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<h1 class="title toc-ignore">Work Term 1 & 2</h1>
</div>
<p><img src="img/pipl-painting.jpg" /></p>
<div id="introduction" class="section level1">
<h1>Introduction</h1>
<p>My first two co-op work terms took place at the University of
Guelph’s School of Computer Science. More specifically, I worked as an
undergraduate research assistant (URA for short) for Dr. Daniel Gillis,
associate professor. Prior to this work term, I had already been working
as a URA for Dan since my first year. Through that time, I became more
and more interested in research and the field of academia. I decided
that I wanted a co-op experience to emulate the life of a researcher in
academia.</p>
<p>Here, I will highlight the ups and downs of that time I tried to be a
researcher.</p>
</div>
<div id="about-the-employer" class="section level1">
<h1>About the Employer</h1>
<p><img src="img/socs.png" /></p>
<p>The School of Computer Science (SoCS) is a department in the College
of Engineering and Physical Sciences at the University of Guelph.
Instituted in 1971, SoCS allows students to choose an “Area of
Application”, which is a minimum of 8 courses in a discipline other than
Computer Science. This encourages a more interdisciplinary approach to
computer science and allows the computer science knowledge to be applied
toward other fields. You can visit the School of Computer Science’s
website <a href="https://www.uoguelph.ca/computing/">here</a>.</p>
<p>Research in SoCS tends to also take an interdisciplinary approach. <a
href="https://danielgillis.wordpress.com/">Dr. Daniel Gillis</a>, an
associate professor in SoCS, spans his research across the fields of
statistics, biology, pedagogy, and community-engaged scholarship. Of
interest to me, however, was his <a
href="https://danielgillis.wordpress.com/research/son-bp-clwrp/">work in
ecological modelling</a>. Most of his ecological modelling work focused
on quantifying the effects anthropogenic activities on animal
populations. One research area that I got involved with early on was the
development of an efficient agent-based model to simulate these
anthropogenic effects. The combination of SoCS’s interdisciplinary focus
and Dan’s research in ecological modelling set the foundation for a work
term that was of major use and interest to me.</p>
</div>
<div id="job-description" class="section level1">
<h1>Job Description</h1>
<p>I will fully admit that I lucked out in how this job was set up from
the get-go. I had been working with Dan and his biological modelling
research team since my second semester at the University of Guelph.
Therefore, I already had a great rapport with Dan. This allowed me to
sort of mould the job to what I wanted it to be, pending his approval of
course. This meant that I was not only in charge of deciding what I was
going to have as deliverables for Dan, but I was also in charge of
designing the experiments and programming that needed to be done for
this job.</p>
<p>I decided that I wanted to use this work term to try to combine my
major interests of computer science and ornithology (the study of
birds). I had been working with a subset of Dan’s biological modelling
team that focused on developing an efficient type of spatially-explicit
agent-based model (known as an environment agent-based model, eABM for
short) to be used for risk assessment on a population of lake whitefish.
However, I wanted to apply this model to birds; in particular, I chose
to apply it to the piping plover, an endangered species of shorebird
native to North America.</p>
<p>At this point, it was determined that I was going to develop an eABM
for use with piping plovers at Sauble Beach, a nesting ground and
popular tourist destination. Once the model was developed, I would
design some experiments to add stressors to the simulated environment of
piping plovers. These stressors might be stressors that would be
experienced by the piping plovers that actually use the beach for
nesting. The overall goal would be to use this model (and therefore the
experiments from the model) to assist in informing management decisions
for piping plover conservation.</p>
<p>This was the research project that I was going to do for my time as a
researcher. We also decided that I was going to try to present the
findings at a conference. If the findings were novel enough, there was
the potential to author a paper.</p>
</div>
<div id="goals" class="section level1">
<h1>Goals</h1>
<p>Because this co-op term ended up turning into an 8-month contiguous
co-op term, I was able to create a variety of small goals that could be
achieved within a couple months as well as larger goals that took close
to the entire work-term. Some goals had solid deliverables that could be
attached with them to show their progress, while the progress for others
had to be subjectively evaluated by both myself and Dan.</p>
<div id="programming-languages" class="section level3">
<h3>Programming Languages</h3>
<p>With this still being a programming-dominated co-op position, I
wanted one of my goals to involve the learning of at least one new
language. In this case, I decided I wanted to learn
<strong>Python</strong>. Python appears to be a popular language used in
the scientific programming world, and I figured it would be a useful
language to learn. As mentioned above, the main task in this job was to
develop an agent-based model; therefore, I decided that I would develop
the model using Python, allowing me to fully immerse myself in the
language.</p>
<p>In addition to Python, I wanted to get more comfortable using
<strong>R</strong>. I had had experience using R in various statistics
courses, but it was fairly simple analyses and plotting. I particularly
wanted to get more comfortable with subsetting data and creating plot
recipes using R’s <em>ggplot2</em> package. In order to achieve this, I
decided that all model analyses would be done using R. At the end of the
work term, I would aim to have an analyses library written in R.</p>
</div>
<div id="scientific-communication" class="section level3">
<h3>Scientific Communication</h3>
<p>Since this job was meant to emulate the life of a researcher, it
would be imperative for me to increase my scientific communication
skills. Scientific communication is important to be able to convey
scientific findings to the public in a manner which does not contain
jargon. Additionally, scientific communication is important for
researchers for funding application through grants.</p>
<p>With this in mind, I wanted to improve three aspects of scientific
communication: <strong>written</strong>, <strong>visual</strong>, and
<strong>oral</strong>. To improve my written communication, I decided
that while I was developing the model and subsequent experiments, I
would try to write about it as much as I could. With this writing, I
wanted to turn them into sections of what would be seen in a scientific
paper, such as abstract, introduction, methods, results, and discussion.
