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2_TOPICS.md

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Topic Areas in this Repository

  • Setup Google Cloud Platform Account
    • Setup GCP Account
    • Setup GCP client tools
    • Setup GCP project security
  • Files & Data
    • Use Google Cloud Storage for files
    • Use public Genomic Datasets on GCP
    • Use Big Query to query files
    • Use Cloud SQL to store data
    • Use Terra.bio reference Genomic Datasets
  • Compute with Virtual Machines & Docker Containers
    • Use Google Compute Engine Virtual Machines
    • Use Jupyter Notebook Instances (specialty GCE VMs)
    • Use Terra.bio Notebooks
    • Test Docker container image for Pipelines
    • Orchestrate containers with Kubernetes
    • Use Google Pipelines API (or PAPI - also called Life Sciences or Genomics API)
    • Use cromwell & WDL for pipelines
    • Use Terra.bio Workflows
    • Use Nextflow.io for pipelines
    • Use dsub for pipelines
    • Use Galaxy Project for pipelines
  • Machine Learning
    • Use ML Vision / Video APIs & AutoML
    • Use ML Text / Natural Language APIs
    • Use ML Table Analysis
    • Use Deep Variant
    • Use TensorQTL
    • Use Google Compute Engine ML (deep learning) image to create a Virtual Machine
    • Use Google optimized Deep Learning container to create your own ML container
    • Use a Jupyter notebook in Google Colabs with BigQuery
    • Use a Jupyter notebook in Google Colabs with BigQuery ML
  • Code & Cloud Service Tools
    • Use Source Repositories for code source control
    • Use Deployment Manager to deploy services
    • Use Google Container Repositories to host docker container images
    • Monitor log with Stackdriver
    • Setup CI/CD with GCP CloudBuild
  • Serverless Compute with Functions
    • Use Serverless Cloud Functions
    • Use Serverless Cloud Run
    • Create Serverless websites with AppEngine
  • Advanced GCP & Scripts
    • Get links to advanced GCP topics
    • Use gsutil to manage Cloud Storage
    • Use gcloud to list Compute Engine instances
    • Use gcloud to manage Cloud SQL
    • Use gcloud and bq to run a genomic analysis with Genomics API & BigQuery
    • Start a container & run a genomic analysis with VariantTransforms on Cloud Dataflow
    • Use a docker command to start a container & run a genomic analysis with VariantTransforms on Cloud Dataflow

📺Link to YouTube playlist of all of the screencasts