Exploring the Riches of the East

A great benefit to studying bioinformatics is the ability to conduct your research anywhere and anytime. Gone are the days of being tethered to a shared laboratory, forcing face-to-face interactions with colleagues on a daily basis. Even collaborations can be carried out exclusively through e-mail. For scientific research, bioinformatics is a hermit’s dream.


Donning archaic implements such as these are no longer required to do research.

However, I’ve always enjoyed interacting with like-minded individuals. But as the only student working on bacterial ecology/human microbiome project in a lab full of parasitic nematode enthusiasts, overlap is rare. So when a chance to visit with Robert Beiko’s lab (http://kiwi.cs.dal.ca/beikolabWordPress/) at Dalhousie University presented itself, I leapt at the opportunity. Getting to work with a stellar metagenomics group (while abandoning the landlocked northern desert of Calgary for a few weeks) was too good to pass up.

I made a brief visit to my native home (Cape Breton) and then joined the lab shortly after Canada Day. Although Rob was away at a conference, his students had me promptly up and running with desk space and a visitor’s network connection. I got to mingle with the group and learn a little about their research interests. The first thing I noticed was the broad diversity in the group; the backgrounds of the students and researchers spanned the fields of computer science, software engineering, evolutionary biology, math/stats, and molecular biology. This really fostered a collaborative environment, as each person’s strengths could be used to aid the research of others.

Upon Rob’s return, sitting down and chatting with him showcased what the lab is about. Although strongly rooted in computer science, the fundamental goal of their research is to understand the biologically meaningful interactions that could be identified in complex metagenomic data. I got to sit in on discussions about identifying novel species of Lachnospiraceae in the human microbiome, expanding analysis of microbial diversity to include broader phylogenetic levels beyond the constrained 97% similar OTU, and get feedback on both technical and biological issues that are involved in my own research.

Feedback on my research came from the whole lab, as I was given the opportunity to commandeer their regular Tuesday morning lab talk. Although I’m used to weekly talks occurring in the labs I’ve been a part of or visited, the Beiko lab had a unique way of conducting theirs. Notably, PowerPoint presentations were banned; all talks were conducted via dry erase markers and a whiteboard. The speaker for the week was selected through a random number generator and was handed a coffee mug containing writing implements on the morning of the talk. Although unconventional, this provided quite a few benefits:
– Speakers get to step away from their computers for a change.
– Discussing your research without being constrained to the “script” of a pre-defined talk allowed for more interaction with the audience.
– This format helps you practice discussing your research without the safety net of your slides.
– You can illustrate other points from your research on the fly.
– As my visitor status let me circumvent the usual random process, the lab was granted a one-week reprieve from being assigned the dreaded presenter’s “Mug of Damocles.” This pretty much guaranteed a happy and attentive audience.
– You get to draw stuff. Drawing is fun.

While I was there, I also got to engage in a microbial meeting led by the senior PhD student, Dennis Wong. The group met to discuss the different analytical methods used to study microbes. Luckily, on this day they were discussing phylogenetics, so I was able to contribute knowledge from my MSc days. It felt good to have something to contribute to the group, as I was gobbling up their time and space!

Near the end of my stay in the Beiko Lab, I had the opportunity to take in a talk by Dr. Jim Brown, director of computational biology at GlaxoSmithKline. His talk was titled “Human-Microbial Interactions in Drug Discovery.” He talked about how drug development is changing to incorporate microbiome data of the hosts/patients. It was directly related to my research and demonstrated new ways in which metagenomic data are driving research and development.

Experiencing how a different lab does business is informative and also great fun. As a grad student, a change of scenery coupled with a semi-vacation is probably the most relaxing way to establish new collaborations and remain productive. I had a blast visiting the Beiko lab, and look forward to interacting with them in the future!