These sections would be sent to Dan for him to make any edits for me to
revise. An overall deliverable I wanted to get out of this was a
scientific paper that I could send to a journal for a chance at
publishing.</p>
<p>For visual communication, I planned on submitted scientific posters
to two conferences: American Ornithology 2017 and CEPS Undergraduate
Poster Session (CUPS). The scientific poster would be used to convey
results of the studies that I conducted in a visually attractive way.
Hopefully, it might increase the communication and comphrehension of the
results. This tied in well with oral communication in that I would have
to present these posters. At American Ornithology 2017, I would have to
present my poster to hundreds of professional scientists; at CUPS, I
would be presenting my poster to judges for a shot at some prizes.</p>
</div>
<div id="time-management" class="section level3">
<h3>Time Management</h3>
<p>I’ve struggled with time management for quite some time. I therefore
wanted to try to use this work-term as an opportunity to improve from my
stereotypical “student-thing” of leaving things to the last minute and
hurriedly finishing them. It would be important for this work term, too.
From the goals above, I’ve already listed that I would need to develop a
model, write analyses for the model, write sections of papers about the
model, create research posters, and travel to conferences to actually
present the research. Clearly, this work-term was going to be a
situation where time management was of utmost importance.</p>
<p>In my Operating Systems class that I took the winter before my co-op
term, we were introduced to <a
href="https://en.wikipedia.org/wiki/Gantt_chart">Gantt charts</a>. In
that case, we were introduced to Gantt charts in the context of process
scheduling; however, Gantt charts can clearly be used for project
scheduling as well. In order to improve my time management skills, I
decided that I would try to make a Gantt chart for all the deliverables
I needed to produce. This allowed me to create a visual representation
of what a week-to-week workflow would look like to meet the deadlines I
needed. It would be a fairly simplistic Gantt chart as it wouldn’t show
dependences (in hindsight, I should have included dependancies), but it
would at least help keep me acountable of knowing what should be done by
when.</p>
</div>
<div id="learn-the-industry" class="section level3">
<h3>Learn the Industry</h3>
<p>This, in my opinion, was a bit more of an “abstract” goal rather than
a goal that could have concrete deliverables. However, I thought it
would be imporant to be able to learn what life is actually like in
academia. Researchers can often be only depicted when the “cool”
scientific discoveries are presented in the news and you see the large
group photo of many happy scientists. However, I was quite sure that it
wasn’t always cool discoveries that were happening during the research
process. I wanted to fully immerse myself in even the minutiae of
academia to fully understand if I think it would be a proper field for
me to pursue. I planned on trying to “achieve” this goal by trying to
get myself involved with everything from the literature review process
to the grant-writing process to the budgeting process.</p>
</div>
</div>
<div id="academic-relation" class="section level1">
<h1>Academic Relation</h1>
<p>As mentioned, I am majoring in Computer Science and minoring in
Statistics. Additionally, I am supplementing my major/minor combination
with some ecology courses to create an overall “Computational Ecology”
major. With that in mind, I don’t think it’s too much of a stretch to
see where this work term fits in with my academic studies. Of course,
much of what I had to do on the job was not explicitly taught in class.
