Ecological Models and Data at Bamfield By Michelle Gordy

“A unique experience” is probably the best way to describe, likely any course at the Bamfield Marine Sciences Center (BMSC), but most definitely the Ecological Models and Data course. Set in the small marine village of Bamfield, on the west coast of Vancouver Island, BC, the BMSC provides a temporary home to researchers and students from all over Canada and beyond. Nestled behind the Broken Islands within Barkley Sound, the BMSC sits between epic forests and the Pacific Ocean. The campus offers outstanding views, all from the comfort of “The Rix” (Rix Centre for Ocean Discoveries) and the library, where we spent about 85% of our time, because this was a computer-based course. We did get the chance to visit some of the amazingly beautiful beaches, hike a bit of the West Coast Trail, and play around in the intertidal zone to see the plethora of marine life surrounding us. Beyond the scenery, this course uniquely offered an intensive three weeks of mathematical modelling, computer programming, ethical discussions on p-values and scientific philosophies, random row boat trips to get ice cream, late nights at the library, and random bouts of sleep-deprived laughter.

The view from The Rix

(Photo credit: Jody Reimer)

The view from the library

Trips to the beach for paper discussions

(Photo credit: Jody Reimer)

The intensity of the course not only created an atmosphere of bonding between the students, but an opportunity to learn through teaching, something I was not expecting. What I mean by this, is that there was a wide variety of backgrounds among the students, ranging from undergraduate students who have never used R to PhD students that use R every day, or are in the math department and learning how to use ecological models. When we would work on our labs together, we would all, at some point during the course (usually late at night in the Rix or the library), would take what we knew and teach it to our fellow classmates, so we would all successfully complete the labs on time. The learning curve associated with this course was high, and the instructors knew it; they were outstanding at being there (some even during the night) to help us through, and guide us. Though the workload was high, and the timeframe short, I believe that being at the BMSC and being away from the business of home helped to provide the best learning atmosphere. The collective knowledge of the instructors and the TA were impressive, and they all presented an incredible ability to teach and relate abstract concepts to real world problems.

This course benefits my professional development in more ways than I expected. I had originally thought it would be a great way to finally learn how to use R, the most widely used computer program for ecologists, and this would be the greatest benefit for my future career. While, yes, I did definitely learn how to use R, I also learned a great deal about statistics, about ethics in publishing, about how learning isn’t always best done by someone telling you exactly how to do something, but rather helping someone to figure it out on their own, and that hard work really pays off. I learned a great deal about getting out of my “comfort zone”, and dealing with complex problems in a short timeframe. I have no doubts that these lessons have impacted the way in which I view a career in science/research, and that they will improve my chances at success in both my current PhD research, and in my future career as well. Having a greater understanding of best practices in ecological research and modelling has already changed the way in which I am considering the analyses I will be using on the data I have collected, and how I communicate that to other students in the lab.

The best quote to summarize the Ecological Models and Data course came from our first lecture. It was “See the ecological forest through the statistical trees. Because if you don’t… there be dragons!!”. This quote not only made it to the back of our class t-shirts, but serves as a reminder that statistics can often be misleading, and we can often use them wrongly. It is important to have a strong understanding of the statistics and models you’re using, because you could be missing what’s really going on, or misinterpreting the true patterns.

The dragon part comes in because every time we learned about “the wrong way to do things”, ‘Hurlbert’ the dragon would appear.


My only advice to other students interested in taking this course would be to come into it knowing that the intensity is worth the payoff.

I’d like to express my sincere thanks to HPI and the University of Alberta for helping to fund this opportunity through professional development awards.


