This is a virtual environment which contains databases, software, workflows, and workshops for Precision Health Data Analysis.
Contact:
Dr. Phillip Richmond (prichmond@bcchr.ca)
Precision Health Initiative, BC Children's Hospital Research Institute (www.bcchr.ca/phi)
- Databases - Info about databases stored on Sockeye and where they are downloaded from.
- Software - How-to on managing software, and some software deployments here as well.
- Open Data - Shared open datasets, staged from Chinook.
- Workshops - Workshop content, including guided and self-paced content.
- Workflows - Functional workflows for processing precision health data.
- Deployments - This contains info about deploying on different systems.
- Overview and Purpose
- Contributions
Emerging technologies which enable in-depth biological profiles of patients are transforming our understanding of health and disease, providing clinicians and researchers with the tools to diagnose and treat both rare and complex diseases in a precise manner tailored to each patient. It is now possible to examine the core components of molecular and cellular physiology, including the genome, proteome, metabolome, microbiome, and epigenome (multi-omic data) of patients in a comprehensive manner, enabling patient-specific diagnosis and treatment options. While these tools carry immense value, they also come with logistical and redundancy challenges for effective deployment within research and clinical settings, including ensuring appropriate ethical consent, knowledgebase, education and training, and computational infrastructure. The Precision Health Initiative at BC Children’s Hospital Research Institute (BCCHR) seeks to address these challenges by coordinating computational infrastructure and education/training efforts for the local community of researchers and clinicians.
UBC’s Advanced Research Computing (ARC) consortium has been providing computational resources to the UBC research community including high performance computing (HPC) on the Sockeye cluster, and data storage on the Chinook system. The ARC team has also been interfacing with the Provincial Health Services Authority in BC (PHSA), to establish data security specifications which enable the analysis of sensitive clinically-derived patient data (e.g. patient genomic sequences) on the Sockeye and Chinook systems. Together, ARC is moving towards a platform which can support precision health data analysis for researchers at UBC, further enabling research excellence in the field of biomedical science. The final obstacle which remains for the broad uptake of the ARC platform for precision health data analysis surrounds the education and training of researchers in the biomedical sciences, many of whom have little-to-no experience in the necessary skills for analyzing, interpreting, and visualizing the “big data” of precision health technologies.
The primary goal of the Precision Health Virtual Environment is to provide a collaborative, open, educational environment for the exchange of knowledge and deployment of training modules on the Sockeye and Chinook systems. The environment will achieve this with four aims:
- Serve as an onboarding platform for new users, which will guide them in the usage of Sockeye and Chinook systems for research data analysis.
- Provide open source workshops developed by the Precision Health Initiative and community members for the analysis of precision health data.
- Establish shared data commons for large shared datasets with utility across research groups in the domain of human precision health.
- Build community around researchers using similar precision health technologies to promote collaboration and sharing of functional workflows, software, and pipelines on the ARC platforms.
This environment is launching in Fall 2021 as a pilot project to demonstrate efficacy, with the hopes of broader long-term adoption by the UBC research community. The rest of this document details a vision for the environment’s disk space footprint, training content, and plan of action. A key component of this space is designing it with some degree of portability, so that it can be re-implemented in different settings (e.g. NDRIO).
The Precision Health Bootcamp will run from July 25th - August 10th, 2022.
For the workshop advertisement, please click here.
For registration, please click here.
For detailed descriptions of the workshops, please click here.
This space is made possible by contributions of researchers in the community. If you are interested in contributing to this space, contact Phil Richmond (prichmond@bcchr.ca).
- Phillip Richmond
- Emilie Theberge
- Nikita Telkar
- Will Casazza
- Lynne Williams
- Amrit Singh
- Alex Weber
- Hayley Sowards
- Amy Inkster
- Derek Tam
- Jane Velghe
- Elizabeth Kinney
- Jeff Gardner
- Jiarui Li