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.envrc
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use flake
layout node
mkdir -p "${HOME}/Library/Application Support/SourceGit"
echo "${PATH}" > "${HOME}/Library/Application Support/SourceGit/PATH"

28
.gitignore vendored
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@ -161,31 +161,3 @@ fontawesome-pro-6.3.0-web
### Nix Flake gitignore ###
result
### MacOS gitignore ###
# General
.DS_Store
.AppleDouble
.LSOverride
# Icon must end with two \r
Icon
# Thumbnails
._*
# Files that might appear in the root of a volume
.DocumentRevisions-V100
.fseventsd
.Spotlight-V100
.TemporaryItems
.Trashes
.VolumeIcon.icns
.com.apple.timemachine.donotpresent
# Directories potentially created on remote AFP share
.AppleDB
.AppleDesktop
Network Trash Folder
Temporary Items
.apdisk

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layouts/_default/index.manifest.json

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@ -4,6 +4,3 @@ overrides:
- files: "*.html"
options:
parser: "go-template"
- files: "*.gotmpl"
options:
parser: "go-template"

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@ -1,15 +1,14 @@
when:
branch: master
event:
- push
- cron
cron: "weekly-build"
event: push
steps:
- name: Build site
image: hugomods/hugo:std-base-non-root-0.141.0
image: nixos/nix:2.24.11
commands:
- hugo --minify
- echo 'experimental-features = flakes nix-command' >> /etc/nix/nix.conf
- nix build
- mkdir public && cp -av result/* public
- name: Deploy to pages
image: codeberg.org/xfix/plugin-codeberg-pages-deploy:1
settings:

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{
"languages": {
"HTML": {
"formatter": {
"external": {
"command": "prettier",
"arguments": ["--stdin-filepath", "{buffer_path}"]
}
}
}
},
"file_types": { "HTML": ["gotmpl"] }
}

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@ -6,20 +6,18 @@ My personal website. Hosted over at <https://millironx.com>
## Notes to self
### Nix dev shell
All developer dependencies are now bundled as a Nix Flake. The only trouble with
this is that npm packages don't play well with Nix (and especially Flakes), so
npm packages are specified twice: once in `package{-lock}.json` and then again
in `node*.nix`.
All dependencies are now bundled as a Nix Flake. The only trouble with this is
that npm packages don't play well with Nix (and especially Flakes), so npm
packages are specified twice: once in `package{-lock}.json` and then again in
`node*.nix`.
Compounding this, there are formatters and commit hooks that require npm to be
functional. So, to develop right now requires allowing direnv to setup the Nix
development shell, then immediately installing npm packages via `npm ci`. VSCode
(with extensions) and Zed are smart enough to figure out how to use direnv, and
direnv will pass the PATH to SourceGit for Mac, but other programs aren't that
smart, so you'll need to launch those programs from inside a direnv shell to
make sure they have Prettier, Husky, and all that jazz to execute the hooks.
(with extensions) and Zed are smart enough to figure out how to use direnv, but
other programs (like SourceGit) not so much, so you'll need to launch those
programs from inside a direnv shell to make sure they have Prettier, Husky, and
all that jazz to execute the hooks.
Last compounding factors: if `node_modules` is present in the root directory,
then node2nix won't create a correct derivation, so `node_modules` will need to
@ -32,11 +30,3 @@ run.
Yes, hopefully I can get completely away from npm here soon, but this is a minor
inconvenience considering how (not) often I install new packages into this site,
and really discourages me from contributing to the website obesity crisis.
### Nix building
Nix building will not work because Hugo reaches out to the internet via content
adapters, and that (by intention) is not perfectly reproducable. As such,
_development_ tools are installed in a Nix shell, but building has been removed
from the Flake. Thankfully, hugomods provides "canonical" Docker images for hugo
now.

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# Characters
Imaginary friends that help me inject personality into my articles. These are
anthropomorphized versions of animals that I have known in real life. I tried to
draw them roughly in the style of Chris Pasquini, but failed myself, then tried
using Perplexity's image generation. The style isn't quite the same, but I like
it for these animals. Also, Perplexity does a horrible job of labeling images,
so ignore the ref sheet emotion labels.
## Spawn of Satan (aka Spawn aka SOS)
![Spawn ref sheet](spawn/_ref-body-perplexity.png)
Spawn of Satan is the name Travis gave to the cannulated cow, and it stuck.
Spawn is old and cynical after having every professor with a new idea experiment
on her. After being in academia for so long, she knows her way around
mathematics and the scientific method reasonably well, even if she's never
formally taken a college course in the sciences. She is the realist to any blog
post's optimist.
## Whelen
![Whelen ref sheet](whelen/_ref-body-perplexity.png)
Whelen is a happy-go-lucky German Shepherd/Husky mix puppy. He's been to school
once - and that was just to get neutered - so his knowledge of math and science,
heck, even of the humanities, isn't very good. He is very naive and thinks
everyone is nice and wants to be his friend, but he is also friendly to everyone
and is very vocal when he feels left out. He will step in when any blog post is
getting too technical and demand an explanation for real people (dogs?).