Recently submitted grant applications

I’m in San Francisco for the Anthelmintics conference that kicks off tomorrow (Wednesday). If you interested I’ll be tweeting away with the ‘#anthelm14‘ hashtag. In the wee bit of spare time I’ve been afforded, my mind has drifted to grants. Oh joy…

I submitted two grant applications in the last few months. I’m not as brave as some, including Titus Brown, who put their applications on their blogs, I thought I’d share the word clouds associated with each application. I like word clouds, mainly because I like words and this presents them in a potentially meaningful light. I’m not sure exactly what they’re telling me. Sometimes I think this is how Sherlock sees things and then uses some Bayesian process or hidden Markov model to reconstruct the underlying text. I do find them useful to ensure that I haven’t used too many of those sentence adverbs that creep into grant applications, which we think help. You know… innovatively, strikingly, etc.

First, back in November, I submitted an application to NSERC (Natural Sciences and Engineering Research Council), entitled: Discovering the role of genome diversity and the molecular basis of parasite adaptations. The decision comes back at the end of March.

generated with Wordle.net

generated with Wordle.net

The second was submitted last week to the CCFC (Crohn’s & Colitis Foundation of Canada). This was not to work with nematodes, rather looking to go beyond the pie-chart to study microbiomes. The title is ‘functional analysis of the microbiome of Crohn’s patients to improve diagnosis and treatment.’ This was for an Innovation grant, their word not mine, so I felt that I could justifiably sneak it in a few times. Not sure when I hear back from these folks. Hopefully it’ll be with a cheque.

created with wordle.net

created with Wordle.net


Helminthology Graduate Course

A month has now passed since the close of the Fall Semester or Michaelmas Term, depending upon your vernacular. Over the last four months I coordinated three courses:

  1. Genetics & Molecular Biology, part of the DMV undergraduate programme.
  2. Advanced Topics in Microbiomes, a graduate course in the Veterinary Medical Sciences (VMS) programme.
  3. Helminthology, another graduate course in VMS.

With the new semester well underway, I thought that a little introspection would be worthwhile. How well did I think each course went? What did I do right? What could be improved upon? And what completely failed? I am able to include informal feedback from students, but the official feedback is withheld until the end of the academic year. Despite, this being an exercise in self-reflection (brooding?), I am at heart, mouth and deed an extravert. Hence, I thought I’d share…
I’m going to start with the Helminthology course, because we tried to go beyond what seems to be the standard for a graduate course.

The University of Calgary’s Faculty of Veterinary Medicine (UCVM) has (unwittingly?) built up research strength in helminthology (parasitic worms) covering Wildlife Ecology ( Susan Kutz, Ale Massolo), Pathology (Padraig Duignan), Molecular Biology (John Gilleard) and Genomics (my goodself). Further, Biological Sciences has Constance Finney and Medicine has Derek McKay, both immunologists working with helminths. Graduate students training in our labs leave knowing (hopefully) a lot about the specific field of study and on the specific species upon which they focused. However, what has been absent is a wider view on field. Is it not important that my students understand the ecosystems which interact with the genomes they’re sequencing? Shouldn’t ecologists know more about how the host tries to expel the helminth and how the helminth fights back? We thought so.

A total of nine graduate students and three postdocs took this course, making it the most populous elective graduate course in the Veterinary Medical Sciences programme.

Course Structure
Each week a different topic was covered, see below. A instructor-led lecture on the Monday was followed by a student-led workshop on Friday.

Topic Instructor
Ecosystems & helminths Andrew Dobson (Princeton) with Susan Kutz
The impact of climate change and helminths of wildlife Peter Molnar (Princeton) with Susan Kutz
Helminth morphology Mani Lejeune
Helminths of livestock John Gilleard
Drug resistance John Gilleard
Helminths of humans James Wasmuth
Genomics James Wasmuth
Host immune response Constance Finney
Immunoregulation by helminths Constance Finney

The lecture component was left up to each instructor; I’ll comment on my two lectures in another post. The student-led workshop were given a basic structure. It was important that students read the primary literature around each topic. However, we wanted to go beyond the traditional journal club presentations, in which one person presents a paper with powerpoint and the others may (or may not) ask questions. The structure we adopted was based on a recommendation by Mani Lejeune. Briefly, each week:

  • All students were expected to read both papers
  • Two students were assigned as moderators