Ethiopia Short Course 2016 | By Joel Bowron and Timothy Jayme

I had the unique privilege to aid Drs. Guido van Marle and Lashitew Gedamu along with fellow graduate student Tim Jayme to travel to Africa and teach a workshop on molecular biology and bioinformatics. I was honoured to be chosen for the trip, and was not disappointed in the thrilling opportunity that awaited me in Africa – the birthplace of humanity.  In the months that led up to the trip itself, there were many meetings, many workshops, and lots of brushing up on rusty molecular microbiology techniques. Tim and I were tasked with developing assignments for the workshop. For my part, the assignment included a number of bioinformatics and virtual molecular biology tools, many of which are available freely on the internet. But how do you access these types of tools in a rural area in a country where the electrical infrastructure is sometimes as simple two exposed live wires that you connect and disconnect when/if you require power (this is how our hotel was powered off the main grid)? This was one of the first challenges that presented itself to me. The short answer to this question is you have a back-up plan, and a back-up plan for your back-up plan, and so on. With internet being even more sporadic than the power grid, you download offline tools, and, when all else fails, you resort to good old fashioned pen and paper. I worked and polished my assignment until I felt I had accounted for almost any contingent.

In addition to working on physical assignments, we were also tasked to act as teaching assistants (TAs) to run the wet lab portion of the workshop. In the wet labs we were running different types of PCR, including sequence specific PCR and qPCR (or real-time PCR). Here we reinforced concepts learned from the lecture portion of the workshop to really enable the students achieve a thorough understanding of the work that they would be doing. This, in my eyes, was one of the most applicable and fundamental lessons for the students. The connection between theory and practical application is where you would see so many of those “lightbulb” moments where you see the students connect the concepts and really start to grasp the power of these types of molecular techniques.

image3-1This experience was unique, not only in its professional challenges, but for me on a more personal level as well. Born and raised in Calgary, Alberta, I have never set foot outside the continent. On this trip alone, I had tripled the amount of continents I have set foot on, adding Europe and Africa to the list. With a short 12-hour layover in London, England, Tim and I decided to make the most of it and take a quick tour of the sites. After a grueling couple days of travel, we finally arrived in Addis Ababa, Ethiopia. Addis was startling to someone like me, and definitely took some getting used to. Traffic is chaotic, there truly appear to be few observed rules of the road. You push, you shove, and eventually you get to where you’re going. During our stay in Addis, we toured around the city, saw some sites, and met with various people from AHRI (Armauer Hansen Research Institute). Here we toured a facility that was being built as a Tuberculosis research lab, as well as the current research laboratories. It was truly amazing and inspiring to see the amount and quality of research being carried out in the labs we toured, and it made me appreciate more fully the amenities of my own lab.

After spending one week in Addis, we flew to Gonder, a rural city up in the north of the country, where we carried out three of the five days of our workshop. It was in Gonder that we met up with Drs. Dylan Pillai and Bonnie Meatherall who were teaching an infectious disease workshop in parallel to ours. The workshops were definitely a resounding success and I think were appreciated by all parties involved. Now, when I say we carried out three of the five days of our workshop, I feel I must admit that our workshop was regrettably cut short in Gonder due to unforeseen protests, that had unfortunately turned violent. I begrudgingly admit this because, while we did end up flying out of Gonder early for safety reasons, I never felt like my safety was in jeopardy. I should further explain that both the University of Gonder and Dr. Gedamu never hesitated when they felt the situation warranted action and were commendable on the mitigation of any possible risks. Furthermore the president of the University of Gonder personally escorted us to the airport and facilitated our departure from the city. I also feel obliged to point out that Dr. van Marle and Dr. Gedamu have never witnessed this type of activity in the 7+ years these types of workshops have been held in Ethiopia.

While the situation during our trip was not ideal, I feel confident in stating that I have walked away from this trip with hundreds of positive experiences and would recommend this experience to anyone remotely interested without hesitation. I can only say positive things about my time in Africa, and wouldn’t skip a beat if asked to return. Africa is such a beautiful place, and the citizens of Ethiopia were warm, welcoming and extremely courteous. I met so many amazing people on this trip and cannot fully express my gratitude towards everyone involved in making this experience a reality for me. For my part, I would like to thank the NSERC-CREATE Host Parasite Interactions groups for facilitating my trip, as well as personally thank Drs. Guido van Marle and Lashitew Gedamu. I would also like to thank our contacts in Ethiopia, at the University of Gonder, who truly made us feel welcomed and comfortable and were always around for us. Finally, I cannot recommend this program enough, and encourage anyone who is thinking about it, to apply. It is a unique and amazing experience, and has opened my eyes to a more global perspective which I believe will help shape my career aspirations in the future.

