Canadian Center for Computational Genomics

Mentors: Student: Jiahuang Lin

<p>There has been a recent surge in the development of open-source computational methods for simulating human evolution and analyzing human genome data. These provide many new opportunities for genomic research, but the integration of these different resources is currently poor. In particular, turning models of human history into evolutionary models is notoriously time-consuming and bug-prone, and it requires knowledge of the specifics of each simulation tool. The major goals of this project are to develop a library of widely used historical models that integrate across multiple simulation tools, and to develop more robust and user-friendly model specification tools to automate the workflow of genomic and evolutionary analyses.</p>

Mentors: Student: Konstantinos Kyriakidis

<p>In this project we will work on the new CC systems (Beluga, Graham, Cedar, Niagara) and potentially mp2 trying to automate the setup of things like the account ID, meaningful default resources limits specific to each system, etc., in order to have zero configuration work done by users before being able to submit jobs. We will also work on creating some built-in safeguards against system abuse by novice users when they use this package. Documentation and tutorials will be easy to read and to understand and will be created at the same time the code is created in order to avoid delays in the delivery of the package. There will be use-case integration with PopSV, a package that could integrate this extension in order to demonstrate how easier this makes life for users of PopSV on CC systems. Time permits, we could potentially provide another software that could benefit from this e.g. SCones.</p>

Mentors: Student: Madhav Vats

<p>Genpipes is a set of software pipelines designed for genomic analysis. There are currently seven different pipelines and three more are in the development phase. These pipelines consist of several steps (10-40). Therefore keeping track of which step was executed, what functionality did it provide, at what time it was executed, whether it failed or succeeded can be a cumbersome task. The project consists of an integrated system that automatically builds a flowchart of the steps executed by the user. This would be a user-friendly add-on to the software as having a flowchart of the steps executed would help in the analysis and understanding of the process performed.</p>

Mentors: Student: Pranav Tharoor

<p>The main objective of McGill initiative in Computational Medicine (MiCM) is to deliver inter-disciplinary research programs and empower the use of Big Data in health research and health care delivery. One of the ways MiCM aims to achieve this objective is to strengthen collaborative research by sharing and transferring knowledge within the community.</p> <p>In order to realize the potential of Computational Medicine at McGill University, there is a need to better connect researchers in life sciences and clinical domains with researchers and students in the data sciences (e.g., statistics, bioinformatics, medical informatics, computer science, epidemiology). The former has interesting datasets and questions, while the latter can apply or develop quantitative methods to look for solutions to these questions.</p> <p>To facilitate this type of matchmaking, this project works on a database-driven, lightweight web application, with the purpose of matching McGill research data projects, with masters and doctoral students seeking looking for interesting projects to analyze.</p>