Centre for Infectious Disease and One Health
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DataHarmonizer
DataHarmonizer PublicA standardized browser-based spreadsheet editor and validator that can be run offline and locally, and which includes templates for SARS-CoV-2 and Monkeypox sampling data. This project, created by …
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pathogen-genomics-package
pathogen-genomics-package PublicThis is the DataHarmonizer spreadsheet web application bundled with pathogen genomics data entry and validation templates
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nf-ncov-voc
nf-ncov-voc PublicA Nextflow wrapped workflow for generating the mutation profiles of SARS-CoV-2 or Mpox genomes. Workflow is developed in collaboration with VIRUS-MVP (https://github.com/cidgoh/VIRUS-MVP) which can…
Repositories
- DataHarmonizer Public
A standardized browser-based spreadsheet editor and validator that can be run offline and locally, and which includes templates for SARS-CoV-2 and Monkeypox sampling data. This project, created by the Centre for Infectious Disease Genomics and One Health (CIDGOH), at Simon Fraser University, is now an open-source collaboration with contributions…
- nf-ncov-voc Public
A Nextflow wrapped workflow for generating the mutation profiles of SARS-CoV-2 or Mpox genomes. Workflow is developed in collaboration with VIRUS-MVP (https://github.com/cidgoh/VIRUS-MVP) which can be used to visualize the mutation profiles and functional annotations.
- iMicroSeq_Contextual_Data_Specification Public
An ontology-based specification for harmonizing contextual data in pathogen genomics. Developed for iMicroSeq to support standardized metadata capture across different water types (including wastewater and environmental), for public health. Includes templates, guides, and SOPs for implementation and curation.
- Soil_Microbiome_Specification Public
A data specification for harmonizing soil microbiome contextual data to improve data quality, data integration, and analysis, supporting consistent and reusable data across research and monitoring initiatives.
- VIRUS-MVP Public
VirusMVP is an interactive heatmap-centric app that integrates viral genomic mutations, lineage information and curated functional impact to study the spread and evolution of viruses in Canada and globally.
- SchemaBLAST Public
- ceur_pdf Public
Converts a Google Doc to a CEUR-WS–formatted PDF by downloading the document directly from its public URL, extracting front-matter content automatically, and compiling to PDF.
- GRDI_AMR_One_Health Public
A data specification for harmonizing One Health AMR pathogen genomics contextual data. The specification provides standardized (ontology-based) fields and terms which are implemented via a spreadsheet collection template, supported by field and reference guides as well as different curation and new term request SOPs.
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