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@ -165,18 +165,7 @@
);
--container-border: light-dark(var(--swiss-brown-6), var(--eclipse-16));
--container-background: light-dark(var(--swiss-brown-4), var(--eclipse-12));
--container-border-alt: light-dark(var(--eclipse-16), var(--swiss-brown-6));
--container-background-alt: light-dark(
var(--eclipse-12),
var(--swiss-brown-4)
);
--motto-background: rgba(0, 0, 0, 0.66);
--page-button-text: var(--prickly-pear-yellow-1);
--page-button-background: var(--prickly-pear-yellow-8);
--page-button-background-hover: var(--prickly-pear-yellow-10);
--page-button-background-active: var(--prickly-pear-yellow-12);
--page-button-background-disabled: var(--prickly-pear-yellow-6);
--page-button-text-disabled: var(--eclipse-7);
/*
Fonts
@ -185,10 +174,7 @@
"URW Bookman L", "Georgia Pro", Georgia, serif;
--font-family-slab-serif: Rockwell, "Rockwell Nova", "Roboto Slab",
"DejaVu Serif", "Sitka Small", serif;
--font-family-transitional: Charter, "Bitstream Charter", "Sitka Text",
Cambria, serif;
--font-family-system-ui: system-ui, sans-serif;
--font-family-monospace: "Nimbus Mono PS", "Courier New", monospace;
}
/*
@ -200,26 +186,6 @@ html {
font-family: var(--font-family-slab-serif);
}
body {
display: flex;
flex-direction: column;
min-height: 98vh;
margin: 0 8px;
align-items: center;
}
.container {
max-width: min(60rem, 100vw - 2rem);
}
.footer-inner {
width: min(60rem, 100vw - 2rem);
display: flex;
justify-content: space-between;
align-items: center;
flex-shrink: 0;
}
a {
color: var(--link-color);
}
@ -269,39 +235,6 @@ nav a:hover {
background-color: var(--nav-button-background-hover);
}
main {
display: flex;
flex-direction: column;
}
article p,
.character-dialog-text,
article li {
font-family: var(--font-family-transitional);
font-size: 1.15rem;
text-justify: inter-word;
text-align: justify;
hyphens: auto;
}
article > p {
text-indent: 2ch;
line-height: 1.5em;
}
article h1 + p,
article h2 + p,
article h3 + p,
article h4 + p,
article h5 + p,
article h6 + p {
text-indent: 0;
}
.footnotes p {
font-size: smaller;
}
figure {
border-color: var(--container-border);
border-width: 1.5pt;
@ -311,41 +244,33 @@ figure {
padding: 1.25pt;
}
figure:has(blockquote) {
blockquote {
background: linear-gradient(
to right,
var(--container-border),
var(--container-background)
);
border: none;
border-radius: 0;
border-left: 6px solid black;
padding: 0.25em 1em;
border-left: 5px solid black;
padding: 1px;
padding-left: 6px;
}
figure:has(blockquote) > blockquote {
margin: 0;
}
figure:has(blockquote) > figcaption::before {
blockquote small::before {
content: "\2014 \00A0";
}
figure:has(blockquote) > figcaption {
margin-top: -1em;
margin-bottom: 1em;
blockquote small {
font-size: 80%;
}
footer {
display: flex;
flex-direction: column;
align-items: center;
background-color: var(--container-background);
margin: 0 0 -1em -1em;
width: calc(100% - 1em);
padding: 0.25em 1.25em;
font-size: smaller;
display: flex;
justify-content: space-between;
align-items: center;
}
form {
@ -370,25 +295,6 @@ textarea:invalid {
border-bottom-color: var(--ear-tag-red);
}
code {
font-family: var(--font-family-monospace);
}
/*
abbr element "tooltip" for mobile
heavily modified from https://bitsofco.de/making-abbr-work-for-touchscreen-keyboard-mouse/
*/
abbr[title]:focus::after {
content: attr(title);
background-color: #1e1e1e;
color: #fff;
border-radius: 0.125em;
box-shadow: 1px 1px 5px 0 rgba(0, 0, 0, 0.4);
font-size: smaller;
padding: 0.5em;
display: block;
}
/*
Container-type helper classes
*/
@ -398,12 +304,6 @@ abbr[title]:focus::after {
width: 100%;
}
.motto-wrapper {
display: block;
flex: 1 0 30vh;
margin-bottom: 1em;
}
.motto {
position: relative;
display: grid;
@ -413,7 +313,6 @@ abbr[title]:focus::after {
font-weight: 600;
text-shadow: 0 0 10px rgba(0, 0, 0, 0.33);
width: 100%;
height: 100%;
padding: 0 0 0.5em 0;
border-radius: 0.25rem;
z-index: 10;
@ -441,7 +340,6 @@ abbr[title]:focus::after {
.motto .motto-inside h1 {
background-color: var(--motto-background);
padding: 0.5rem;
}
.card {
@ -453,23 +351,11 @@ abbr[title]:focus::after {
margin: 1rem 0;
padding: 0.5rem;
padding-top: 0;
position: relative;
display: flex;
flex-direction: column;
}
.card-content {
display: flex;
flex-direction: column;
flex-grow: 1;
}
.card-header {
display: flex;
flex-direction: row;
justify-content: space-between;
flex-grow: 1;
}
.card-link {
white-space: nowrap;
display: inline-flex;
@ -477,26 +363,22 @@ abbr[title]:focus::after {
align-items: center;
text-underline-offset: 0.25em;
backface-visibility: hidden;
margin: 0.1em 0.25em;
padding: 0.33em;
padding-right: 0.45em;
}
.card-body {
margin-top: 0.33em;
margin: 0 0.5em;
}
.category-button {
position: absolute;
top: 1em;
right: 1em;
display: grid;
align-items: center;
justify-items: center;
color: white;
background-color: var(--ear-tag-red);
border-radius: 0.5em;
padding: 1em;
margin: 1em;
height: 2em;
aspect-ratio: 1 / 1;
}
.card-title a h3 {
margin-right: 3.5em;
}
.card-title > a {
@ -539,118 +421,6 @@ abbr[title]:focus::after {
fill: currentColor;
}
.account-bucket {
