First: Principles

Ramblings of a software developer with a degree in bioinformatics. Agile development mixed with DNA sequencing - what could go wrong?

Saturday, March 04, 2023

New "No Turn On Red" signs posted in downtown Bloomington

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In 2021, Indiana University law school student Purva Sethi was attempting to cross a street in downtown Bloomington. A driver attempting to...
Wednesday, December 14, 2022

New Leaf, New Life – Statement on a New Jail

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 The Bloomingtonian published a press release from New Leaf, New Life on the new jail being planned in Monroe County. Their comments: A bigg...
Friday, December 09, 2022

Reporting bias against scooters

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  Here's what happened: On September 18, 2022, Madelyn Howard, heavily intoxicated, came cruising in her Mercedes northbound on Walnut S...
Tuesday, November 29, 2022

The High Cost of Free Black Friday Parking

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On this Giving Tuesday, I heard a plug for a donation from my local public radio station, WFIU. As I was getting out my wallet to send somet...
Monday, March 29, 2021

Limit CPU/Memory When using Docker

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After having trouble with the Singularity Pull command on a computing cluster, I decided it might be easier to download the image via Docke...
Thursday, February 25, 2021

Including config.h in every file in Visual Studio

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Rather than explicitly including a header file in every source file, I like to use gcc's - include flag to add a config.h file, a file h...
Tuesday, October 20, 2020

Julia on a multi-user system

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Had occasion to install Julia  on a multi-user system today. I downloaded the tarball to my own directory and ran Make. The instructions say...
Tuesday, October 13, 2020

WSL permissions bits

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Conflicts between Linux permissions and Windows permissions are a perennial problem for people who switch back and forth between WSL and Win...
Thursday, September 03, 2020

Research Computing and Data Capabilities Model

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The capabilities model allow an institution to evaluate how well it supports various data and research requirements. https://carcc.org/2020/...
Friday, August 21, 2020

Traversing a graph database with Gremlin

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This is an invaluable tutorial on how to use the Gremlin query language to get results from a graph database. For some reason, all the inter...
Thursday, July 23, 2020

GDB in threaded code

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GDB ( https://www.gnu.org/software/gdb/  ) is a handy way to debug command line applications. But in the case of applications that are runni...
Sunday, July 19, 2020

Creating a Hyperbook in Microsoft Word

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When someone creates a document they'll possibly set up a table of contents which conveniently links to the chapter headings they've...
Thursday, July 02, 2020

Force-closing an SSH connection

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On occasion when I'm using SSH to connect to a remote server, I run an application that hangs. If the terminal's running inside a GU...
Friday, June 05, 2020

Downloading files from Google Cloud

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In doing some testing with GATK 4 , I found myself in need of downloading files from Google Cloud. Google Cloud likes to use URL's that...
Friday, May 15, 2020

Github offers successor options

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Github is putting some thought into what happens to to your repositories if you're "unable" to manage them - a kind way of say...
Thursday, April 30, 2020

Covid-19 infections by county, rate of increase

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So this image shows rate of increase of the number of cases on a daily basis. It's not as smooth as I would like.
Wednesday, April 29, 2020

Generating sequentially increasing values in C++

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Say you need to generate a sequence, in C++, simply consisting of the first so many integers, like, 1,2,3,4,5. With a little programming e...
Saturday, April 11, 2020

Command Line tips from CLI Magic

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Tips for working with the command line from CLI magic . I like this one to s how all listening TCP/UDP ports for the current user: $ lsof ...
Wednesday, April 01, 2020

Covid-19 infections by county, over time

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This is a visualization choropleth I put together of Covid-19 infections for each county over time. It's based on the NY Times data set...
4 comments:
Tuesday, March 31, 2020

BeautifulSoup4 in Python

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A lot of code available that uses BeautifulSoup tells you to call it like so: from beautifulsoup import BeautifulSoup If you'v...
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