Carrières

Le C3G s’engage à offrir de nouvelles opportunités aux candidats intéressés à poursuivre une carrière dans le domaine de la recherche en génomique. Si vous êtes un penseur créatif et innovateur, si vous aimez les défis, si vous avez un forts intérêt pour le développement de logiciels, si vous êtes passionné par les sciences de la vie et la technologie, nous serions ravis de vous lire.

Postes ouverts

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Programme de stages d’été

Le C3G, en collaboration avec le Laboratoire Bourque de l’Université McGill, a élaboré ce programme de stages afin d’offrir aux étudiants de premier et de deuxième cycle la possibilité d’acquérir une expérience pratique en bio-informatique appliquée, en développement de logiciels/web ou en recherche génomique. Les stagiaires travaillent avec des bio-informaticiens et des développeurs de logiciels au sein de C3G sur un projet pendant les mois d’été.

Stage d’été 2022

Le programme de stages d’été pour 2022 est fermé. Veuillez nous contacter en complétant le formulaire

Rejoindre notre équipe

Veuillez nous contacter en complétant le formulaire ci-dessous si vous souhaitez vous joindre à notre équipe. Tous les champs marqués d’un astérisque sont obligatoires. Veuillez noter que le C3G s’engage à assurer l’équité en matière d’emploi et de diversité. Nous accueillons favorablement les demandes des peuples autochtones, des minorités visibles, des minorités ethniques, des personnes handicapées, des femmes, des personnes d’orientation sexuelle et des identités de genre minoritaires et d’autres personnes qui pourraient contribuer à une plus grande diversification.

Témoignages

During my internship at C3G, I had the opportunity to work on multiple projects doing hands-on bioinformatics.
The first project was to look at a transgenic mouse’s genome sequencing data for an insertion/deletion event which wasn’t picked up on by the usual detection methods. Afterwards, I compared the differences between using the GRCh37 and GRCh38 genome references by applying the GenPipes RNA-seq pipeline on previously analyzed data. I made a few interesting discoveries that proved useful to C3G in order to improve their analyses. Next, I worked on a project with the goal of replicating results from a previous study looking into optimizing the sequencing and detection of cassava mosaic viruses (CMV) present in African crops (TreeLab).The end goal of said project being to be able to detect CMV with a laptop unconnected from the Internet directly in the fields.

LinkedIn profile

Étienne Collette, Current Summer Intern at C3G

During my internship at C3G, I had the opportunity to work on multiple projects doing hands-on bioinformatics.
The first project was to look at a transgenic mouse’s genome sequencing data for an insertion/deletion event which wasn’t picked up on by the usual detection methods. Afterwards, I compared the differences between using the GRCh37 and GRCh38 genome references by applying the GenPipes RNA-seq pipeline on previously analyzed data. I made a few interesting discoveries that proved useful to C3G in order to improve their analyses. Next, I worked on a project with the goal of replicating results from a previous study looking into optimizing the sequencing and detection of cassava mosaic viruses (CMV) present in African crops (TreeLab).The end goal of said project being to be able to detect CMV with a laptop unconnected from the Internet directly in the fields.

For the whole time that I was here, I was able to learn a lot about the workings of HPC systems and furthering my knowledge of both R and BASH.

LinkedIn Profile

Sebastian Ballesteros Ramirez, Software Engineer at C3G; Previous Summer Intern 2020

I was tasked with organizing massive sets of epigenomic data in accordance with IHEC standards during my internship. When I arrived, data was very loosely organized by consortium, all of which had different naming conventions and internal organizational structures. There were three steps to organize the data. First, I wrote a script to scrape information for the IHEC database and store it as a master metadata file. With IHEC IDs and consortium IDs linked, I then wrote a program to move data files into a structure that better followed the international standard. The most interesting part of my internship was writing a search program that allowed users to quickly locate files based on dataset characteristics, such as donor age, tissue type, or experiment type. I quickly learned that even the best file organizational system would not work for everyone, so the search function was key to meet the goals of my internship.

I loved working with C3G. I had an opportunity for the first time to use powerful computing clusters, became more familiar working in a UNIX environment, and thoroughly developed my python skills.

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Soulaine Theocharides, Computer Engineering Student at Queens University; Previous Summer Intern 2020

Over the course of my internship with C3G, I was involved with a few key projects. More specifically, I was tasked with generating synthetic FHIR datasets using FHIR APIs. These datasets were created with the goal of ingesting them into the metadata service and to test the ingestion algorithm. All synthetic datasets that I generated were published on C3G’s public repository, so other developers and researchers will have access to already prepared datasets. A large aspect of my internship involved mapping across data standards. I worked on mapping the GA4GH Phenopackets standard used by the metadata service to the mCODE standard. This mapping will be used in future C3G projects that will benefit from incorporating specific mCODE data elements. Finally, I was tasked with mapping data elements collected by a COVID-19 initative, CanCOGen, to the Phenopackets schema. Ultimately, the mapping I completed was sufficient for building a synthetic dataset for a prototype to be used for the CanCOGen project.

My time as an intern with C3G has been very hands-on and educational. I learned a lot through my work with APIs and extensive documentation of data standards as well as through interactions with my colleagues. As I have a more clinical background, rather than computer science background, my internship has made me eager to continue to strengthen my programming skills.

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Solomia Yanishevsky, Data Administrator at C3G; Previous Summer Intern 2020

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.

LinkedIn profile

Rami Coles, Software Developer at Deloitte Canada; Previous Summer Intern 2019

Summer of 2019, 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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Shereen Elaidi, Undergraduate Student Researcher at McGill University; Previous Summer Intern 2019

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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Nick Zombolas, Software Engineer at Wavo.me; Previous Summer Intern 2019

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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David Lougheed, MSc Human Genetics student at McGill University ; Previous Summer Intern 2018