Articles by tag: software
Lots of work goes into writing documents. Lots of that work is rule-based and can be made programmatic. This makes working with documents as a form of code that needs to be compiled as useful way to think about them, as well as working with them. LaTeX can handle these kinds of documents and may be the right place to start.
In Rust, I have always had trouble dealing with paths and how they differ from strings. Here, I want to break down how these types are related to each other, why they're different, and how to convert between them.
This post is about Org mode, an exemplary Emacs package, and why I think so many people love this piece of software.
This post is a walkthrough of how to get these Linux GUI applications running on Windows using the Windows Subsystem for Linux.
My friend, Finn M-K, makes music for a living. I wanted to buy his most recent album and keep the MP3 files. The process was miserable and the easiest route was to pirate it. This is not a sustainable ecosystem for musicians.
Here is a brief rundown of file permissions on Unix systems and how to change them.
I use Anaconda managing my computational software environments. Here are some pragmatic tips for making conda environments easier to deal with.
Dependencies are complicated for computational biologists. Adapting a different development strategy can help your end users.
Here is a reason why I like the Rust language and community, but also why developers may not like them.
This blog post is an experiment in running the web monetization protocol on this blog. If you don't have web monetization enabled in your browser, you won't see the contents of this post.
Emacs is a text editor that has a lot of history and a lot of functionality. Because of its history and the philosophy behind it, it can be hard to find the "right" way to do anything with it. In this post, I want to compile some information that I've found over time, and things that have worked for me.
The PATH environment variable is key for getting software to run on your computer. Sometimes you have to edit it by hand for your development purposes. Here is a tool to make that process a little more sane.
Command line utilities are great. Here are a few of my favourites.
I made a command line tool for keeping track of financial statements for various accounts called Quill. Here's a breakdown of how I developed a solution.
A cursory look at the economics of scientific software, and the implications on its usability and longevity.
Rust is rapidly becoming a powerful and popular programming language. Running it on Windows can be a bit of a pain, so here's a guide to make it easier.
HiGlass is an interactive genome browser that's particularly useful for Hi-C data. Here, I describe how to create your own genome annotation file for HiGlass, allowing you to more easily display your work, regardless of the organism you work in.
Brief thoughts on how to cleanly write ggplot code in R
As a long-time Vim user, it took me some time to figure out what emacs was an how to use it. I hope to make that transition a bit easier and clearer for others.
I offer 10 practical suggestions for designing robust, intuitive, and user-friendly software tools for bioinformatics.
A brief introduction to creating your own conda packages.
Making high-quality bioinformatics software is hard. Installing and using it shouldn't be, though. Here's a detailed description of all the work I did to try and install the ChAMP package.
A quick method for keeping updated on works published by specific authors using PubMed's not so well known RSS feature.
A brief description of how I try my best to keep a low-maintenance and reproducible software environment.
I ported PubPeer's Chrome extension for Microsoft Edge.
I run this site using GitHub Pages, so here's my setup of how I make it easier to test my site before I make changes, using Visual Studio Code.