display: grid;
grid-template-columns: 3em 1em 1fr;
background-color: var(--container-background-alt);
padding: 1em 0;
border-radius: 0.5em;
border-color: var(--container-border-alt);
border-style: solid;
color: light-dark(white, black);
margin: 1em 0;
align-items: center;
}
.account-bucket h3 {
align-self: center;
writing-mode: sideways-lr;
}
.account-bucket details {
grid-column: 3;
}
.account-bucket .crypto-list {
grid-column: 3;
max-width: 100%;
}
.account-list {
display: flex;
justify-content: space-between;
flex-wrap: wrap;
width: calc(100% - 1.5em);
}
.account-bucket .account-list {
grid-column: 3;
}
.account-list a {
font-size: xx-large;
text-decoration: none;
color: inherit;
padding: 0.5em;
}
.account-list a:hover {
background-color: var(--container-background);
border-color: var(--container-border);
border-width: 2.5px;
border-radius: 0.5em;
border-style: solid;
padding: calc(0.5em - 2.5px);
}
figcaption .mono {
color: light-dark(black, white);
overflow-wrap: anywhere;
}
.crypto-list details {
max-width: 100%;
}
.character-dialog {
display: grid;
width: calc(100% - 1rem);
grid-template-columns: 5rem 1fr;
grid-template-rows: auto auto;
gap: 1em;
margin: 0.5rem;
}
.character-avatar {
display: grid;
max-width: 100%;
grid-row: 1 / span 2;
grid-column: 1;
align-self: start;
align-items: center;
justify-items: center;
min-width: 5rem;
min-height: 5rem;
border-radius: 5rem;
align-items: center;
border-style: solid;
border-color: var(--nav-button-background-hover);
background-color: var(--cowhide-2);
}
.character-avatar > img {
max-width: 4rem;
max-height: 4rem;
}
.character-dialog-bubble {
display: grid;
grid-template-rows: auto auto;
align-self: start;
border-radius: 0.5em;
border-width: 0.2rem;
border-color: var(--nav-button-background);
border-style: outset;
row-gap: 0.5rem;
padding: 0.5rem;
background-color: var(--container-border);
min-height: 5rem;
}
.character-dialog-title {
font-weight: bolder;
}
/*
Helper classes
*/
@ -661,9 +431,6 @@ figcaption .mono {
.img-fluid {
max-width: 100%;
height: auto;
display: grid;
align-items: center;
justify-items: center;
}
.float-left {
@ -676,68 +443,6 @@ figcaption .mono {
max-width: 100%;
}
.pagination {
display: flex;
justify-content: center;
gap: 0.5em;
padding-left: 0;
}
.pagination li {
list-style-type: none;
color: var(--nav-button-text);
}
.pagination li a {
color: var(--page-button-text);
background-color: var(--page-button-background);
border-radius: 0.05rem;
border-style: outset;
border-width: 0.2rem;
border-color: var(--page-button-background);
width: 2rem;
max-width: 1.8vw;
aspect-ratio: 1 / 1;
display: flex;
justify-content: center;
align-items: center;
margin: 0.2rem;
text-decoration: none;
padding: 0 0.2rem;
font-family: var(--font-family-system-ui);
}
.pagination li a:hover {
background-color: var(--page-button-background-hover);
}
.pagination li.active a {
background-color: var(--page-button-background-active);
}
.pagination li.disabled a {
cursor: not-allowed;
background-color: var(--page-button-background-disabled);
color: var(--page-button-text-disabled);
border-style: solid;
}
.mono {
font-family: var(--font-family-monospace);
font-weight: 600;
}
.bolder {
font-weight: bolder;
background-color: rgba(0, 0, 0, 0.33);
border-radius: 0.25em;
}
/* Specific elements */
#content {
flex: 1 0 max-content;
}
/*
Desktop screen size adjustments
*/
@ -775,15 +480,6 @@ figcaption .mono {
flex-direction: row;
}
.person-profile {
position: sticky;
top: 0;
width: 300px;
min-width: 20vw;
max-width: 30vw;
margin-bottom: 5vh;
}
/*
Helper classes
*/
@ -805,19 +501,20 @@ figcaption .mono {
margin-right: 1rem;
}
.card-thumbnail {
.card-header {
width: 20vw;
flex-shrink: 0;
}
.card-thumbnail:not(
:has(~ .card-content > .card-header > .card-title > .dt-published)
) {
width: 10vw;
.card-body {
margin-left: 1rem;
}
.card-content {
margin-left: 1rem;
.bolder {
font-weight: bolder;
background-color: rgba(0, 0, 0, 0.33);
border-radius: 0.25em;
padding: 0.25em 0.75em 0.5em 0.33em;
}
/*
@ -837,3 +534,79 @@ figcaption .mono {
clear: both;
}
} /* end @media */
@media (prefers-reduced-motion: no-preference) {
@supports (animation-timeline: scroll()) and (animation-range: 0 50vh) {
@keyframes sticky-header {
from {
height: 50vh;
top: 6rem;
}
to {
height: 10vh;
top: -1rem;
}
}
@keyframes blurry-header {
from {
filter: blur(0);
}
to {
filter: blur(2px);
}
}
@keyframes transparent-text-bg {
from {
background-color: var(--motto-background);
}
to {
background-color: rgba(0, 0, 0, 0);
}
}
main,
footer {
position: relative;
top: 55vh;
}
.motto {
position: fixed;
top: 12rem;
animation: sticky-header linear forwards;
animation-timeline: scroll();
animation-range: 0 50vh;
}
.motto::before {
filter: blur(12px);
top: 2rem;
animation: blurry-header linear forwards;
animation-timeline: scroll();
animation-range: 0 50vh;
}
.motto-inside h1 {
animation: transparent-text-bg linear forwards;
animation-timeline: scroll();
animation-range: 0 40vh;
}
@media (min-width: 768px) {
.motto {
width: calc(100% - 8rem);
}
.motto::before {
top: 0;
}
}
} /* end @supports */
} /* end @media */