However, what <i>was</i> taught in class gave at least a foundation to
help me better understand what I had to teach myself in order to succeed
at this position.</p>
<div id="computer-science" class="section level3">
<h3>Computer Science</h3>
<p>Object-oriented programming (CIS*2430), Data Structures (CIS*2520),
and Algorithms (CIS*3490) were probably the most useful classes for this
work term. Object-oriented program was an important part of developing
the model. Most of the simulated entities in the model had to be
developed with objects in mind, such as piping plover attributes or
environmental attributes. While I didn’t have to develop the data
structures myself (Python provides them), knowing which data structure
to use was important for writing an efficient simulation model. This, of
course, ties in with the use of the proper algorithm for certain data
structures, especially when it came to sorting and searching for
elements of a list of elements.</p>
</div>
<div id="statistics" class="section level3">
<h3>Statistics</h3>
<p>Prior to this work term, I had taken three statistics courses. The
key takeaways from these classes that I was able to apply to this work
term was the use of hypothesis testing and regression. Hypothesis tests
mirrored those done in the classroom in that it was usually a simple
comparison between two means (i.e. simply using a t-test). Prior to this
work-term, I had only delved into linear regression and some small-order
polynomial regression. What I ended up needing was logistical
regression. While I had to learn that on my own, the background
knowledge of linear regression allowed me to better understand what was
happening in a logistical regression model run.</p>
</div>
<div id="ecology" class="section level3">
<h3>Ecology</h3>
<p>I hadn’t actually taken any ecology courses prior to this work term.
I had only decided during this work term that I wanted to start
supplementing my major with some ecology courses. Nonetheless, I was
able to gain some ecological knowledge, especially when it comes to
ecological modelling and some of the submodel that governed the overall
eABM that I developed. If I do a work-term similar to this one again, I
will have more ecology courses that may benefit me.</p>
</div>
</div>
<div id="opportunities" class="section level1">
<h1>Opportunities</h1>
<div id="american-ornithology-2017" class="section level3">
<h3>American Ornithology 2017</h3>
<p>One of the most unique experiences I was able to have during this
co-op term was the ability to travel to a conference. Prior to the co-op
work term (but when I knew what I was going to be doing for the
work-term), I submitted an abstract to <a
href="http://aossco2017.fw.msu.edu/">American Ornithology 2017</a>,
which was going to be the joint meeting between the American
Ornithological Society and Society of Canadian Ornithologists/Société
des ornithologistes du Canada, both of which I am a member of. I got
notified in late-May that my abstract was accepted for a poster
presentation, which meant that I was going to travel to East Lansing, MI
at the beginning of August for this conference.</p>
<p>Overall, the conference exceeded my expectations. I was surrounded by
so many like-minded scientists, and I found out that “Computational
Ecology” was not as exotic of a field as I initially thought. In fact,
it was actually a field that was in somewhat of a demand, especially for
those that have computer science knowledge. I was able to present my <a
href="https://figshare.com/articles/Modelling_habitat_loss_in_Piping_Plovers_using_an_environmental_agent-based_model/5280931">scientific
poster</a> to a variety of scientists who all seemed to find it to be a
very interested topic. I made a number of valuable connections that I
still chat with from time to time.</p>
<p>The absolute highlight of the conference actually came at the
beginning of the conference from the keynote speaker, <a
href="http://www.deborahcramer.com/">Deborah Cramer</a>. A quote that
she said stuck with me and will continue to stick with me for a long
time:</p>
<blockquote>
<p><em>“Who hears the birds when they cry? You do.”</em></p>
</blockquote>
<p>That quote stuck with me because I was able to see that I did, in
some way, belong at that conference and I did indeed have something
important to offer. Everyone in the room had one thing in common: the
conservation of birds. Originally, this work term was scheduled as a
4-month term; however, this quote inspired me to continue for the second
4-month block. It sparked the flame of wanting to go to graduate school
and wanting to help the conservation of birds using the skills that I
gain in computer science.</p>
</div>
<div id="ceps-undergraduate-poster-session" class="section level3">
<h3>CEPS Undergraduate Poster Session</h3>
<p>After American Ornithology 2017, I presented a similar poster at the
CEPS Undergraduate Poster Session at the University of Guelph. Instead
of presenting to hundreds of people in a more casual environment, this
one involved judges that scored your poster and overall presentation. I
actually participated in this poster session last year when I was first
working for Dan and his team. This year, I came in with the goal of
winning either the Best in Department award or one of the Top 3 posters
in the session. <a href="img/cups_award.jpg">Mission
accomplished!</a></p>
</div>
<div id="scientific-paper" class="section level3">
<h3>Scientific Paper</h3>
<p>As mentioned as part of my goals, I was going to improve my written
scientific communication by writing sections of a scientific paper
thoughout the work-term. These would be submitted to my advisor
