Kelly Sovacool, PhD kelly-sovacool

Google Drive file I/O with Colab Jupyter notebooks

A minimal working example.

Instructions

Place the Jupyter notebook in your Google Drive.
In Google Drive in your web browser, open the Jupyter notebook with Colaboratory.
Run the cells in this notebook to mount the drive and practice reading & writing files.

Notes

test-conda-env-hpc

Question

Does the conda environment that you have activated on the login node also get used in the compute nodes when submitting a job?

Methods

Used conda version 4.6.14

Activate a conda env with snakemake installed.

Keybase proof

I hereby claim:

I am kelly-sovacool on github.
I am kellysovacool (https://keybase.io/kellysovacool) on keybase.
I have a public key ASBMlXzLKCSXdzRoABp2hzLAnUTCeiJezimIZ4iS22kGrgo

To claim this, I am signing this object:

Kelly studied biology with a minor in computer science at the University of Kentucky. While working as an undergraduate lab assistant, she discovered a passion for applying computer science to answer biological questions. In 2018, Kelly joined the Bioinformatics PhD program at the University of Michigan. She develops computational tools and data analysis pipelines for microbiome research under the mentorship of Pat Schloss. See her personal website for more information: https://sovacool.dev.

software-performance

Measuring & improving performance of scientific software.

Compiled vs. Interpreted Languages

Static vs. Duck typing

Static: variable types are declared at initialization and cannot change. [C++]

monte-carlo-pi

Monte Carlo simulation to estimate the value of Pi

Runtime

Original Python 2 version

time python monte-carlo-pi.py
3.142226

	#!/usr/local/bin/python3
	"""
	CS315 Homework 4 through 6: Binary numbers and arithmetic
	Author: Kelly Sovacool
	Email: [email protected]
	Date: 21 Sept. 2017
	Updated: 16 Nov. 2017
	Usage:
	./binaryNumber.py
	./binaryNumber.py human-readable

	#include <cstdio>
	#include <iostream>
	#include <string>
	using namespace std;

	int main ()
	{

	while (true) { //This repeats the program. You close console window manually by clicking "x".

	---
	title: "Lab Meeting Code Review 2019-09-30: Visualizing weights of model features"
	output: html_notebook
	---

	```{r}
	library(tidyverse)
	feature_data = readr::read_csv('combined_all_imp_features_non_cor_results_L2_Logistic_Regression.csv')
	head(feature_data)
	```