heejongkim’s gists

heejongkim / Dockerfile

Created November 13, 2024 04:51

DiaNN 1.9.2 Dockerfile

	FROM ubuntu
	USER root
	ENV DEBIAN_FRONTEND=noninteractive

	# Update package lists and ensure package versions are up to date
	RUN apt-get update && apt-get upgrade -y

	# Install necessary packages including locales
	RUN apt-get install wget unzip libgomp1 locales -y

heejongkim / cuda_pytorch.sh

Created June 12, 2022 15:13 — forked from unnir/cuda_pytorch.sh

Install CUDA v8.0, cuDNN v6.0, Anaconda, and PyTorch GPU on Ubuntu 16.04

	#!/bin/bash

	CUDA_REPO_PKG="cuda-repo-ubuntu1604_8.0.61-1_amd64.deb"
	wget http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1604/x86_64/${CUDA_REPO_PKG}
	sudo dpkg -i ${CUDA_REPO_PKG}
	sudo apt-get update
	sudo apt-get -y install cuda-8-0
	#nvidia-smi
	echo 'export PATH=$PATH:$CUDA_HOME/bin' >> ~/.bashrc
	echo 'export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CUDA_HOME/lib64' >> ~/.bashrc

heejongkim / protein_calc.py

Last active October 23, 2022 02:47

(protein, complex) concentration calculator

	### HOW TO USE:

	##### python protein_calc.py <Uniprot Accession Number(s)> <Nanodrop Reading> <Total Sample Volume in ul>

	## Example:
	### For Single Protein:
	##### python protein_calc.py P61830 0.44 200

	### For Protein Complex: (comma separated proteins)
	##### python protein_calc.py P61830,P02309 0.44 200

heejongkim / mzTab2tables.R

Created May 7, 2021 18:51

generalized mzTab parsing tool in R

	## mzTab parsing to tsv files
	## Unlike MSnbase, this will dumbly crawl over mzTab file and generate multiple tsv files
	## The logic is that, except "MTD" which is the mzTab header, the first column's unique identifier for each sub-table
	## will be utilized to sort each row out to corresponding tsv file(s).

	mzTab2list <- function(mzTab_filename){
	nested_lines <- lapply(readLines(mztab_filename), function(x) unlist(strsplit(x, "\t")))
	nested_lines <- nested_lines[lapply(nested_lines,length)>0] # clean up empty lines

	nested_lines_identifiers <- unlist(lapply(nested_lines, `[[`, 1)) # extract first column value as it tells you where this line belongs to

heejongkim / ipi2uniprot.R

Last active May 8, 2021 03:52

Convert IPI accession number to Uniprot accession number via local BLAST

	### Purpose
	# This is a simple single function that takes a list of IPI accession numbers, query their sequences from IPI fasta DB,
	# blast against given uniprot fasta, report the best hit in a table format, which contains both IPI and uniprot accession number
	# side by side along with BLAST result and its sequence
	# rudimentary exception handlings are included but not even close to production quality

	### dependencies
	# Biostrings
	# rBLAST + BLAST 2.9.0+ local installation

heejongkim / Vreg click code

Created March 22, 2021 04:38 — forked from Electronza/Vreg click code

VREG Click: adjustable power supply with Arduino Uno

	# Project page
	# https://medium.com/electronza/vreg-click-adjustable-power-supply-with-arduino-uno-2c61422e17bd