View file

@ -1,68 +0,0 @@
@media (prefers-reduced-motion: no-preference) {
@supports (animation-timeline: scroll()) and (animation-range: 0 50vh) {
@keyframes sticky-header {
from {
flex-basis: 30vh;
}
to {
flex-basis: 0;
}
}
.motto-wrapper {
position: sticky;
top: 0;
z-index: 100;
animation: sticky-header linear forwards;
animation-timeline: scroll();
animation-range: 0 30vh;
contain: content;
}
@keyframes blurry-header {
from {
filter: blur(0);
}
to {
filter: blur(3.5px);
}
}
.motto::before {
animation: blurry-header linear forwards;
animation-timeline: scroll();
animation-range: 0 30vh;
}
@keyframes transparent-text-bg {
from {
background-color: var(--motto-background);
text-shadow: 0 0 10px rgba(0, 0, 0, 0.33);
}
to {
background-color: rgba(0, 0, 0, 0);
text-shadow: 0 0 10px rgba(0, 0, 0, 1);
}
}
.motto-inside h1 {
animation: transparent-text-bg linear forwards;
animation-timeline: scroll();
animation-range: 0 30vh;
}
.motto-inside h1 small {
display: block;
font-size: calc(1vh + 1vw);
line-height: calc(1vh + 1vw);
}
main section {
margin: 0 0.25em;
contain: content;
}
} /* end @supports */
} /* end @media */

View file

@ -1,9 +1,7 @@
baseURL = "https://millironx.com"
languageCode = "en-us"
title = "Milliron X"
[pagination]
pagerSize = 5
title = "MillironX"
paginate = 5
[build]
writeStats = true
@ -11,47 +9,8 @@ writeStats = true
[Params]
cardImage = "saddles"
motto = ""
images = ["saddles.jpg"]
categories = []
[taxonomies]
people = "people"
tag = "tags"
category = "categories"
[mediaTypes]
[mediaTypes."application/atom+xml"]
suffixes = ["xml"]
[outputs]
home = ["atom", "html", "manifest"]
page = ["html"]
section = ["html", "atom"]
term = ["html", "atom"]
[outputFormats]
[outputFormats.atom]
mediaType = "application/atom+xml"
baseName = "feed"
[outputFormats.manifest]
name = "manifest"
baseName = "manifest"
mediaType = "application/json"
notAlternative = "true"
[markup]
[markup.goldmark]
[markup.goldmark.parser]
[markup.goldmark.parser.attribute]
block = true
[markup.goldmark.renderHooks]
[markup.goldmark.renderHooks.link]
enableDefault = true

View file

@ -1,11 +1,12 @@
---
title: Home
cardImage: charolette
cardImageDescription: She almost looks like she's in her native country again.
motto: <small>My name is Thomas Christensen</small><br />I am Milliron X
description: The homepage of Thomas A. Christensen II
layout: _default/list
menu:
main:
name: Home
params:
icon: home
weight: -1000
@ -28,3 +29,58 @@ to a sense of withholding, prestige, and power.
Together, these two symbols represent the qualities I strive for in each of my
works: authenticity, originality, power, depth, and prestige.
## Who am I?
{{< imgproc me-and-lady Resize "768x" "float-right" >}} Image courtesy
[Guy McCutcheon Photography](https://www.guymccutcheon.com/) {{< /imgproc >}}
I am
- 🧬 A bioinformatician (by profession)
- 📐 An engineer (by education)
- 🐂 A rancher (by lifestyle)
- 🖥️ A techie (self-taught)
- 🎥 And a filmmaker (at heart)
I've got a soft spot for Brown Swiss dairy cows (just in case you couldn't tell
by the pictures), and am sometimes called "one of those crazy, Wyoming dairy cow
people." I love anything to do with cattle or technology, but especially
anything to do with both of them.
_{{< abbr "Born again, fundamentalist, dispensationalist, King James Bible-believing, independent Baptist" >}}Christian{{< /abbr >}},
American, Convervative, Pro-gun, Heterosexual - any questions?_
## Where am I?
{{< imgproc wy-in-ks Resize "768x" "float-left" / >}}
I am a Wyomingite sojurning in Kansas. That ought to lead to some interesting
stories.
Around the web you can find me at (in order of subjective importance)
- {{< fa github >}} GitHub: [@MillironX](https://github.com/MillironX)
- {{< fa orcid >}} ORDiD:
[0000-0003-1219-9320](https://orcid.org/0000-0003-1219-9320)
- {{< fa gitlab >}} GitLab: [@MillironX](https://gitlab.com/MillironX)
- {{< fa vimeo >}} Vimeo:
[Thomas Christensen II](https://vimeo.com/tchristensenii)
- {{< fa stack-overflow >}} StackExchange:
[Milliron X](https://stackexchange.com/users/4863541/milliron-x)
- {{< fa steam >}} Steam: [MillironX](https://steamcommunity.com/id/millironx)
This list is intended to verify my identity on other sites. Please do _not_ use
it as fodder to try and "follow" me on each of these platforms. I stand with
RMS:
{{< blockquote "Richard Stallman _in_ [If you feel your organization needs a 'presence' in Facebook](https://stallman.org/facebook-presence.html)" >}}
Facebook is a bad place for a person to be. When people find us on Facebook, we
lead them away from Facebook and then talk with them elsewhere.
{{< /blockquote >}}
I typically don't respond to inquiries made on these platforms. Please use
[my contact form](/contact), instead.
</div>
</div>