A moderator’s job was to summarise the papers and then promote discussion among all those in attendance. Each student was assigned two sessions and when possible, the topics were outside his/her research focus. The PI for each topic was present during the discussion. My briefly guidelines were that PIs remain in the background and participate when asked a question or when prudent to do so.
After the discussion sessions, the moderators were then charged with writing a blog post each: http://ucvmhelminthology.wordpress.com/. They could decide between themselves how they wanted to split it up. They were also encouraged to go beyond a description of the paper and incorporate discussion points from the class. The students were also to set-up and administer the blog.
As it’s a course, the students needed to be awarded a grade. Each instructor scored the students’ participation in class, which was 50% of the grade and I reviewed the blog posts which accounted for the other 50%.

So… how did it go?
From a PI point-of-view, the course seems a success and we hope to run it again in 2015. I know, I know, you want to know that the students thought. Once I get the official anonymous feedback, I’ll share the love. As this may not be until the summer, I ran a one hour feedback session with the attendees.

What they liked:

  • The breadth of topics
  • Discussing the papers
  • The idea of writing the blog posts

What they didn’t like:

  • Not enough genomics
  • Writing a blog post outside their comfort-zone
  • The time spent writing the blog posts

I’m happy that the students enjoyed the structure of the course. I has been apprehensive of how the discussion sessions would pan out. After a slow start, all of the students got involved, some excellently so.

I’ve spent some time dwelling on their reservations towards writing blog posts. Among the PIs, we felt it important that they write more and embrace a form of communication that’s increasingly popular, if not commonplace in science literacy. Also, I thought that the blog posts were great. Check ’em out: http://ucvmhelminthology.wordpress.com/. Therefore, I was initially disappointed by the feedback. Now, I feel that there were two core problems: 1) Blogging is new to them, 2) they were being graded. While, I do not believe the tail should wag the dog, I will probably make some changes for the next running of the course:

  • Award a pass/fail for the blog – if they write something, they pass.
  • Allow the students to write one a topic of their choosing, rather than assigning all of the topics.

I asked the students and postdocs if they wanted to carry on contributing to the blog and there was nodding of heads. I asked if they would try and spend 90mins each month, writing about an aspect of helminthology they found interesting. That’s not much time and I hope that some of the students can embrace the opportunity. I look forward to reading and learning…

Bioinformaticians wanted in Calgary

Bioinformatics Analyst
In the Faculty of Veterinary Medicine, we’re recruiting a Bioinformatics Analyst to support the growing number of bioinformatics and genomics projects undertaken by our researchers. For more details check out the posting.

Faculty position in Genomics/Computational Biology
The Department of Biochemistry & Molecular Biology, Faculty of Medicine is looking for someone to join the faculty. For more details check out the posting.

Voluminous Veterinary Medical Sciences

Within the Veterinary Medical Sciences graduate program we are aware of the broad range of research undertaken by students with an even more extensive range of backgrounds (e.g. DVMs, biomedical sciences, ecologists and policy). I carried out my PhD studies in the now defunct Institute of Cell, Animal and Population Biology, part of the University of Edinburgh’s School of Biology. Here, I shared the cafeteria with immunologists, quantitative geneticists & entomologists. I cannot speak highly enough of being in such a dynamic environment. During my time, ICAPB was split into two –  Evolutionary Biology and Immunology and Infection. However, they still share a building and a social lounge, splendidly named the Darwin Dance Hall.

My postdoc was at a hospital’s research institute. The research focus of the departments was considerably more narrow than my previous experiences, and with good cause. However, I often found myself wandering over to the biology-based departments at the University.

When I was applying for faculty of jobs, how academic expansive the research interests of the faculty/department wasn’t high of the list of requirements. However, it should have been. I’m back in such an environment and loving it. I wish that the School of Biological Sciences was a little closer than a 30min stroll, especially in January & February. At least I earn the cookie.

