Sean Davis seandavi

prelim

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

quarto add r-wasm/quarto-live

Template for use

Powerpoint from code

Using code for a powerpoint is a useful approach to have chatgpt and other LLMs create powerpoint slides from documents or a textual description.

Usage

pip install -r requirements.txt

Nextflow on Google Cloud at CU Anschutz

Nextflow is a powerful workflow management system designed for creating scalable and reproducible scientific workflows. It enables you to write workflows in a declarative language, making it easy to define complex pipelines that can be executed on various platforms, including local machines, clusters, and cloud environments like Google Cloud.

This short tutorial is meant for informatics users who are comfortable with a command line interface. It also assumes that the user is familiar with and has run nextflow on a local computer or HPC system.

Roughly, this document will walk through:

Sure! Here's the converted Docker Compose YAML file with a MySQL server as a separate container and a Docker volume for storage:

version: '3'
services:
  wandb-local:
    image: wandb/local
    container_name: wandb-local
    environment:
 - HOST=https://YOUR_DNS_NAME

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

	## Required packages

	# 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

	You are an HR specialist and are evaluating the qualifications of job applicants
	for a high-performance computing (HPC) specialist position.
	You have been given a set of criteria to evaluate each candidate.
	The candidate materials are in the attached PDF.
	For each job applicant, fill in the following YAML-format criteria document. You
	may use the "comment" field to provide additional context or justification for
	your evaluation.

	---
	# candidate name

	# convert all CMGD SummarizedExperiments to CSV files
	# Should run more-or-less directly as a script
	# Requires more than 128GB RAM to complete
	# Generates about 200GB of files

	# BiocManager::install('curatedMetagenomicData')
	# BiocManager::install(c('arrow','data.table','dplyr', 'readr'))

	library(curatedMetagenomicData)convert all CMGD SummarizedExperiments to CSV files

	#!/bin/bash
	# results in json format
	# Actual data in "results" array
	#
	# Opportunity numbers taken from https://commonfund.nih.gov/dataecosystem/FundedResearch
	curl \
	-X POST \
	https://api.reporter.nih.gov/v2/projects/search \
	-d '{"criteria":{"opportunity_numbers": ["RFA-RM-23-003", "PA20-185", "OTA-23-004", "RFA-RM-22-007", "OTA-23-005", "RFA-RM-17-026", "RFA-RM-21-007", "RFA-RM-19-012"]}}' \
	-H 'Content-Type: application/json'

	#!/bin/bash
	curl https://gis.cdc.gov/Cancer/DataVizApi/GetJSON/USCS_County \| sed -e 's/<string xmlns="http:\/\/schemas.microsoft.com\/2003\/10\/Serialization\/">//g' -e 's/<\/string>//g'\| jq -c '.[] \| .USCS_County[]' > output.jsonl