Great Lakes Bioinformatics Conference by Sonja Dunemann

Blue sky; the Toronto skyline on the close horizon. A church tower to my right – I think it is my right. There is a delightful hubbub in my head – I am in Canada! I am in Toronto! I am lying on a rooftop patio of the most recommended hostel by The Lonely Planet, my favorite travel adviser. I am thinking that I want to implement all the terrific things I have learned at the conference, and about where I am going to go next.

Okay, this is a challenge: which Great Lakes Bioinformatics

(GLBIO)/Canadian Computational Biology (CCBC) workshop should I sign up for? There are several workshops that are of major interest to me and could potentially be helpful for my current research project: proteomics of the zombie ant parasite. Before I can decide, the machine learning (ML) workshop is full, so I sign up for the Cytoscape Networks workshop (Networks, proteins! This might be helpful!).

In the end, I shouldn’t have worried too much. There was space left in both workshops that I did not sign up for, namely software engineering and machine learning, so I could go to all the workshops I was interested in. The software engineering workshop was as basic as expected (thanks to well informing websites of the organizer), but I figured I could learn a couple of helpful tricks to improve upon my coding. The Cytoscape Network workshop was more directed to Biologists than to Bioinformaticians. It presented the Cytoscape software and how to use it. But luckily, I could finally learn something about algorithms such as random forests in the ML workshop (thankfully it was in the evening so I could – miraculously – find a spot for myself). Material for the ML workshop can be found on GitHub (

Before going to the CCBC conference, I became familiar with the field of proteomics. I read a lot of papers and tutorials by authors not yet known to me. It has always been a highlight for me to meet the authors of papers I studied, especially if these papers were of high relevance to my own research. At the CCBC conference, I had the privilege to talk to the leader of the proteomics field, Alexey Nesvizhskii, in person.

My own contribution to the conference was a poster about my proteomics project. Although the project was not yet complete, I presented some preliminary results. Due to numerous questions of people that were not familiar with the project, I could remind myself of the big picture behind it, and its necessity. A fellow German student presented her poster next to mine, and we exchanged our thoughts and challenges.

Going to many talks a day, our attention might wander off from time to time. The keynote speaker Jennifer Gardy however told us a captivating crime story about a tuberculosis outbreak, and how genomics can come to the rescue. Yes, that is what we like! More of that!

In conclusion, I gained a lot from the conference: networking, making friends, and learning new things about my own field. I would like to thank the NSERC-CREATE HPI program for providing travel funds that helped me attend this conference.

Conference of post-secondary learning and teaching at U of C | By Anna Manko

In May 2016 I had an opportunity to attend the 2016 Conference on Learning and Teaching at our Alma Mater, University of Calgary.This event was held in the Taylor Institute of Teaching and Learning at U of C.  The conference focused on the creativity in teaching and learning. It was a very new experience for me to attend this type of scientific event. This year there were around 250 participants from all over the country: from Montreal to Vancouver, and some participants came from USA.

It was too difficult to choose which sessions to attend; I tried to attend as many sessions as possible however. The first keynote speaker was Dr. Robert Kelly; his talk was devoted to the creative development in education through thinking, innovation and invention. He convinced the audience that people use creativity in their life from day to day, just they don’t name it “creativity”. It was of special interest for me to understand that in the scientific discipline where it seems like there is no room for much creativity when communicating research. However, through the different approach learned in this session, the use of words and techniques make it possible to engage and inspire an audience.

At the end of the day we had poster sessions where students and teachers presented their results. One poster that caught my attention was related to how the creative-organized learning space at the university affect the efficiency of studying. Using many pictures, the observational research project demonstrated how students working space could be organized in the effective manner.

The next day consisted of a couple of active workshops where we had chance to discuss with colleagues what the role of a teacher is in the formation of learning desire in modern students is. One of the memorable sessions was a workshop related to the creative ways to teach biosciences, historical and sociological classes. Presenters had a lot of visual materials that helped the audience follow their talk.

I would like to thank NSERC CREATE HPI for providing some of the funding that allowed me to attend this meeting.