Matt Ralston

Bioinformatician | Gamer | Powerlifter

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Not Very Humerus

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Source code and documentation


Who's this guy?

Hello, I’m Matt, a laboratory scientist and bioinformatics programmer. I have a serious passion for computers, bioinformatics and algorithms. Bioinformatician who enjoys studying microbiological genomics and algorithms. Not currently enrolled in a program but still studying the disciplines nonetheless. I look for disciplines that are synergistic with biological fundamentals (chemistry, compuster science, and mathematics) to balance potential applied science areas with my quantitative reasoning.

Philosophically, I admire the spirit of the Gnu Public License, Creative Commons, Arduino, and open-science communities. Some day, I'd love to work on some blog posts about citizen science with Arduino instruments.

A challenge in biological sciences is system complexity and the number of system components available to study. For this reason, there has been an increase in the number of multiplexed measurement technologies, as well as an increase in the cost of instrumentation. Multiplexed assay formats like the microarray and Illumina sequencing provide a broad, survey arm to detect changes worth investigating at the classical level. However, determining the sensitivity of such measurements or confronting the quantitative aspects of biology remains a challenge that is often addressed by software and statistical thresholding.

Quantitative fundamentals are often pushed aside in exchange for a broad applied science survey in many undergraduate biology programs. For this reason, I elected to focus on classical biochemistry book work, applied molecular fundamentals in a cancer laboratory, and a masters degree in computer science with a focus on sequencing technology and multiplexed gene expression.

If there was one thing I'd fix from my masters degree, it would be that I didn't build the library from scratch with cheap ligases and random hexamers. I elected instead to use a Illumina TruSeq sequencing kit, which produced an RNA library with good fragment length and excellent fastq quality scores. However, these kits should be used as a high-caliber basis to judge the quality of alternative library preparation protocols utilizing cheaper reagents and custom barcoding strategies. In short: I wish I had used a more DIY approach.

Open source fanboy, powerlifter, guitarist.


  • Molecular Biology
  • Physiology
  • Genetics/Genomics
  • Organic Chemistry
  • Biochemistry
  • Algorithms
  • Database Systems
  • Biostatistics
  • Regression Analysis
  • Machine Learning

Organic, Phyical, Analytical Chemistry:

  • GC-MS
  • HPLC
  • ITC


  • Fed-batch fermentation
  • Plate/colony culture
  • Flux-balance analysis


  • Fluorescence-Activated Cell Sorting (FACS)
  • Immunofluorescence / Immunohistochemistry
  • Western blot

Molecular Biology:

  • Northern blot
  • q-RT-PCR
  • Next Generation Sequencing


  • MySQL/PostgreSQL/Oracle
  • MongoDB/DynamoDB
  • Sqlalchemy/Rails/Express ORMs

Statistics / Visualization:

  • R + KnitR + Shiny
  • Pandas + matplotlib + Seaborn
  • Data-Driven Documents (D3.js)

Web Development:

  • HTML + CSS + JS

Functional Programming:

  • Scheme
  • Haskell

UNIX Shell:

  • Bash on RHEL/Debian/Arch Linux/OSX

Scripting / Full-stack:

  • Bash
  • Python / Flask
  • Ruby / Rails
  • Perl
  • NodeJS / Express


Work History



Data Science Workstation Build

#meta #prose #beginner #sysadmin
22 Apr 2021

In this blog post we’ll be reviewing the essentials of a mature workstation build, in this case, for graduate school....

How Do I Become A Bioinformatician

#meta #prose #education #beginner
05 Sep 2020

I see plenty of posts on /r/bioinformatics of students or mid-career professionals asking what it takes to become a bioinformatician....

Sorting Out Modules In Python

#python #beginner #noob
26 Feb 2020

Oh yeah, it’s all coming together If you’re comfortable with the differences between dictionaries and modules, skip ahead to the...