24 July 2015

Getting ready for Botany 2015!

I'm heading off to Edmonton this weekend for Botany 2015. This conference is co-hosted by a handful of professional societies, a few for which I've maintained membership for several years (Botanical Society of America and American Society of Plant Taxonomists). I'm excited to be returning to this conference after attending Evolution for several years. My dance card is very full for this conference, but I'm looking forward to each part:
  1. Ecological niche modeling workshop: A few of my undergraduate researchers are pursuing some projects involving species distributions and niche modeling. Pam Soltis (who was on sabbatical at NESCent when I was there) is hosting a workshop on this very topic, and I'm elated to have some time to sit down and formally learn methods using QGIS, an open-source modeling tool.
  2. Oral presentation: I'll be presenting preliminary results from my characterization of transposable elements in Agavoideae (agave/tequila, yucca, etc). I'm really excited for this collaboration with two other early career scientists, Michael McKain and Alexandros Bousios, to finally come to fruition. You can read my presentation abstract here, and I'll be posted the slides to SlideShare after the presentation. 
  3. PLANTS mentor: The Botanical Society of America sponsors undergraduates from under-represented groups to attend their annual meeting, and I'll be acting as a mentor for one of these students during the conference. He'll be giving a talk on palm evolution that sounds great! I'm looking forward to meeting him this weekend.
  4. Student career luncheon: I've been invited to speak at a luncheon for student conference attendees about careers in botany. This sounds like a great way to share my experiences in my path to research and teaching. My short talk will be followed by "speed dating," where students will be able to interact with professionals.
  5. Professional society service: I have some additional obligations to serve a professional society during the conference, which makes me feel like a Very Adult Scientist but also will keep me pretty busy!

13 July 2015

Debriefing from TACC Summer Supercomputing Institute

I had such good intentions to blog more this summer during my reprieve from class planning, but that obviously didn't work out. A short blog post describing my adventure at the Texas Advanced Computing Center (TACC) Summer Supercomputing Institute (SSI) in Austin, Texas last week seemed a good way to reinforce my lessons learned (as well as provide a convenient way to ease back into a normal work schedule). Here are the highlights:

  • Students in the class were from a variety of disciplines, including applied math, physical science, and life science. Some folks were proficient programmers, others (like me) were familiar with running programs but had little experience writing their own compiled programs (consequently, I'm looking into taking more formal courses in CS).
  • The class covered a variety of topics, including parallel programming (OpenMP and MPI), debugging/optimization, data management, and data visualization. You can see some of TACC's previous course materials here (and I hope they'll add public access for materials used for our class, some of which were new!). I was especially enthralled with the session on data management, and am intrigued by exploring Hadoop for genomics.
  • Given that this class (as well as many of TACC's other training sessions) are geared towards folks with a background in programming, I spent some time talking to folks there about whether the resource is appropriate for entry-level folks (i.e., biologists rather than computer scientists). As it turns out, the marketing and education folks there are very interested in continuing to expand the user base, including folks who may not be very proficient at the command line. To that end, I've started a GitHub repo to develop materials for folks new to TACC (which I'll rely on heavily for my graduate-level bioinformatics class this fall). These materials might also be of use to folks who access HPC resources through XSEDE, which has a campus champions program that I'm thinking of joining. 
All in all, it was an intense but intellectually profitable week. Plus, I learned to make fancy figures! I don't know what it means, but the units are PARSECS! Super cool.