View file

@ -14,15 +14,13 @@ menu:
fa-thumbnail: university
---
> I have spent too long in school and not enough time in the middle of nowhere
>
> -- Baxter Black, DVM
During my time in academia, I have amassed a few notable accomplishments. Of
course, as the old saying goes, "if it isn't published, then it never happened,"
so here is a list of everything that actually happened.
Academia is not the be-all and end-all of life (contrary to what your professor
might have told you). I've found the side-effects to be similar to this guy's:
<!-- prettier-ignore-start -->
> I have spent too long in school and not enough time in the middle of nowhere,
> and it has inhibited my ability to learn the simple things.
{author="Baxter Black, DVM"}
<!-- prettier-ignore-end -->
so here is a list of everything that actually happened. Several of these
articles are also available on
[my Google Scholar page](https://scholar.google.com/citations?user=gbP4RDgAAAAJ),
but this is the complete list.

View file

@ -1,42 +0,0 @@
---
title: "Genetic analysis of bovine papillomas"
date: 2024-09-19
categories:
- poster
people:
- Thomas A. Christensen II
- Rachel Palinski
- Bob Gentry
journal:
"National Association of Animal Breeders Technical Conference Student Poster
session"
location: "Middleton, Wisconsin"
---
Bovine papillomavirus (BPV) is a major cause of reproductive failure in cattle.
In bulls, penile papillomas caused by BPV may cause reluctance to breed, and is
always a cause to fail an animal on a breeding soundness exam. Historically, it
has been thought that BPV was transmitted via direct contact and could be
controlled by managing clinically presenting animals in the herd, but more
recent evidence suggests alternative modes of transmission. BPV has been found
repeatably in clinically healthy animals, and in non-cutaneous secretions
including milk, blood, urine and semen. Currently, no commercially available BPV
vaccine uses isolated viral particles and naturally occurring virus does not
produce cross-protective immunity. In order to develop a proper vaccine for
penile papillomas further studies are required to understand the epidemiology of
BPV in herds. While vulvar, cutaneous, and mammary papillomas have been
genotyped in recent years, this information is not available for penile
papillomas. In this study there were 31 submissions, collected from 7 states,
NE, KS, NY, TX, AL, MO and SD (14 different cattle operations) Samples were
collected between August of 2022 and April 2024. Twenty-two submissions were
penile papillomas and with pooling of samples represented over 50 penile
papillomas. Samples were metagenomically sequenced at the Kansas State
Veterinary Diagnostic Lab, and the genotype of each sample was determined using
the phylogenetic analysis. The clade of each sample was determined by aligning
consensus sequences of the L1 gene (used for both for phylogeny and as a vaccine
target) using MAFFT and a maximum-likelihood phylogeny generated in Mega X.
Analysis found that all penile papilloma submissions were composed of BPV type
2, with one sample showing co-infection with BPV type 1. Conversely, cutaneous
and teat papillomas had BPV genotypes that were more variable with genotypes of
1,2,7,12,14,29 and 40. These results indicate that BPV type 2 and type 1 provide
a unified target for bovine penile papilloma vaccine development.

View file

@ -1,14 +0,0 @@
---
title:
"Got Warts? Bovine Papillomavirus Pathogenesis, Transmission, and Vaccination"
date: 2024-09-19
featured: false
categories:
- presentation
people:
- Bob Gentry
- Thomas A. Christensen II
journal:
"National Association of Animal Breeders Technical Conference Sponsor session"
location: "Middleton, Wisconsin"
---

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@ -1,7 +1,6 @@
---
title:
"nf-core/taxprofiler: highly parallelised and flexible pipeline for
metagenomic taxonomic classification and profiling"
"nf-core/taxprofiler: highly parallelised and flexible pipeline for metagenomic taxonomic classification and profiling"
date: 2023-10-23
featured: true
tags:
@ -17,25 +16,9 @@ people:
- Maxime Borry
- Mahwash Jamy
- nf-core community
- James A. Fellows Yates
- James A. Fellows Yate
link: https://doi.org/10.1101/2023.10.20.563221
journal: bioRxiv
---
Metagenomic classification tackles the problem of characterising the taxonomic
source of all DNA sequencing reads in a sample. A common approach to address the
differences and biases between the many different taxonomic classification tools
is to run metagenomic data through multiple classification tools and databases.
This, however, is a very time-consuming task when performed manually -
particularly when combined with the appropriate preprocessing of sequencing
reads before the classification. Here we present nf-core/taxprofiler, a highly
parallelised read-processing and taxonomic classification pipeline. It is
designed for the automated and simultaneous classification and/or profiling of
both short- and long-read metagenomic sequencing libraries against a 11
taxonomic classifiers and profilers as well as databases within a single
pipeline run. Implemented in Nextflow and as part of the nf-core initiative, the
pipeline benefits from high levels of scalability and portability, accommodating
from small to extremely large projects on a wide range of computing
infrastructure. It has been developed following best-practise software
development practises and community support to ensure longevity and adaptability
of the pipeline, to help keep it up to date with the field of metagenomics.
Metagenomic classification tackles the problem of characterising the taxonomic source of all DNA sequencing reads in a sample. A common approach to address the differences and biases between the many different taxonomic classification tools is to run metagenomic data through multiple classification tools and databases. This, however, is a very time-consuming task when performed manually - particularly when combined with the appropriate preprocessing of sequencing reads before the classification. Here we present nf-core/taxprofiler, a highly parallelised read-processing and taxonomic classification pipeline. It is designed for the automated and simultaneous classification and/or profiling of both short- and long-read metagenomic sequencing libraries against a 11 taxonomic classifiers and profilers as well as databases within a single pipeline run. Implemented in Nextflow and as part of the nf-core initiative, the pipeline benefits from high levels of scalability and portability, accommodating from small to extremely large projects on a wide range of computing infrastructure. It has been developed following best-practise software development practises and community support to ensure longevity and adaptability of the pipeline, to help keep it up to date with the field of metagenomics.

