C3G Interns

Our teams have a broad expertise in bioinformatics and significant experience in personalized medicine applications

Want to be a intern?

Internships at C3G

Through internships, C3G and the Bourque Lab offer students an opportunity to get hands-on experience in applied bioinformatics, software/web development or genomics research.

How to Apply: Available summer internship positions will be posted here around December each year. Outstanding candidates are also welcome to contact us here to apply outside of the regular summer internship program.

Meet our past interns:

Rami Coles

During my internship, I worked on the development of a new pipeline for GenPipes called EpiQC. EpiQC can be used on C3G’s computer clusters. The pipeline’s objective is to assess the quality of a ChIP-Seq signal track (bigwig) dataset and determine if it should be used or not. I implemented different metrics to verify the quality of those bigwig files using 3rd party tools such as BigWigInfo, ChromImpute and EpiGeEC and also coded multiple python scripts to facilitate the use of the pipeline. After having tested the pipeline on small datasets (~100 files), I ran it on the whole ChIP-Seq data available through the IHEC data portal (~2500 files) to see how the pipeline runs on a big dataset. While most of the features worked, I had some issues with ChromImpute. I successfully trained ChromImpute on the whole dataset but could not impute the predicted files.

I learned a lot about computer clusters since I had no previous experience with them and how to handle large datasets, and while coding the pipeline and various scripts, I further improved my skill in using python.

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Summer Intern 2019

Shereen Elaidi

This summer, I worked on metagenomics analysis. In particular, I installed the whole genome shotgun (WGS) pipeline, MOCAT2, on C3G’s computing clusters. Since it did not work out-of-box, we did a lot of debugging and wrote our own wrapper scripts that were tested to work on C3G’s servers (since the ones shipped with MOCAT2 were depreciated). Additionally, we modified some of the MOCAT2 code to bring the run time of one of the pipeline’s steps down from several hours (and sometimes days, depending on the sample size) to only minutes and reduced RAM usage from 250 – 500GB of RAM down to less than 1GB of RAM. We used MOCAT2 to analyze 156 stool samples to examine the relationship between the gut microbiome and fibromyalgia.
Since I had no bioinformatics experience, and minimal computer science experience, I learned a lot during this internship, including genome sequencing and the importance of the gut microbiome, how to debug large pipelines and write my own wrapper scripts, how to process very large datasets, and how to use computing clusters.

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Summer Intern 2019

Nick Zombolas

During my time as a web development intern at C3G, I worked to improve the GenPipes Dashboard for viewing pipeline execution. I got a lot of great experience working with modern frameworks in the frontend and backend, such as React, Redux, Node.js, and Express. My main focuses throughout the internship were to improve the performance of the website, as well as add new features to provide a better user experience. Performance enhancements include adding an efficient sample search feature, as well as lazy-loading and virtual scrolling for samples. I also added a graphical view of sample execution, created a page to view project statistics, and provided a general cleanup of the user interface.

Throughout the internship I got a lot of experience with modern web frameworks, as well as learned the best practices for keeping code clean and concise.

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Summer Intern 2019

David Lougheed

As a software development intern at C3G, I worked on three projects: a tool to look at the research output of Genome Canada, a website which displays research connections between professors at McGill and especially the McGill initiative in Computational Medicine, and a browser for data produced by the MHcut tool (a collaboration between Dr. Bourque’s lab and the Woltgen lab at Kyoto University.) During my internship, I primarily used Python to write scripts and web service backends, and D3 to produce interactive data-driven JavaScript-based front-ends.

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Summer Intern 2018