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BHKLab Handbook

Cell Line Viability Screens

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bhklab/handbook

General
Disciplines
Software Development
Grants
Onboarding / Offboarding
Resources
Contributing

BHKLab Handbook

bhklab/handbook

General
General
- Mission Statement
- Lab Space
  Lab Space
- Summary of Work (SOW)
  Summary of Work (SOW)
  - Confluence SOW Tutorial (outdated)
- Communications
  Communications
- Meetings
  Meetings
- Presentations
  Presentations
  - Presentations Database
  - Presentation Tools
- Manuscripts
  Manuscripts
- Projects
  Projects
  - Student Project Ideas
- Accomplishments Tracking
  Accomplishments Tracking
- Code Of Conduct
  Code Of Conduct
Disciplines
Disciplines
- Data Science
  Data Science
  - Data Access
    
    Data Access
    
    EGA Data Upload
  - Data Curation
    
    Data Curation
    
    Snakemake
    
    ORCESTRA
    
    IO Clinical Trial Curation
    
    IO Clinical Trial Curation
    
    Non-IO Clinical Trial Curation
    
    Non-IO Clinical Trial Curation
  - Visualization
    
    Visualization
    
    Sankey Plots in R
- Machine Learning
  Machine Learning
  - Learning Resources
  - Tools
  - Supervised Learning
    Supervised Learning
    
    Supervised Learning Algorithms
  - Unsupervised Learning
    
    Unsupervised Learning
    
    Clustering
    
    Clustering
    
    GMM
    
    K-Means Clustering
    
    Spectral Clustering
    
    Dimensionality Reduction
    
    Dimensionality Reduction
    
    Laplacian Eigenmaps
    
    Locally Linear Embeddings
    
    Principal Component Analysis (PCA)
    
    Random Projections
    
    T-SNE
    
    UMAP
    
    Generative Modeling
    
    Generative Modeling
    
    VAE
- Bioinformatics
  Bioinformatics
  - Data Types
    Data Types
    
    RNA-Seq
  - Tools
    Tools
    
    RNA-Seq Pipelines
    RNA-Seq Pipelines
    
    DESeq2
    
    Kallisto
    
    STAR
  - Methods
    Methods
    
    Survival Analysis
- Pharmacogenomics
  Pharmacogenomics
- Imaging
  Imaging
  - Data Sources
    
    Data Sources
  - Data Types
    Data Types
    
    DICOM (Digital Imaging and Communications in Medicine)
    
    NIfTi Format
  - Radiomics
    
    Radiomics
    
    Extraction Tools
    
    Extraction Tools
    
    LifeX
    
    Radiomics Score
  - Tools
    
    Tools
    
    QIPCM
    
    QIPCM
    
    Querying Data from the QIPCM PACS
Software Development
Software Development
- Development Environment
  Development Environment
  - Shells
    
    Shells
    
    Windows Subsystem for Linux (WSL)
  - Integrated Development Environments (IDEs)
    
    Integrated Development Environments (IDEs)
    
    RStudio
    
    Visual Studio Code
  - Package Managers
    
    Package Managers
    
    Pixi Package Manager
  - CLI Tools
    
    CLI Tools
    
    zoxide
  - Containerization
    
    Containerization
    
    Containerization on H4H
- Languages
  Languages
  - Javascript Typescript
    
    Javascript Typescript
    
    Learning Resources
  - Markdown
    
    Markdown
    
    Mkdocs
    
    Mkdocs
    
    Tabbed Code/Content Blocks
  - Python
    
    Python
    
    Rich
    
    Rich
  - R
    
    R
    
    MultiAssayExperiment
    
    R Coding Best Practices
    
    SummarizedExperiment and Ranged
    
    Tidyverse
    
    Tidyverse
    
    Plotting with ggplot2
    
    networkD3
    
    networkD3
    
    Sankey Plot
  - Rust
    
    Rust
  - SQL
    
    SQL
- Version Control
  Version Control
  - Git
    Git
    
    Introduction
    
    Quick Git Tips
  - Code Reviews
    Code Reviews
    
    Introduction to Code Reviews
    
    Mindsets in Code Reviews
    
    Common Challenges and Solutions in Code Reviews
    
    Conducting a Review
    
    Code Review Presentation
  - ORCESTRA Version Controlling
- Remote Development
  Remote Development
  - Google Cloud Platform
    
    Google Cloud Platform
    
    Project Proposal
    
    Monthly Billing Reports
    
    Serving Images and Videos
    
    Artifact Registry
    
    Big Query
    
    Cloud Build/Run
    
    Cloud SQL
    
    Cloud Storage
    
    Compute Engine
    
    Vertex AI
    
    Virtual Machines (VMs)
  - High Performance Computing for Health
    
    High Performance Computing for Health
    
    Quick Start
  - Lab Server
    
    Lab Server
    
    GitHub Access
  - Compute Canada Cloud
    
    Compute Canada Cloud
- Web Development
  Web Development
  - Back end
    
    Back end
    
    Libraries and frameworks
    
    Libraries and frameworks
    
    ExpressJS
    
    NestJS
    
    Node
    Node
    
    NodeJS
    
    npm (Node Package Manager)
    
    Tools
    Tools
    
    Postman
  - Front end
    
    Front end
    
    DOM
    
    Libraries and frameworks
    
    Libraries and frameworks
    
    React
    React
    
    React
    
    React Hooks
    
    Styling libraries and frameworks
    
    Styling libraries and frameworks
    
    PrimeReact
    
    Styled-components
    
    TailwindCSS
Grants
Grants
- Identifying Suitable Grants
- Preparing for Submission
  Preparing for Submission
  - UHN Budget Process
- Writing a Strong Grant Proposal
- Submission Process
- Templates & Resources
Onboarding / Offboarding
Onboarding / Offboarding
- Onboarding
  Onboarding
- Offboarding
  Offboarding
  - Admin Offboarding Instructions
Resources
Resources
- Trainee funding opportunities
- Guide for mentors and supervisors
- Literature Review
  Literature Review
  - Covidence
  - Paperpile
  - How to Read a Paper
    
    How to Read a Paper
Contributing
Contributing

Cell Line Viability Screens#

TODO

June 26, 2025 June 26, 2025

James Bannon

Navigating PSets