View file

@ -1,54 +0,0 @@
---
title: "YAVSAP: versatile viral quasispecies analysis for veterinary samples"
date: 2024-03-05
featured: false
categories:
- presentation
people:
- Thomas A. Christensen II
- Steven Stancic
- Andrea Lu
- Dana Mitzel
- William Wilson
- Rachel Palinski
journal: "Phi Zeta Research Day"
location: "Manhattan, Kansas"
tags:
- virus
- quasispecies
- next-generation sequencing
- pipeline
awards:
- "2nd Place Large Animal Applied Research Presentation"
link: "/academia/yavsap/yavsap.pdf"
---
Viral populations within an infected host are composed of viral particles with a
spectrum of genetic mutations rather than a unified genome. This phenomenon is
referred to as viral "quasispecies," and has been useful for the understanding
of viral transmission and early detection of new viral variants. Next generation
sequencing (NGS) has enabled the study of these quasispecies for many viral
species, notably Influenza A and B, Human Immunodeficiency Virus (HIV), Foot and
Mouth Disease Virus (FMDV), and Severe Acute Respiratory Syndrome Coronavirus 2
(SARS CoV2), and established protocols and computer analysis tools have been
developed for these species. Some of the most important viruses, such as
emerging and exotic disease agents, however, do not have replicatable protocols
or software tools capable of producing valid output from their sequence data.
Here, we present Yet Another Viral Subspecies Analysis Pipeline (YAVSAP). YAVSAP
is a fully automated bioinformatic pipeline built from the ground up to identify
and analyze viral quasispecies of any arbitrary virus in human and veterinary
samples. YAVSAP provides reference-based genome mapping of both long- and
short-read sequencing reads to any reference genome that the user chooses,
identifies subconsensus variants and haplotypes, and assesses the phylogenies of
all viral sequences found within a sample. YAVSAP is written in Nextflow and
conforms to the nf-core initiative's standards, which allows it to run on
low-end computers, high performance computing (HPC) clusters, or anything in
between with zero configuration. YAVSAP has been tested on viruses of interest
to veterinary medicine and public health, including Japanese Encephalitis Virus
(JEV), Influenza D Virus (IDV), Bovine Coronavirus (BCoV), SARS CoV2, and Rift
Valley Fever Virus (RVFV), and can correctly identify consensus genomes and
quasispecies within samples containing each of these viruses. This tool provides
a means for biologists with little bioinformatic experience to analyze deep
sequence data while correcting for many of the pitfalls associated with previous
and current analysis platforms. YAVSAP is open source software and is publicly
available at https://github.com/ksumngs/yavsap.

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---
title: "Blogroll"
menu:
main:
name: Blogroll
params:
icon: scroll
weight: -800
cardImage: eclipse
cardImageDescription: |
Randall Monroe was right. Eclipses are way cooler than they sound.
suppressRss: true
draft: true
---
## Stuff I like on the internet
@ -17,4 +7,39 @@ suppressRss: true
This section of a website used to be called a "blogroll." I don't know what it's
called now. In order to be on this list, I must have been subscribed or
otherwise follow it for over a year. It's amazing how little stuff on the
internet can make that cut.
internet can't make that cut.
### [Thru the Bible](https://ttb.org/)
I'm convinced that the word of God is timeless, and we need less commentary and
cherry-picking of favorite verses, and more study of the complete Bible. Dr.
McGee does just that.
### [Enoch the Cow Vet](https://youtube.com/channel/UC6PPmHUbcdOSzX5tLB3uXdw)
A veterinarian/agricultural channel that doesn't make me cringe. "God built
these things for cows for vets ... [there are] so many aspects of the cow that
are just designed for vets." Amen, Enoch. Amen.
### [Proglogion](https://blog.drwile.com/)
The blog of my high school science teacher (of sorts). It is refreshing to find
a creationist who can still think critically. I love his "bad sermon
illustrations" posts.
### [The Milk Check](https://www.jacoby.com/learning-center/podcasts-overview/)
A pragmatic inside look at dairy marketing. I only understand half of what
they're talking about, but I learn something new every episode.
### [Brian Harry's Blog](https://devblogs.microsoft.com/bharry/)
Where else are you going to find a blog about cows _and_ version control? The
blog is basically dead now, but it's still fun to go back and read the farm
stories.
### [Car Talk](https://cartalk.com/)
The antics of these guys are enough to make anyone have to pull over to the side
of the road from laughing too much. I dread the day when NPR fully axes the only
good program to cross their airwaves.

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@ -1,8 +0,0 @@
---
title: Brian Harry's blog
link: https://devblogs.microsoft.com/bharry/
---
Where else are you going to find a blog about cows _and_ version control? The
blog is basically dead now, but it's still fun to go back and read the farm
stories.

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---
title: Car Talk
link: https://cartalk.com
---
The antics of these guys are enough to make anyone have to pull over to the side
of the road from laughing too much. I dread the day when NPR fully axes the only
good program to cross their airwaves.

