much trouble.

My happy face at
Fall Festival food.
As a kid, I was pretty invested in the games and rides at the festival. As an adult, I didn't even step foot into those areas, instead preferring to walk along the 4+ blocks of food vendors (each booth is a fundraiser for a group in the community, including several of my old school groups). My mom was kind enough to accompany me on my meanderings, which makes for great food-grazing because we could share twice the number of different menu options. I could wax philosophical about the virtues of various chili and cheese covered, deep fried concoctions, or you could take a look at the index of foods from this year's Munchie Map. Some items, like brain sandwiches and burgoo, are regional specialties. Some booth attract patrons with weirder options, like pickle juice slushies. I stuck with more traditional choices, like turkey burgers, stromboli, and cobbler with ice cream.

Of course, watching people is my favorite pastime at these events. The best overheard comment this year was from a family that stood in a semi-circle sharing corn dogs. One woman remarked (ever so sagely and without accusation), "Well, if one of us has ebola, I guess all of us do now." Indeed.

A rather large gingko tree.
The purpose of my trip was to give a seminar for the Department of Biology at my alma mater, Western Kentucky University. Part of the reason I'm enjoying my new job at UTTyler is because, as a regional school, it feels familiar to WKU. Campus has grown since I left, and the science folks have some great new teaching facilities. Despite these renovations, I was pleased to see this fantastic old ginkgo tree still standing between buildings.

It was a pleasure to meet with both mentors from my undergraduate years as well as with other assistant professors. After my graduate education and postdoc work at R1 universities, it's refreshing to talk to folks who are making a real difference in under-served parts of the country, both by helping students conduct science research as well as teaching classes in evolution.

It was gratifying to see a lecture room near full to bursting with students for my seminar that afternoon. I'm sure it was due in part to extra credit being offered for classes, but I hope a few of them gleaned some sort of benefit from my discussion linking the evolution of organisms to that of genomes and transposons (the powerpoint is available on Slideshare if you'd care to take a gander). After all, I graduated with my bachelor's degree from WKU less than ten years ago; if I were to believe the words of several folks I've encountered lately, I'm a shining example of a "success story."

Historic letterpress prints from Hatch Show Print
Why do I feel the need to qualify my "success" with quotation marks? For now, suffice it to say that I'm way too excited about developing classes and proposing new research to feel like I've accomplished anything more than the promise of more work! As my undergrad advisor, Larry Alice, reminded me when I saw him last week, I also need to enjoy myself. Recalling my previous obsession with mosses, he remarked: "Don't forget to stop and smell the bryophytes." In the spirit of following his advice, I allowed myself to make my travel back to Texas a little less miserable by sipping a caramel latte and perusing the Hatch Show Print display of historic letterpress designs in the Nashville Airport. Mmm...whole hog sausage.

13 October 2014

Managing your academic identity.

A friend from Facebook posted today that she stumbled across another academic with her same first and last name, working on similar research topics, and remarked that mistaken identities were bound to happen.

There are few other Hertwecks out there, but I still do what I can to manage and maintain my academic identity, so that other folks can find this blog, the papers I write, my research website, etc. There are social media style sites for maintaining your research products (Academia.edu, ResearchGate), but here are my favorite alternatives:

  1. Get an account on ORCID. It's free, and you'll get a unique identifier to include when you submit grants, manuscripts, etc. This is also a nice segue into checking out your Scopus author identifier (if your organization has access).  
  2. Curate your Google Scholar profile. This is another free tool, and there's nice documentation and explanations if you click through the link. Citation tracking tools and the ability to manually adjust which articles show up in your profile makes this a quick go-to for academics, plus there are other functionalities built in (i.e., citation alerts for topics which might interest you).
  3. Sign up for Impactstory. This is a great option if you have an active presence in social media or invest energy in other types of non-traditional academic deliverables. Although they recently transitioned to a paid subscription service, they are a non-profit and your money goes towards keeping the data and software open-source.
These were the first options that came to mind, although there are others which might be of interest. What am I missing? Who's got a better resource for maintaining your academic identity online?

06 October 2014

Two of three.

I believe in borrowing professional inspiration from any available source. My partner, Matt, and I were talking about working effectively with others awhile back and something he said stuck with me.

To be successful, you need to do two of three things:

  1. Have brilliant ideas
  2. Meet deadlines
  3. Be pleasant in working relationships
I think the simplicity of it is what appealed to me. Academics are expected to be outstanding researchers, effective teachers, and committed to service. Doing even one of those tasks well can be a full-time job, so performing all three brilliantly seems nearly insurmountable. Conceptually, meeting two of the three listed criteria above is very much in line with my personal philosophy: it implies plurality (multiple paths to success) and allows for imperfection (you don't have to do everything well all of the time).

Most importantly, it seems attainable. Indulge me a moment while I break these criteria down for myself. Can I have brilliant ideas? Well, I must have something ok to say every once in awhile to have finished my dissertation, published some papers, and gotten a job. I think I can keep doing the brain-thinking-stuff the way I have up until this point. Can I meet deadlines? I think so! See above comment related to past precedent. Can I be a nice person to work with? Hmm. I'm loathe to admit that this last option is the hardest for me at times. I've worked really hard to moderate my attacks of grumpiness, especially when dealing with students. Presenting myself as friendly, open, and approachable is still a struggle at times (especially if I'm distracted by some program debugging or it's allergy season), but I can do a decent job at ameliorating my intensity.

Like all recipes for success, this one is by no means fool-proof. I won't be including a personal assessment of each of these things in my tenure packet. But as a way of thinking about my day-to-day interactions, I find it a fairly workable solution. After cogitating on this advice for a year or so, I finally asked Matt where he found it. I was immensely pleased to learn it came from one of my favorite authors, Neil Gaiman. You can read his full speech and see a recording here (the excerpt listed below starts at 14:10).

From Neil Gaiman's keynote address at the University of the Arts, 2012:

People keep working, in a freelance world, and more and more of today's world is freelance, because their work is good, and because they are easy to get along with, and because they deliver the work on time. And you don't even need all three. Two out of three is fine. People will tolerate how unpleasant you are if your work is good and you deliver it on time. They'll forgive the lateness of the work if it's good, and if they like you. And you don't have to be as good as the others if you're on time and it's always a pleasure to hear from you.
Of course, he's talking about succeeding in the arts, but I'd like to think the general framework is transferable to other types of professions. As a science educator and researcher, there's perhaps less flexibility in adherence to these criteria than if I were a freelance artist. For example, when a grant application is due or a classroom of students is depending on me, deadlines are not negotiable. But when I think about the variety of successful scientists I know, they actually do fit into this "two-of-three" framework. There are actually even cliches about scientists that follow this rule. Think about the friendly, absent-minded professor (pleasant, brilliant, but misses deadlines), or the acerbic and curmudgeonly professor (brilliant, insists on deadlines, but won't show up at happy hour).

Personally, I'm going to aim for doing a pretty good job at all three things, at least most of the time. "Two of three" will be my mantra to cut through anxiety fueled by perfectionism. Next time I'm a day late returning a manuscript review, I'll be able to forgive myself bit more easily, because I know the review will be thorough and polite. Two of three...not too bad.

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.

Considerations:

  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.