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Step 1: install duckdb

DuckDB is the database tool that we use to access the files living in cloud storage.

• Installation instructions

Step 2: create a duckdb with the parquet views

curl https://raw.githubusercontent.com/omicidx/omicidx-etl/refs/heads/main/omicidx_etl/sql/020_base_parquet_views.sql | duckdb omicidx.duckdb

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nih-repo-summary — Copilot CLI Skill

A GitHub Copilot CLI skill that generates a polished, one-page NIH funder-ready summary of any code repository. The summary is written for non-technical scientific audiences — program officers, grant reviewers, and NIH staff — not software developers.

The skill instructs Copilot to act as an observer only: it reads and reports but never modifies the repository.

---

What It Produces

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/* 1.  give every row a sequence number */
WITH ordered AS (
    SELECT
        package,
        stage,
        status,
        startedat,
        row_number() OVER (PARTITION BY package ORDER BY startedat) AS rn
    FROM t_build_summary where stage='buildsrc'
),

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Constructive Use of AI in Clinical Reasoning: Transitioning to Residency with Reflection and Safety

1. Why AI Matters

Artificial intelligence (AI), including large language models (LLMs), is becoming a daily companion in medicine — from documentation to diagnostic reasoning. Used thoughtfully, AI can enhance learning and efficiency. Used uncritically, it risks deskilling, never-skilling, and mis-skilling.

Opportunity	Risk
Off-loads routine cognitive work	Overreliance → weaker independent reasoning

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Frontier of AI & Medicine, October 2025 Christina Olson Christina.Olson@childrenscolorado.org

Self-Directed Learning Exercises: AI Tools for Clinical Care

Clinical Decision Making

*For this exercise, ensure that you do not enter PHI or other details that potentially could identify specific patients or our institution in Open Evidence or ChatGPT, as these are not secure systems. It is ok to

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Connecting

Start duckdb, either on the command line or in R, etc. To connect to and then use the biodatalake ducklake, do the following inside the duckdb connection:

install httpfs;
load httpfs;
.read 'https://store.cancerdatasci.org/ducklake_config/ducklake_ro_connect.sql'

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#' Workshop cost calculator
#' 
#' This cost calculator give the **minimum** cost for a workshop of the
#' requested size, number or participants, and hours. 
#'
#' @param vcpu numeric() amount of virtual cpu requested (can be fractional)
#' @param memory numeric() in GB the amount of requested memory
#' @param hours numeric() the number of hours for each instance to run
#'   The workshops will run for this amount of time even if a participant
#'   is not using it. So, every launch results in a cost. 

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---
title: "Github Repos for Topic"
author: "Sean Davis"
format: html
params:
  gh_topic: "r01ca230551"
---

## Required packages

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prelim

To use the live-html (webr/pyodide) in quarto:

quarto add r-wasm/quarto-live

Template for use

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# Install Bioconductor and required packages
# This command installs the BiocManager package for managing Bioconductor packages
install.packages("BiocManager")

# Use BiocManager to install specific packages for data analysis and visualization
BiocManager::install(c("GEOquery", "SummarizedExperiment", "ggplot2",
                       "party", "ggparty", "partykit", "randomForest"))

# Load necessary packages for modeling and visualization
library(party)          # For creating classification trees