I sit on the graduate education committee, and we’ve been working very hard to ensure that the capacious nature of VMS is a strength. A seminar series is being implemented, where students will present their work to peers. The skill will be reaching out to students with different backgrounds. Equally, the attendees will become immersed in various research topics and approaches. This can only help with their own thinking. It’s gonna be fun.

Parasites @ Calgary Science Cafe

On the evening of May 28th, almost 100 members of the public and a smattering of UofC students crammed into the back room of the Ironwood Grill, Inglewood, to hear about parasites. Dr Patrick Hanington, of the University of Alberta’s School of Public Health and UCVM’s Dr John Gilleard, were the guest speakers at a Science Cafe, co-hosted by the TELUS Spark Science Cafe and the UofC’s NSERC CREATE program in Host-Parasite Interactions.

Dr Patrick Hanington & Dr John Gilleard

Dr Patrick Hanington & Dr John Gilleard

Dr Gilleard started proceedings by providing the audience with an overview of the impact of parasitic diseases, specifically those caused by parasitic worms, i.e. helminths. Usually thought of as diseases of the poor in sub-Saharan Africa and South-East Asia, many in the audience were surprised to learn of the negative impact caused by helminths in the livestock industry in the developed world. The cost in Alberta runs into the tens of millions of dollars. Many of the anti-parasitic drugs currently used were first developed for the livestock industry and later licensed for use in humans; a great example of comparative medicine in action. Unfortunately, resistance to these drugs is now commonplace in parasites of livestock and an emerging concern for humans. Not to paint a completely bleak picture, Dr Gilleard highlighted how new approaches in molecular biology and genomics are helping find new treatments.

Dr Hanington focused on a helminth disease called schistosomaisis, which is caused by the Schistosoma worms. These worms spend part of their life-cycle in snails, from where they emerge in aquatic habitats to seek a mammalian host, including humans. Drawing on his own research, Dr Hanington described how this complex life-cycle makes it difficult to eradicate the parasites through drug treatment. As effective are simple changes in human behaviour. For example, lakeside workers wearing knee-length rubber boots and the need for decent sanitation.

During the break, the public gathered around a table upon which sat specimen jars containing various helminth species, ranging from microscopic to meter-long. The over-riding emotions were one of mild horror and intense fascination.


A question period followed, where the audience asked about a broad range of topics, including: the potential effects of climate change to the likelihood of helminth infection in Alberta, and how research into these parasites could be better funded. The event was a huge success and hopefully just the first collaboration of many between the Host-Parasite Interaction program and the city’s cultural institutions.

Organized by TELUS Spark, Science Café is held on the fourth Tuesday of every month at 6:30pm to 8:30pm from September through May at the Ironwood Stage and Grill (1229 – 9 Avenue SE). For more details, please visit: http://www.sparkscience.ca/events/science-cafe/

During the morning of Tuesday, May 28th, Dr. John Gilleard was interviewed by Dave Norris, radio host of “My Two Cents Flat” from CJSW 90.9FM. Click here to hear the interview.

More Photos of the Science Cafe and Dr. Hanington’s Seminar in the afternoon of May 28th at the UofC and the trainee pizza lunch.

Summer addition to the lab

A warm welcome to Jeff Wintersinger to the lab. Jeff has just completed the third year of his BHSc in Bioinformatics, here at UofC. He’ll be investigating the extent of in silico miss-assembly in parasite genomes and the effect this has on identifying large gene families. The work is an spin-off from the mBio paper. This work on the SRS gene superfamily in Toxoplasma was complicated by very similar and distinct gene sequences being collapsed into one locus by the genome assembly algorithm. The result was either a single representative gene model for four or more in vivo genes, or, sometimes, no gene model. If this has happened for a relatively small and deeply sequenced genome as that of Toxoplasma, then I fear for the larger, more complex helminth genomes. I eagerly await Jeff’s results in August.

Jeff joins Ivan Kryukov as an undergraduate student in the group. Ivan’s staying on from successful winter term projects, one of which was his honours thesis, for which he was awarded an A grade. Ivan will be turning his attention to characterising the Cathepsins in nematode species. He’ll be finally scratching an itch to learn more about phylogenetics.