Kelly Sovacool

@kelly

Bioinformatics Software Engineer. PhD from Schloss Lab at UMich. 🏃🏻‍♀️🚴🏻‍♀️🧗🏻‍♀️ #python #rstats #nextflow #snakemake she/her My views are my own.

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Kelly Sovacool@kelly· 10d

First-year butterfly milkweed in bloom — the first to bloom in my new native garden! Featuring a monarch caterpillar munching away.

A photo of butterfly weed (asclepias tuberosa), just starting to bloom. This plant was started from seed 8 months ago. A monarch caterpillar can be seen near the flower buds.

Kelly Sovacool@kelly· Jul 13

I'm presenting poster C-049 at #ISMB2026 #BOSC2026 on Wednesday: "Anatomy of a modular toolchain for reproducible bioinformatics workflows" (Poster C-049). Please reach out if you're here and would like to meet up, and stop by my poster if you want to talk about reproducible software!

The anatomy of our modular toolchain for reproducible bioinformatics workflows. The central component is a Bioinformatics Workflow or Pipeline repository. Lines extend out of the Workflow to the other components: a Python package containing helper functions for a custom CLI, reusable Nextflow modules and sub workflows, Docker recipes, Documentation website, and Continuous integration. Each of these components contribute to scalability, reusability, and reproducibility of bioinformatics pipelines.

Kelly Sovacool@kelly· Jul 11

We‘re doing it! A few days ago I bought a 20” planter, acquired free bricks/rocks, and just today I added a couple of pond plants! Need to get some logs for more wild looking ramps into and out of the pond.

A large planter that has been repurposed into a mini wildlife pond. There are bricks and rocks stacked to create shallow areas of the pond for wildlife to enjoy, as well as a ramp into and out of the water. A small solar powered fountain provides gentle movement to keep mosquito larvae at bay. The newest additions are two aquatic plants: pickerel weed and common duckweed.

Kelly Sovacool@kelly· Jan 9

From last June: an opossum friend found their way to our pile!

Photo of an opossum peaking it's head through the leaves of a compost bin.

Kelly Sovacool@kelly· Sep 18

it's been one of those days...

A screenshot of a git commit that says "ci(docker): throw spaghetti at the wall". Sometimes, the only thing you can do to make a docker recipe build successfully is throw spaghetti at the wall and see what sticks.

Kelly Sovacool@kelly· Mar 21

Haha thanks for the support ✨ There are services where you can build a webpage with a layout that mirrors your Instagram posts, so you can have different specific links for each post. Eg NYT uses this to link to posts about their stories. I wanna do something similar but more DIY!

The New York Times instagram page. They have a link in their bio to nytimes.com/instagram

A screenshot of nytimes.com/instagram. All of the images in this grid correspond to NYT Instagram posts, and clicking one will take you to the NYT article that the post is about.

Kelly Sovacool@kelly· Mar 19

Everything else is spiraling right now so we have to revel in the small joys. The microbes are waking up from their winter slumber!

A thermometer inserted into a compost bin. The compost temperature is 88 F, a new high for this year as winter draws to close in Michigan.

Kelly Sovacool@kelly· Mar 3

quick example

# pip install qrcode pillow
import qrcode
from qrcode.image.styledpil import StyledPilImage
from qrcode.image.styles.colormasks import SolidFillColorMask
qr = qrcode.QRCode(error_correction=qrcode.constants.ERROR_CORRECT_H)
qr.add_data('https://neighborhoodscientist.org/')
img = qr.make_image(image_factor=StyledPilImage,
color_mask=SolidFillColorMask(),
fill_color="#197278")
img.save("qrcode.png")

Kelly Sovacool@kelly· Jan 31

one of many many reasons to use testthat: positive & encouraging messages! (testthat.r-lib.org) #rstats #testthat

A screenshot of the RStudio console showing results from testthat, an R package for unit testing. After running tests, testthat printed a motivational message: "Your tests are magnificent!"

Kelly Sovacool@kelly· Jan 13

FWIW this is in their FAQ:

screenshot of the frequently asked questions section from https://freeourfeeds.com/

Kelly Sovacool@kelly· Dec 4

Spouse found the spreadsheet in our shared Google Drive account 🤓

A chain of text messages:
“Are you really taking measurements”
“On the compost temp pile?”
“LMAO”

Kelly Sovacool@kelly· Dec 4

Kelly Sovacool@kelly· Nov 25

Recently started a compost bin and I’m wayyyy too excited that the compost is warmer than the ambient air temperature for the first time. It’s 48 F outside and the pile is now ~73 F 🥳 Go microbes go!

A thermometer inserted into a compost bin. The compost temperature is 73 F while the ambient air temp is 48 F.

Kelly Sovacool@kelly· Nov 20

There are only 10 hard problems in computer science...

$A screenshot of an introductory Python coding tutorial from https://www.schlosslab.org/just-enough-python/. A chunk of Python code demonstrates creating a dictionary with 3 key-value pairs and how to iterate over the keys and values in the dictionary. The printed output shows: "There are only 10 hard problems in computer science: 1 naming things, 2 understanding binary, 3 off-by-one errors". The code is below: problems = {1: "naming things", 2: "understanding binary", 3: "off-by-one errors"} print('There are only 10 hard problems in computer science:') for num in problems: print(f"\t {num} {problems[num]}")$

Kelly Sovacool@kelly· Dec 19

holiday brain: my git commit messages aren't making a whole lotta sense... but at least they pass the conventional commits hook 🤷🏻‍♀️

A screenshot of a commit message on GitHub. The message reads "fix(cli): only prevent citation is flag set". The message format adheres to "conventional commits" guidelines, but doesn't make any sense.

Kelly Sovacool@kelly· Nov 8

when you have the esteemed privilege of deleting files that were accidentally committed by the maintainer 🫡 #git #software