Projects

The Metabolomics Innovation Centre (TMIC) is a nationally-funded core facility that has a unique combination of infrastructure and personnel to perform a wide range of cutting-edge metabolomic studies for clinical trials research, biomedical studies, bioproducts studies, nutrient profiling and environmental testing.

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The Genome Canada Help Desk was a Genome Canada funded project that ran from 2003-2011. The HelpDesk offered bioinformatics services, research, tools, and databases to the scientific community. Databases such as DrugBank were created with Help Desk funding. The Help Desk software repository is available for free, without restriction on our bitbucket site.

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Point of Care, Real-Time Urine Metabolomics Test to Diagnose Colorectal Cancers and Polyps in Low-and Middle-Income Countries

This grant supports research to introduce a rapid, non-invasive screening test for colorectal cancer in Nigeria to curb the incidence and mortality rates of colorectal cancer. This project funds the development and refinement of a multi-compound, low-cost colorimetric sensor system that detects and quantifies creatinine, N,N-diacetylspermine and hippuric acid in urine. The sensor device is designed to produce results in <20 minutes, to work off battery power, to be no larger than a shoebox and to cost <$100. The cost of the assays is limited to $3/test.

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New Resources for Chemical Genomics and Metabolomics in Biomedicine
This grant supports research towards the development of comprehensive databases and chemical/spectral libraries for metabolomics, chemical genomics and systems biology. It also provides support towards the development of bioinformatics software for metabolomic data analysis. This project is being used to support the development of FooDB (a database of 25,000 food constituents), HMDB, DrugBank and other metabolomic informatics resources.

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Novel Approaches to Spectral Prediction and Spectral Deconvolution for Metabolomics
This grant supports research into the development of new software tools and techniques to predict and interpret both NMR and MS spectra for metabolomics. It uses machine learning techniques to accurately predict small-molecule NMR or MS spectra from their structure and novel, innovative spectral processing methods to identify metabolites from the NMR or MS spectra of complex mixtures.

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The Natural Product Magnetic Resonance Database Project

This project will develop the NP-MRD (the Natural Product Magnetic Resonance Database), the central clearing house for all NMR data generated by the natural products community. The NP-MRD will be an open-access, web-enabled, FAIR-compliant database containing NMR spectra and structure data for all known natural products. The database accepts raw (time domain data, processed spectra, assigned chemical shifts, J-couplings, RDCs, etc.) and meta-data (structures, sources, methods, taxonomy, geospatial data, etc) from natural products. The NP-MRD will be an electronically accessible database that allows key information about the world’s natural products to be openly shared and used by all.​

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Comprehensive pathway generation of drug action and drug metabolism for DrugBank

The goal of this project is to expand the number of machine-readable pathways covering drug action, drug metabolism and xenobiotic metabolism in DrugBank (and other metabolome databases). The pathways will be identified via literature searches. Approximately 2300 approved drug action pathways and 200 high-priority drug metabolism pathways will be generated. The project will use case studies/examples to demonstrate the pathways’ usefulness in education, training, and drug discovery research.

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An Analytic App for Arm-Chair Ranching

The main objective of this project is to develop an app, called Arm-Chair Rancher that will provide data-driven, artificial intelligence tools to support customized, farm-specific planning, prediction and forecasting to optimize individual beef cattle ranch operations in Alberta. Arm-Chair Rancher will be the first publicly available app to use big data analytics and machine learning to enable farm-specific planning and forecasting. These are the key differentiating features of Arm-Chair Rancher

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Pacific North West Advanced Compound Identification Core

This project aims to bring together innovations in instrument engineering, advanced computational chemistry and informatics to create a transformative platform for standards-free metabolomics and identification of unknown compounds. A major focus of this project has been the development of improved methods for metabolite or metabolism prediction (via BioTransformer) and MS/MS spectral prediction (via CFM-ID).

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Comprehensive pathway generation of drug action and drug metabolism for DrugBank

The main objective of this project is to apply machine learning methods to predict the metabolic reactions and metabolites for 2000 drugs in DrugBank that do not have metabolism/metabolite data. In addition, the project will map the predicted metabolites and reactions onto pathway diagrams using a modified PathWhiz program. All of the predicted metabolites, metabolic reactions and pathway data will be uploaded into DrugBank.

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A novel rapid, liquid biopsy early stage lung cancer diagnostic test

The goal of this project is to develop a low cost, highly sensitive and accurate lung cancer test for patient screening. The metabolite test will be based on using technologies that are routinely used in clinical diagnostic laboratories. The test will be minimally invasive, requiring only a small amount of blood for analysis and will detect lung cancer at stage I or stage II, which is when it is most treatable. This project builds off exciting early stage lung cancer biomarker discoveries in our lab.

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