Let’s Have Some Data Driven Fun! The Parasitology Data Analysis Workshop 2019

As a member of the Host Parasite Interaction group, I have come to appreciate that research in parasitology can range from genomic studies on parasite diversity to studying the ecological impact of parasites in wild animals. It is no surprise then that data in parasitology research also come in all shapes and sizes. The Parasitology Data Analysis Workshop sought to address this diversity in parasitology research by providing a platform to discuss and learn about analyzing, processing, and depicting different types of biological data.

The Parasitology Data Analysis Workshop was held at the University of Calgary from the 12^th to 15^th of November 2019 and was attended by twenty trainees from both HPI as well universities across Canada and the United States. Over four days, we engaged in multiple sessions that were thoughtfully designed to help us connect the gaps between the different domains of parasitology research that were our individual comfort zones. In addition to covering numerous topics ranging from statistical analysis and modeling of data to the ethical considerations of scientific research, the workshop also provided us with a valuable experience in networking in the semi-formal setting of the sessions. The recurrent theme of the workshop could easily have been “team work”, as we found ourselves working in collaborative assignments and discussions within carefully organized smaller groups before sharing ideas and concepts with the whole class.

Each day of the workshop had three major segments that often tied to each other in a general theme. Ample time was interweaved for delicious refreshments, coffee, and a hot lunch. Every evening, the faculty/facilitators of the workshop made themselves available for chatting with trainees about their work and questions about data interpretation in the informal setting of a lounge.

Day one

Day one of the workshop revolved around learning to work with raw data — from being able to statistically test the data to depicting results graphically. The first segment of the workshop was conducted by Dr. Rob Deardon regarding statistical testing of experimental data. He elegantly presented the threat of “p-hacking” our data or etching out erroneous significance by not understanding the statistical meaning behind the tests we use on big data sets.

During the lunch session, we started the first segment of a two-part session on research integrity by exploring hypothetical scenarios of mitigating scientific fraud in a “choose-your-own-adventure” video series.

The next session was Dr. Constance Finney’s data visualization course on audience driven, but accurate and clear graphical depiction of our data. Based on our prior submissions of what we as trainees identified as “clear” and “hard to understand”, this session gave us a fundamental run through of the key elements that encompass a good graph. A follow-up exercise of correcting our own graphical representations of a previously provided data set gave us a chance to apply our newly learnt tips for good data visualization.

The first day ended with a team dinner at a Thai restaurant outside campus, giving us all a great opportunity to network with the faculty and other trainees and setting the tone for the workshop as a friendly environment where we can share our views and learn from each other.

Day two

Day two of the workshop was genomics-oriented. Working in groups, under Dr. James Wasmuth’s guidance, we identified key concepts in genomics-heavy research papers. For trainees like me who don’t have a strong background in genomics and sequencing, discussions with Dr. Wasmuth and Dr. Mark Blaxter brought us reasonably up-to-speed with general techniques and the lingo of a typical genomics paper.

Armed with a basic idea of how genomes are sequenced and the methods to identify good genomics papers, we went forward with Dr. Blaxter’s afternoon public lecture. Dr. Blaxter elegantly showed how they used genomic sequencing of the bacteria Wolbachia for phylogenetic tracing of nematode co-evolution. Dr. Blaxter also spoke about the magnificent “Darwin’s Tree of Life” project he is heading at the Sanger Institute, and the aim they have to sequence all species on the earth! The subsequent session, also led by Dr. Blaxter, introduced us to Blobplots — a tool used to separate out contaminating genomes from genomic sequencing data.

Day three

Day 3 of the workshop focused on exploring different toolkits available to study cell biology, with a special emphasis on the analysis of imaging data. We began the day with an overview of several cell biology techniques like flow cytometry, PCR, and ELISA. The next segment in this session was my personal favorite, where each group was given a hypothetical scenario in the lab and were told to design our own work plan to execute the idea. This was a great exercise in protocol design and helped us appreciate not only the different techniques available, but also the minute variations that can make or break such experimental conditions.

As a second part of the session on ethics, during lunch, we were visited by the scientific integrity officer at the University of Calgary, Ms. Shirley Voyna Wilson, for discussing the frameworks available for students and faculty to discreetly voice concerns about incidents of scientific misconduct.

The session after lunch, Dr. Lucy Swift and Dr. Andrew Chojnacki from the Live Cell Imaging Resource lab at the University of Calgary briefed us on the important aspects of image quality. We also had a hand-on training exercise in using ImageJ for image analysis.

Day four

The fourth and final day of the workshop focused on parasites in ecological studies as well as exploring the different kinds of model systems available for answering our research questions. Guided by Dr. Jillian Detwiler in groups, we started by exploring the ecological approaches established for studying the emergence of diseases and ecological phenomena. Following this, we built causal diagrams for these diseases using coloured post-it notes, an exercise that revealed the complicated nets of factors at play. After this session, Dr. Detwiler gave us a great introduction on using the programming language R to analyse and model ecological correlations in the statistical data.

With an introduction to how interconnected and intriguing the data from ecological studies of parasites can be, we went on to attend Dr. Detwiler’s public lecture on her studies about the behavioural impacts of trematode parasites on infected snails. The last session of the workshop, conducted by Dr. Finney and Dr. Peters, focused on discussing the vast variety of model systems available and in use for answering research questions. Based on our homework reading material, we set out to inspect the pros and cons of different model systems and appreciated the need to be vigilant of how suitable our chosen model is for the research we want to do.

With this last session, our four days of learning to deal with all sorts of parasitology data had come to an end. Apart from having immersed ourselves with the topics of the workshop, we walked out having made great friends with our peers in parasitology and holding our very own ceramic “parasitology” mugs! It would be amiss of me not to acknowledge and thank the organizers and instructors of the workshop for their careful planning and dedication not only throughout the four days, but also for all the effort they put into tailoring the material according to our requirements many months in advance. I am also grateful to the sponsors who made organizing this valuable workshop possible.