Augustin Luna cannin

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RETRIEVE CaImAn DOCKER IMAGE

https://hub.docker.com/r/cannin/caiman

docker pull cannin/caiman:1.9.15-20230906

RUN CaImAn DOCKER CONTAINER

sudo docker rm -f cm; sudo docker run --name cm -d -p 4444:4444 -p 5900:5900 -8888:8888 -e SE_VNC_PASSWORD=password -v /home/ubuntu/tmp:/home/seluser/tmp --shm-size="4g" cannin/caiman:1.9.15-20230906

cancer_type	cancer_type_color	organ_system	organ_system_color
BRCA	#ED2891	Breast	#e6308e
GBM	#B2509E	Central Nervous System	#c48cbc
LGG	#D49DC7	Central Nervous System	#c48cbc
COAD	#00AEEF	Core_GI	#7aa8d9
ESCA	#007EB5	Core_GI	#7aa8d9
READ	#DAF1FC	Core_GI	#7aa8d9
STAD	#00AEEF	Core_GI	#7aa8d9
COADREAD	#00AEEF	Core_GI	#7aa8d9
STES	#007EB5	Core_GI	#7aa8d9

Getting Started

Go to https://chat.openai.com/ and sign in (make an account if you do not have one)
Copy and paste the following text into the text bar at the bottom of the page (after accepting the various terms and disclosures):

Imagine you are helping me interact with several dataset of cancer genomics data. At any given point of time, you have the following abilities. You are also required to output code for some of the requests.

Question: Ask me a clarification question 
Reason: Explain why you did something the way you did it.

	import requests
	from diskcache import Cache
	import os

	# Ensure cache directory exists
	os.makedirs('cache', exist_ok=True)
	cache = Cache('cache')


	def check_pmcid(pmid, email="[email protected]"):

	library(ggplot2)
	library(yaml)

	# Function to summarize a ggplot object
	# TODO: dendrograms with hclust do not work
	summarize_ggplot <- function(object) {
	wrap <- function(x) paste(
	paste(strwrap(x, exdent = 2), collapse = "\n"),
	"\n", sep = ""
	)

	// ==UserScript==
	// @name PubMed Central LLM Summaries
	// @namespace http://example.com
	// @version 0.2
	// @description Add LLM Summaries to PMC
	// @author cannin
	// @match https://pubmed.ncbi.nlm.nih.gov/?term=*
	// @match https://pubmed.ncbi.nlm.nih.gov/*/
	// @match https://www.ncbi.nlm.nih.gov/labs/pmc/articles/*/
	// @match https://www.ncbi.nlm.nih.gov/pmc/articles/*/

	import json

	import dspy
	from dspy.teleprompt import BootstrapFewShot, LabeledFewShot
	from dspy.evaluate import Evaluate, answer_exact_match
	from dspy.datasets import DataLoader


	# PURPOSE ----
	# Example with dataset read from CSV using LLM judge to evaluate the answer

	\begingroup
	\fontsize{6pt}{12pt}\selectfont
	\begin{verbatim}
	6pt-tiny
	\end{verbatim}
	\endgroup

	library(lintr)

	# Excluded linters
	# closed_curly_linter
	# camel_case_linter
	# implicit_integer_linter
	# paren_brace_linter
	# pipe_continuation_linter
	# trailing_blank_lines_linter
	# commented_code_linter