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@ -1,8 +0,0 @@
---
title: Enoch the Cow Vet
link: https://youtube.com/channel/UC6PPmHUbcdOSzX5tLB3uXdw
---
A veterinarian/agricultural channel that doesn't make me cringe. "God built
these things for cows for vets ... [there are] so many aspects of the cow that
are just designed for vets." Amen, Enoch. Amen.

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---
title: Proslogion
link: https://blog.drwile.com
---
The blog of my high school science teacher (of sorts). It is refreshing to find
a creationist who can still think critically. I love his "bad sermon
illustrations" posts.

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@ -1,8 +0,0 @@
---
title: Thru the Bible
link: https://ttb.org
---
I'm convinced that the word of God is timeless, and we need less commentary and
cherry-picking of favorite verses, and more study of the complete Bible. Dr.
McGee does just that.

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@ -1,75 +0,0 @@
{{ $data := dict }}
{{ $url := "https://code.millironx.com/api/v1/users/millironx/repos" }}
{{ with try (resources.GetRemote $url) }}
{{ with .Err }}
{{ errorf "Unable to get remote resource %s: %s" $url . }}
{{ else with .Value }}
{{ $data = . | transform.Unmarshal }}
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{{ else }}
{{ errorf "Unable to get remote resource %s" $url }}
{{ end }}
{{ range $data }}
{{/* Get tags of this repository. To quote Steve Edstrom, "If it doesn't have a
tag, it doesn't count."
*/}}
{{ $tagUrl := print "https://code.millironx.com/api/v1/repos/millironx/" .name "/tags" }}
{{ $tagData := dict }}
{{ with try (resources.GetRemote $tagUrl) }}
{{ with .Err }}
{{ errorf "Unable to get remote resource %s: %s" $tagUrl . }}
{{ else with .Value }}
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{{ else }}
{{ errorf "Unable to get remote resource %s" $tagUrl }}
{{ end }}
{{ $firstTag := index $tagData 0 }}
{{ if $firstTag }}
{{ $dates := dict "date" (time.AsTime $firstTag.commit.created) }}
{{ $content := dict "mediaType" "text/markdown" "value" .description }}
{{ $categories := slice "code" }}
{{ $people := slice "Thomas A. Christensen II" }}
{{ $link := .html_url }}
{{ $featured := (gt .stars_count 0) }}
{{ $tags := .topics }}
{{ $params := dict
"categories" $categories
"people" $people
"link" $link
"featured" $featured
"tags" $tags
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"content" $content
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"title" .name
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{{ $.AddPage $page }}
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{{ with .Err }}
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{{ else }}
{{ $content := dict "mediaType" .MediaType.Type "value" .Content }}
{{ $resource := dict
"content" $content
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{{ $.AddResource $resource }}
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{{ else }}
{{ errorf "Unable to get remote resource %s" $url }}
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{{ end }}
{{ end }}
{{ end }}

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@ -1,14 +0,0 @@
---
title: Coding projects
menu:
main:
name: Code
params:
icon: code
link: https://code.millironx.com
weight: 50
fa-thumbnail: code
link: https://code.millironx.com
---
A Forgejo instance dedicated to cows and technology

View file

@ -15,21 +15,12 @@ menu:
weight: 1
fa-thumbnail: file-signature
validation: true
suppressRss: true
---
<script src="https://js.hcaptcha.com/1/api.js" async defer></script>
<form action="https://usebasin.com/f/787df7bfd22e" method="post">
<fieldset>
<legend>Contact Me</legend>
<input
type="hidden"
class="form-control"
id="honorific"
name="honorific"
placeholder="Dr."
/>
<input type="hidden" name="_gotcha" />
<label for="name">Name</label>
<input
type="text"
@ -74,13 +65,6 @@ suppressRss: true
required
style="min-height: 72pt;"
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<span>Submit</span>

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link: https://youtu.be/dQw4w9WgXcQ
weight: 99
fa-thumbnail: right-to-bracket
link: https://youtu.be/dQw4w9WgXcQ
---
The password is "Open sesame!"

BIN
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---
title: "Thomas A. Christensen II"
menu:
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name: About
params:
icon: circle-info
me: true
weight: -900
homepage: https://millironx.com
accounts:
google-scholar: gbP4RDgAAAAJ
github: MillironX
hacker-news: millironx
matrix: "@millironx:matrix.org"
orcid: 0000-0003-1219-9320
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bitcoin: bc1q66u7fqmptr4sczfmvxxfckzl6566633umx40n7
lightning: "millironx@coinos.io"
ethereum: 0x97610b550a5eB6eB2c4a57d3D2b317816c413Fb4
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---
Hi! I'm Thomas. I love anything to do with cattle or technology, but especially
anything to do with both of them. I spend way more time in beef country with
beef cows, but I've got a soft spot for Brown Swiss dairy cows (just in case you
couldn't tell by the pictures). I've worn a lot of different hats:
| | |
| ------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
| First and foremost | ✝️ {{< abbr "Born again, fundamentalist, dispensationalist, King James Bible-believing, independent Baptist" >}}Christian{{< /abbr >}} |
| Location | 🦬 {{< abbr "I want to keep claiming Wyoming, but they're pretty strict about residency there, and I don't want to repeat the Liz Cheney fishing license incident" >}}Wyomingite{{< /abbr >}} sojourning in 🌻 {{< abbr "Yes, Toto, we are in Kansas now" >}}Kansas{{< /abbr >}} (this ought to be interesting) |
| Education | 📐 {{< abbr "noun. A person who cannot build cool things like airplanes or bridges, but can blow up an entire neighborhood and kill dozens of children by misplacing a decimal point. See also: self-hating chemist" >}}Chemical Engineer{{< /abbr >}} |
| Profession | 🧬 {{< abbr "I do genetics and computers" >}}Bioinformatician{{< /abbr >}} and 🐄🩺 {{< abbr "I can't rope well enough to be a cowboy, so being a cow doctor will have to suffice" >}}Veterinarian{{< /abbr >}} (soon!) |
| Politics | 🗽 {{< abbr "Refers to the belief in natural social and political laws created by God that are as inflexible as the laws of physics" >}}Juris naturalist{{< /abbr >}} |
| Hobbies | 🎥 {{< abbr "Storytelling at 24 frames per second" >}}Filmmaker{{< /abbr >}} and 💃🏻 {{< abbr "Square dancing is more musically rigid and is standardized across the country. Swing dancing is more freeform and differs regionally. It's like the difference between classical music and jazz. I like both." >}}Square/swing dancer{{< /abbr >}} |