throughout the term and would be revised throughout.</p>
<p>In the fall 4-month portion of this work term, we invited <a
href="https://www.uoguelph.ca/ib/jacobs">Dr. Shoshanah Jacobs</a> to the
team and officially created the Great Lakes Piping Plover Biological
Modelling Program. Dr. Jacobs was able to collaborate on the paper
sections and add in her biological expertise to the paper. As of writing
this, we plan on submitted our paper, entitled “Exploring the Use of
Environmental Agent-Based Models on Great Lakes Piping Plovers”, to the
Journal of Avian Biology. Of course, that doesn’t mean that it will be
published there, or even at any other journal. However, the fact that a
fully written manuscript came out of this work term is much more than I
could have asked for.</p>
</div>
<div id="professional-memberships" class="section level3">
<h3>Professional Memberships</h3>
<p>Although I didn’t explicitly make a goal for it, I wanted to start
getting myself more known in the ornithology community. One way to
achieve this was through joining professional societies. The two that I
decided to join during my co-op term were the Society of Canadian
Ornithologists/Société des ornithologistes (SCO-SOC) du Canada and the
Ontario Field Ornithologists (OFO). SCO-SOC allowed me to apply for
student awards and travel bursaries where OFO allowed me to connect with
some of the very well-known birders of Ontario.</p>
<p>One of the very last tasks I completed for my co-op was applying for
a student memebership award through the American Ornithological Society
(AOS) for the 2018 pool. This year, I was one of roughly 40 students
across the world awarded a student membership for the AOS.</p>
</div>
<div id="future-work" class="section level3">
<h3>Future Work</h3>
<p>One of the lesser concrete things I was able to take away from this
position was the idea of “never hurting to ask; the worst they can say
is ‘no’”. Using the various connections I made, either through promoting
my work or attending conferences, I now have a variety of leads for
future co-op positions, many of which will involve ecological modelling
of some sort. Many of these came from cold leads; they simply involved
me putting myself out there and asking if there was any way I could
assist with research given my background and training. I look forward to
seeing what these leads may turn into.</p>
</div>
</div>
<div id="conclusion" class="section level1">
<h1>Conclusion</h1>
<p>An easy way to sum up this work term is “exceeded expectations”. I
continually describe my experience that way, but it still holds true. I
was happy just to have a co-op job that combined my passion for computer
science and ornithology, but to have been able to travel to a
conference, create a new research program, and author a scientific paper
simply was above and beyond what I expected to get out of this. As I
mentioned in my blurb about American Ornithology 2017, I also gained a
sense of direction and, as cliche as it may be, a sense of purpose in my
undergraduate studies. I found meaning in the work I was doing in the
classroom as I was finally able to translate it to real-world issues,
and issues I care greatly about. This co-op term has greatly shaped what
the rest of my undergraduate career will look like, both in future
courses and future co-op terms.</p>
<p>While still a work in progress, I was able to create a model which
can simulate breeding piping plovers at Sauble Beach. This model was
written fully in Python, a language I was able to learn over this co-op
work term. I have made the model open source which you can view <a
href="https://github.com/BrandonEdwards/melodus">here</a>. Additionally,
I was able to make a collection of analysis scripts in R to analyze the
output of the model. This included learning to make some
<em>ggplot2</em> recipes and creating meaningful plots out of the data.
These scripts can be viewed <a
href="https://github.com/BrandonEdwards/melodus-analysis">here</a>.</p>
<p>As I discovered, research and the subsequent field of academia is not
an easy field. However, at this point, I think I am willing to accept
the trials and tribulations of academia, maybe even strive to push for
change in some of the tribulations, and start to aim my career
directions toward that field.</p>
</div>
<div id="acknowledgements" class="section level1">
<h1>Acknowledgements</h1>
<p>I would like to firstly thank Dr. Daniel Gillis for allowing me to
have this amazing opportunity. I would not have been able to achieve any
of this without your support. Thank you to Dr. Shoshanah Jacobs, first
for accepting the invitiation to join the team, but for also providing
your biological expertise and angles. I look forward to continuing to
work with both of you!</p>
<p>Thank you to Alicia Fortin from <a
href="http://ploverlovers.com/">Plover Lovers</a>, a volunteer
organization in Sauble Beach who oversee piping plover monitoring.
Alicia and I communicated data back in forth in order to help inform the
model and to potentially create a research program with Sauble
Beach.</p>
<p>This work term was partially funded by the Co-op on Campus grant
through <a href="https://www.recruitguelph.ca/cecs/">Co-operative
Education & Career Services</a>, University of Guelph.</p>
<p>The University of Guelph resides on the ancestral lands of the
Attawandaron people and the treaty lands and territory of the
Mississaugas of the Credit. We recognize the significance of the Dish
with One Spoon Covenant to this land and offer our respect to our
Anishinaabe, Haudenosaunee and Métis neighbours as we strive to
strengthen our relationships with them.</p>
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