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Sean Davis seandavi

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@seandavi
seandavi / scrape_state_cancer_profiles.py
Last active October 19, 2023 23:32
Scrape the cancer incidence from https://statecancerprofiles.gov
"""This script scrapes the state cancer profiles website
and saves the results as csv files.
The website is a bit of a mess, so this script is a bit of a mess.
It requires scraping the select options from the website
and then iterating over all the possible combinations of
select options to get the data.
The script is designed to be run from the command line
with the following command:
@seandavi
seandavi / README.md
Last active August 2, 2023 14:41
Basic google LLM API quickstart and example

See: https://cloud.google.com/vertex-ai/docs/generative-ai/chat/test-chat-prompts

You'll need:

  1. A project id
  2. An installed and working gcloud command-line tool
  3. A service account that has been granted access to vertex AI
  4. A json key file associated with the service account
  5. Set up local environment to use the json key for authentication

Tasks 1, 3, and 4 can be performed using the console OR using gcloud by a user authorized to create resources. Note that the

@seandavi
seandavi / Dockerfile
Last active April 15, 2025 04:26
Run a google cloud batch job set up in python
from python:3.11
RUN pip install --upgrade pip
RUN pip install omicidx
RUN pip install fsspec gcsfs s3fs
COPY abc.py .
@seandavi
seandavi / chatgpt.R
Created July 11, 2023 21:35
Small play function for interacting with Azure openai playground (chatgpt)
library(httr2)
ChatGPT <- function(prompt='Tell me about Bioconductor') {
base_request = httr2::request('https://openai-playground-asdf.openai.azure.com/openai/deployments/gpt-4/chat/completions?api-version=2023-03-15-preview')
res = base_request |>
httr2::req_headers('api-key'=Sys.getenv('API_KEY')) |>
httr2::req_body_json(list(
messages=
list(
list(role="system",content="You are a helpful AI assistant"),
list(role="user", content=prompt)
@seandavi
seandavi / dataflow_chatgpt.dot
Created June 8, 2023 20:33
digraph ChatGPT {
node [shape=box]
subgraph cluster_0 {
label="Microsoft Asure"
style=dashed
ChatGPT
}
subgraph cluster_1 {
label="On Prem or Cloud"
style="dashed"
@seandavi
seandavi / annotationhub_alabaster.R
Created June 7, 2023 16:30
Alabaster process all of annotationhub....
library(alabaster)
library(AnnotationHub)
library(jsonlite)
ah = AnnotationHub()
STAGE_DIR = '/tmp/ah_staging'
dir.create(STAGE_DIR, showWarnings = FALSE)
write_error = function(dirname, e) {
jsonlite::write_json(list(message=jsonlite::unbox(e$message)), file.path(dirname,'error.json'))
@seandavi
seandavi / prompts.md
Created June 2, 2023 23:44
LLM prompts

Meetings

Summary from zoom transcript

You are an AI assistant that summarizes meeting notes generated by Zoom. For the meeting notes provided as input, provide these items if possible from the content:

  • meeting date, time, and title
  • meeting attendees as a bulleted list
  • executive summary (3-5 sentences)
@seandavi
seandavi / bioconductor_ehub_ahub_dataconductor.dot
Created May 31, 2023 13:00
Graphviz dot version of experimenthub and annotationhub replacement by dataconductor
# Place the cursor inside "graph" to get some refactoring options
digraph G {
fontname="Helvetica,Arial,sans-serif"
node [fontname="Helvetica,Arial,sans-serif"]
edge [fontname="Helvetica,Arial,sans-serif"]
edge[color="#00000050"]
subgraph cluster_0 {
@seandavi
seandavi / cytoband_table_prompt.txt
Last active May 10, 2023 21:22
Using GPT-4 to augment AnnotationHub resource metadata
I would like you to describe the UCSC genome browser table called "cytoBand". The first few lines of the table are here:
chrom chromStart chromEnd name gieStain
chr1 0 2300000 p36.33 gneg
chr1 2300000 5300000 p36.32 gpos25
chr1 5300000 7100000 p36.31 gneg
chr1 7100000 9100000 p36.23 gpos25
chr1 9100000 12500000 p36.22 gneg
chr1 12500000 15900000 p36.21 gpos50
chr1 15900000 20100000 p36.13 gneg
@seandavi
seandavi / main.tf
Last active June 4, 2023 01:19
Terraform for setting up OpenAI APIs on Microsoft Azure
# <[email protected]>, 2023-06-02
#
# Terraform for setting up GPT-4, GPT-3.5-turbo, and text-embedding-ada-002
# endpoints. Note that not all models are available in all regions, so
# check before changing the region here, currently set to "southcentralus"
#
# Assumes az-cli authenticated (requires Azure subscription) and terraform
# available and installed
#
terraform {