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---
title: "ChemE Cows"
cardImage: stable-diffusion-cheme-cow-08
cardImageDescription: |
black and white dairy cow wearing a bright yellow hard hat at an oil refinery on a clear sunny day
Fooocus v2.5.5 realisticStockPhoto_v20.safetensors
Hopefully someday I can replace this with a real image
motto:
ChemE Cows<br /><small>A blog about cattle, technology, or anything remotely
affecting either of them</small>
menu:
main:
name: Blog
params:
icon: block-quote
weight: 2
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---
A blog where I might post stuff some day.

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@ -1,104 +0,0 @@
---
title:
"On Baptist habits (or why Baptist churches feel like they're run by the
Mafia)"
date: 2024-03-01
people:
- Thomas A. Christensen II
draft: true
tags:
- religion
- baptist
- christianity
- love
- doctrine
featured: true
categories:
- blog
---
<!--
This is not a real blog post - this is just an idea for a provocative article
that I fed into Llama3.2 to generate some text that is slightly more
interesting than lorem ipsum. Gee howdy, is this writing crap, but I have
committed it to the repository so I can rebase around it. If you are here
reading this somehow, please understand that these are not my thoughts.
-->
In the grand tapestry of American religiosity, there exists a peculiar breed of
Christian denomination that stands out for its unique blend of fervent devotion
and...let's be honest, a hint of authoritarianism. I'm, of course, referring to
Baptist churches. Yes, those churches that make you wonder if they're being run
by the Mafia.
Now, before I proceed, let me just clarify that this isn't an attempt to
disparage the good people who worship in these esteemed institutions. No, no,
nothing like that. It's merely a case of observational reporting, where I'm
poking around the fringes of Baptist culture to get a better understanding of
what makes them tick.
As someone who's spent considerable time within the fold (hello, 20+ years of
being born again), I've come to realize that there are certain habits,
practices, and attitudes that seem endemic to Baptist churches. Now, keep in
mind that this isn't a generalization, but rather an observation born out of
personal experience.
One of these habits is an extraordinary level of fervor and zealotry. Baptists
tend to be deeply invested in their faith, often to the point where it borders
on fanaticism. I've seen folks who will passionately argue for or against just
about anything that's perceived as contrary to their interpretation of
scripture. Now, while this can be a laudable trait in moderation, excessive
fervor can quickly turn toxic.
Another peculiar habit of Baptist churches is an unsettling preoccupation with
hierarchy and authority. It's not uncommon to see senior pastors wielding near
absolute power within the church, often based on factors such as age,
experience, or heaven forbid personal popularity. This can lead to a culture
where dissenting voices are stifled, and nonconformity is discouraged.
The worship services themselves often feel more like formal lectures or
performances than genuinely communal gatherings. Don't get me wrong; I love a
good hymn or sermon as much as the next person, but sometimes it feels like
you're trapped in a 90-minute lecture on theology. And if you're sitting too far
forward, forget about trying to contribute to the conversation your
participation will be met with stern disapproval.
In addition, there's an omnipresent air of suspicion and mistrust that seems to
pervade every aspect of Baptist life. If someone doesn't toe the party line,
they're often met with swift reprimand or outright ostracism. This creates a
toxic environment where people feel pressured into conformity rather than being
encouraged to explore their own spirituality.
Of course, there are always exceptions to the rule, just like in any other human
endeavor. I've encountered Baptist churches that embody the very opposite of
these described habits places where worship is genuine, inclusive, and
welcoming, where individual freedom and creativity are cherished, and where the
emphasis is on community rather than control.
So what drives this peculiar breed of authoritarianism within some Baptist
churches? Is it a genuine misunderstanding of scripture, or perhaps a result of
historical context? Or is there something deeper at play perhaps an inherent
tension between the democratic values of American society and the hierarchical
structures of traditional Christianity?
These questions are central to my exploration of this topic. I'll delve into the
complexities of Baptist history, the role of patriarchal ideology, and the ways
in which cultural and social factors have shaped the institution over time.
In conclusion, while I'm not ready to declare war on all things Baptist just yet
(although, I must admit, it's tempting), I do hope that this exploration will
shed some light on a fascinating aspect of American religiosity. Perhaps,
through a better understanding of these peculiar habits and practices, we can
foster a more inclusive and compassionate community one where faith and
conviction are tempered by empathy and respect for differing viewpoints.
Ultimately, as someone who's found their own spiritual home within the Baptist
fold, I believe it's essential to approach this conversation with sensitivity,
curiosity, and an open mind. By embracing our shared humanity rather than
perpetuating artificial divisions, we can work towards creating a more vibrant
tapestry of faith in America one that celebrates diversity while remaining
committed to core principles of love and service.
But for now, I'll leave you with these final thoughts on Baptist habits habits
that may seem baffling or even disturbing at times, but are ultimately part of
what makes the Baptist experience so richly textured.

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