├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md ├── PULL_REQUEST_TEMPLATE.md └── workflows │ ├── check-links-self.yaml │ ├── check-links.yaml │ ├── check_links.py │ ├── lint.py │ ├── notebook-lint-self.yaml │ ├── notebook-lint.yaml │ └── requirements.txt ├── README.md ├── docs ├── AWS-Batch-Setup.md ├── GoogleCloudPlatformResources.md ├── HowToCreateAzureMLNotebooks.md ├── HowToCreateNewTerminalConsoleJupyterLab.md ├── HowToCreateNextflowServiceAccount.md ├── HowToCreateVertexAINotebooks.md ├── HowToForkRepository.md ├── HowToLaunchAWSBatch.md ├── HowToMountABucketWithGcsfuse.ipynb ├── HowToPullRequest.md ├── HowToPushImageToECR.md ├── HowToReUseAWSBatchResources.md ├── HowToSelectAWSSageMakerKernel.md ├── HowToUseCondaEnvsAsKernels.ipynb ├── HowToUseNextflowandGCPLifeSciences.ipynb ├── SageMakerNotebook&StudioSetup.md ├── account_registration.md ├── image_builder.sh └── open_GCP_project.md ├── idle-shutdown.sh └── images ├── 1_NIH_login.png ├── 1_clone_repo_gcp.png ├── 1_connect_google.png ├── 1_select_vertexAI.png ├── 2_input_university.png ├── 2_nih_org.png ├── 2_select_kernel_R.png ├── 2_select_project.png ├── 3_busy_cell.png ├── 3_grant_access.png ├── 3_name_notebook.png ├── 3_select_project.png ├── 4_final_form.png ├── 4_select_environment.png ├── 5_launch_notebooks.png ├── 5_logingov.png ├── 6_signin_logingov.png ├── 7_final_form_logingov.png ├── 7_mfa.png ├── ECR ├── 1.PNG ├── 10.PNG ├── 2.PNG ├── 3.PNG ├── 4.PNG ├── 5.PNG ├── 6.PNG ├── 7.PNG ├── 8.PNG └── 9.PNG ├── NIGMS_README_Graphic.svg ├── Universities.png ├── aws-small.png ├── aws_container_setup_thumbnail.jpeg ├── aws_notebook_setup_thumbnail.jpeg ├── azure-small.png ├── batch-compute1.PNG ├── batch-compute2.PNG ├── batch-compute3.PNG ├── batch-compute4.PNG ├── batch-permission1.PNG ├── batch-policis.PNG ├── batch-queue1.PNG ├── google-cloud-small.png ├── google-cloud.png ├── images_custom_kernel ├── Capture1.PNG ├── Capture10.PNG ├── Capture2.PNG ├── Capture3.PNG ├── Capture4.PNG ├── Capture5.PNG ├── Capture6.PNG ├── Capture7.PNG ├── Capture8.PNG └── Capture9.PNG ├── images_for_creating_AWSBatch ├── LaunchStack.jpg ├── LaunchStack_configure.png ├── LaunchStack_review.png ├── LaunchStack_select.png ├── LaunchStack_specify.png └── SageMaker_IAM_Role.png ├── images_for_creating_AWS_notebooks ├── 1-sagemakerAI.png ├── 2-sagemaker-instance.png ├── 3-idle-shutdown.png ├── 4-click-create.png ├── Clone_CodeEditor.png ├── Clone_Terminal.png ├── Clone_UI.png ├── Screenshot1.png ├── Screenshot10.png ├── Screenshot11.png ├── Screenshot12.png ├── Screenshot13.png ├── Screenshot14.png ├── Screenshot15.png ├── Screenshot16.png ├── Screenshot17.png ├── Screenshot18.png ├── Screenshot19.png ├── Screenshot2.png ├── Screenshot20.png ├── Screenshot21.png ├── Screenshot22.png ├── Screenshot23.png ├── Screenshot24.png ├── Screenshot25.png ├── Screenshot26.png ├── Screenshot27.png ├── Screenshot28.png ├── Screenshot29.png ├── Screenshot3.png ├── Screenshot30.png ├── Screenshot31.png ├── Screenshot32.png ├── Screenshot33.png ├── Screenshot34.png ├── Screenshot35.png ├── Screenshot36.png ├── Screenshot4.png ├── Screenshot5.png ├── Screenshot6.png ├── Screenshot7.png ├── Screenshot8.png ├── Screenshot9.png ├── terminal1.PNG └── terminal2.PNG ├── images_for_creating_Azure_ML_notebooks ├── 1.png ├── 10.png ├── 2.png ├── 3.png ├── 4.png ├── 5.png ├── 6.png ├── 7.png ├── 8.png ├── 9.png ├── Azure_run_cell.png ├── jl_kernel.png ├── kernel.png ├── launcher.png ├── select_compute.png └── start_open_jl.png ├── images_for_creating_GCP_instances ├── 1_instance_details.png ├── 2_select_workbench_instance.png ├── 3_select_advanced_options.png ├── 4_instance_environment.png ├── 5_instance_machine_type.png ├── 6_instance_idle_shutdown.png └── custom_container.png ├── images_for_creating_new_console ├── New_console.png ├── Right_click_notebook.png ├── Right_click_notebook_highlighted.png ├── Split_view.png └── Terminal_launcher.png ├── images_for_ecr_shellscript ├── step_1.png ├── step_2.png ├── step_3.png ├── step_4.png ├── step_5.png ├── step_6.png └── step_7.png ├── images_for_github_fork ├── CreateLocal.png ├── ForkCommand.png └── final.png ├── images_for_pull_request ├── CreatePull.png ├── PullRequestBranch.png ├── PullRequestMain.png └── PullRequestMessage.png ├── images_for_resuing_AWSBatch_Resources ├── AWSConsoleLambda.png ├── CloudFormation.png ├── ConfirmDelete.png ├── DeleteStack.png ├── ResourcesBatchBucket.png ├── ResourcesIDs.png ├── SageMakerNotebook_IAMrole.png ├── SageMakerNotebook_Permissions.png ├── SelectFunctionDelete.png ├── StackDelete.png └── StackHyperlink.png ├── images_for_selecting_kernel ├── SageMaker_Kernel_Select.png └── SageMaker_Kernel_layout.png ├── service_account_1.jpeg ├── service_account_2.jpeg ├── service_account_3.jpeg ├── service_account_4.jpg ├── service_account_5.jpg ├── service_account_6.jpg ├── service_account_7.jpg └── service_account_8.jpg 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