Matt Ralston

Matt Ralston

M.Sc. Bioinfo + 5 years industry exp. - - - Currently writing a DNA sequence alignment, quasi-mapper, and graph algorithm and manuscript (for bioRxiv). I play math rock on my guitar, I write open-source software on GitHub, I pay my bills in the DE-NJ-PA tri-state area near Delco, and I'm launching a DE-based LLC for Univ. of Delaware and local NGS sequencing projects.

Blog posts

2025

Thoughts on ML deployments, containerized workflows, and notebooks.

6 minute read

Published:

This article hopes to bring the reader up to date (ca. 2017-2022) on modern cloud-native and scalable solutions for data science and natural science research application stacks using the Docker container standard for container specification (vs Singularity, Podman, or containerd containers that are equally valid). First I will provide a brief description of the goal of Docker containers. Next I’ll touch on the kubernetes architecture for distributed data processing and application service management. Finally, I’ll describe code repository, container registries, and Markdown/Rmarkdown/LaTeX documentation as it purtains to a service’s lifespan w.r.t. notebooks and documentation of custom services and their orchestration.

2024

Benchmarking Aligners

1 minute read

Published:

Short-read aligners make up the core of modern bioinformatics program technologies. The aligners are responsible for mapping (rather than aligning) short reads (typically produced by Illumina sequencers) to their most likely originating loci with gapped and ungapped, genomic and transcriptomic methods. For lists of both aligners and short-read mappers and their pros/cons, see the Wikipedia article.

Youth Falls In Night

less than 1 minute read

Published:

I came to life from two unknown trees, Roots tangled deep in mystery’s seas. Yet arms reached out, so strong, so kind, To plant me anew, a love redesigned.

Roots And Wings

less than 1 minute read

Published:

I came to life from two unknown trees, Roots tangled deep in mystery’s seas. Yet arms reached out, so strong, so kind, To plant me anew, a love redesigned.

Basic Python 2

16 minute read

Published:

Skip the description, let’s get to the code!

Ricing In 2024

less than 1 minute read

Published:

Customization is essential for maximizing visual appeal and ease of use of the computer system.

Linear Runtimes For Quasimapping And Alignment Free

1 minute read

Published:

I want to discuss linear runtimes and what that means in alignment-free methods for bioinformatics and sequence alignments and quasi alignments. First, it is the splitting of the sequences, as they are read, into, let’s say, ‘a’ De Bruijn graph. This graph consists of the k-mers, their neighborhoods, and of course the walks or paths through the graph that constitute optimal criteria and local maxima of course for traversal and contig/walk/path maximization. Typically, a search through the De Bruijn structure may be Breadth-First to find optimal depths for traversal of the path through the De Bruijn structure, optimizing for creating some sequence. This leads to read collapse along the sequence unidirectionally (bidirectionally in a unidimensional space) along the sequence space.

2022

2020

How do I become a bioinformatician?

22 minute read

Published:

I see plenty of posts on /r/bioinformatics of students or mid-career professionals asking what it takes to become a bioinformatician. What skills should I have? What programming languages should I learn? What course should I take? Do I need a masters or PhD? Here is my answer to the question 'How do I become a bioinformatician?'

2019

Kmer Database Format (Part 1.)

33 minute read

Published:

The goal of this blog post is to introduce the concepts of k-mer subsequences and blocked GNU-zip file (.bgzf) and suggest that they be used together to form a new file specification for younger bioinformaticians. If I'm successful, the reader should have a basic understanding of common k-mer packages, my opinion on the algorithms and APIs, and the challenge of understanding advanced computer science and benchmarking concepts utilized by those packages/algorithms from the eyes of novice, beginner, and even intermediate bioinformatics students.

Views of the ‘Second Shift’ Phenomenon in Children - Domestic Egalitarianism

10 minute read

Published:

Review notes

These are some notes I jotted down while reading a study from Psychological Science linked by /r/science Reddit at 2.3k updoots. This article had a somewhat clearer design and premise than a more popular post (8.8k currently) this morning in the same subreddit. PDF to the former article and the Springer link to the latter. I am reviewing the article to talk with a new acquaintance on the phone about feminism and gender equality.

Magika - A Sword Art Online fanfiction

43 minute read

Published:

Officially, magic was a forbidden component of Sword Art. Magical skills, item stats, criticals, and ability leveling may have elements beyond the typical diagnostic expertise of the players. Yet, enchanted items, durability, and other components of the material realm of Sword Art have mechanics of randomness, high-level crafting, beyond the scope the typical player will invest into the game. Additionally, defensive and offensive techniques also have randomness and executional nuance beyond the scope of most players’ level of interest. The code of the game actively encourages this obfuscation to provide a simple experience for the players, and even goes so far as to encode a level of instinct that Kirito granted Cline in the West Field. The user interface and neurological link was indeed part of harnessing full potential in the battlefield, involving physical, mental, and psychological nuances. The West Field had reminded him of other MMO’s he had played online; a pointless grind for experience and loot, almost deliberately trivial in comparison to the dungeons and party mechanics. Sure the social components of the game were important, but you never know who’s going to fail to support your flank and ensure survival. Since Kirito was a solo player, it had always seemed easier to grind in the fields so he had something to bring to the table when he actually joined a party.

2018

AWS S3 System Backup Tutorial

13 minute read

Published:

This article is geared for novice to intermediate users of OSX and Linux, perhaps a 20min read.

Review of Ken Robinson’s Changing Education Paradigms

11 minute read

Published:

In this post I’m going to try something a little bit different. I’m presenting at my alma matter this fall to talk about my research for Bristol Myers Squibb. As I’ve been reflecting on objective differences in project longevity, rigor, or collaborative style in preparation for some early-mid 20’s students, I revisited one of my favorite RSA Animate talks: Ken Robinson’s ‘Changing Education Paradigms’.

Pro-Pharma Rant and the Nebula Network

3 minute read

Published:

Hi everyone, have you ever wondered what would be a good idea for an app? Since I became a developer, now I have *some* of the tools to potentially create some basic web applications, command line tools, etc. For some developers who aren't creating regularly, it may seem like your work actually gets in the way of the creative process, and you might not get the time to make that killer app you really wanted to build.

On Python Documentation with Sphinx

1 minute read

Published:

I’ve been exploring the Python documentation system for ReadTheDocs with Sphinx. It could be that I’m dense, but the sphinx-quickstart command seems horribly divorced from most of the automagic documentation goals of the Sphinx project. After following several guides1, 2 I noticed that only an index.rst had been created in the _sources directory. Brandon’s guide suggests that adding your module to either your PYTHONPATH or to your conf.py before make html would lead to autodoc recognizing your package. I wasn’t able to get this to work on OSX Sierra using a virtualenv. After looking through more tutorials, I encountered some suggestions for the sphinx-apidoc command, without actual invocation details.

Hello World

less than 1 minute read

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Hello world, I am building my first blog for science and technical topics called Not Very Humerus (NVH). I’ll be adding periodically to this collection and focusing on the technical side of my journey for a bit. I’ll try to proceed chronologically with some retrospectives at the beginning of the blog to focus on my experiences in University.

2015

Code Syntax

less than 1 minute read

Published:

Popovers