David Eccles 🌻🇵🇸7x🩹🛡️
LightNews LightNews
banner
gringene.org
David Eccles 🌻🇵🇸7x🩹🛡️
@gringene.org
1.5K followers 1.3K following 3.6K posts
Neurodivergent freelance bioinformatician, cuddler of data, and theoretical geneticist, with a love for Free Software and the hacking thereof. Rangitāne o Wairau. He/they.

https://ko-fi.com/gringer

Website: https://www.gringene.org
Posts Replies Media Videos
gringene.org
"THEN They FIGHT YOU..." written in the font and colouring of the "ZOHRAN FOR NEW YORK" logo; golden text on a blue background, with red shadow on the first word.
November 10, 2025 at 5:31 AM
gringene.org
Here's my attempt:

It's not exactly the same "FOR" font, but then again the previous version didn't have the same "ZOHRAN" font. I'm happy to change it, if someone can find a closer match.

www.gringene.org/for.html
GRINGENE Does BIOINFORMATICS in Mamdani's political sign font and colors
November 9, 2025 at 6:30 AM
gringene.org
Silver DNA on a pale grey background, showing individual bases as extruded hexagons/pentagons, with stalks to connect them to the tubular backbone.
November 7, 2025 at 8:45 PM
gringene.org
Here's an alternative DNA image, which includes a major / minor groove.
Coloured DNA (using Blender's toon shader) on a white background, with A = green, C=blue, G=gold, T=salmon, and a red backbone. The DNA is oriented vertically.
November 7, 2025 at 8:19 PM
gringene.org
Here's a closer attempt, with bubbles and a thinner DNA backbone.
Three DNA double helices represented as rough metal oriented at around 30° with a positive gradient. One double helix spanning from the bottom left to the top right diagonal is medium sized and in clear focus; the two other double helices in the top left and bottom right region of the image are blurry and out-of-focus, with the top left one further away and the bottom right one being closer. The surrounding area is filled with bubbles.
November 7, 2025 at 7:48 PM
gringene.org
So trying to be as favourable as possible to Vega with the numbers, and normalising for system count, I'm getting about 12.9% of sequencing runs carried out on Vega.

It seems like those numbers support a statement that PacBio sequencing is typically done on non-Vega systems.
Q3 2025 summary from PacBio, showing $21.3M Consumable Revenue, with stated $236,000 annualised Revio pull-through, and 310 total Revio shipments. Assuming an exact quarterly equivalent, that ends up as $18.29M for Revio, and $3.01M for non-Revio systems. Assuming advertised run costs of $995 for Revio and $1100 for Vega, and *all* those non-Revio systems were Vega, that ends up with 18,380 Revio runs and 2,736 Vega runs (12.9% total runs).
November 6, 2025 at 8:29 PM
gringene.org
I had a couple of months of anger, but I've mostly put that behind me now. I wrote some lyrics to the tune of "my kink is karma", which helped me a lot.
Screenshot of a portion of lyrics from "My code is karma": It's hard, it's hard People say I'm jealous, but my code was stopping You ruin your life You losing your mind You failing software People say I'm jealous, but my code was stopping You breaking your script You crashing your bot You living nightmares People say I'm jealous, but my code is karma
November 6, 2025 at 1:22 PM
gringene.org
Have you looked at the DNA sequence itself to see if there's any correlation between DNA similarity and contact distance?
Figure 5G from the paper, showing the Trp53 region in WT. There are three regions of similarity forming a matrix / cross repeat pattern. REPAVER plot (dotplot mode, k=10bp), showing DNA sequence identity for sequences of at least 10bp in length in the the region corresponding to the Trp53 gene. There are a few repetitive block shapes, which seem vaguely similar to the contact pattern from the paper.
November 6, 2025 at 11:04 AM
gringene.org
Because the sequencing machine capital cost is high, and yield-per-run for long-read sequencing is low, PacBio sequencing has historically been done by large service centres with large queues and substantial turnaround times, often measured in weeks or months.
Image of defoliated trees in a purple misty region. Overlay text reads "Slow Turnaround That Haunty Your Workflow... HiFi gives fast, reliable sequencing so you can rest easy"
November 5, 2025 at 6:56 PM
gringene.org
Like this, for example:
A DNA silhouette spanning approximately 12 bases, recoloured in turquoise
November 4, 2025 at 11:18 AM
gringene.org
#SVGTank Took me *ages* to get the MIRV dialog properly centred on the playing field. It turns out...

* Dialogs don't have a width until they're open
* Dialogs have huge margins
* I wanted it centred on the just the background bit, not the whole SVG
SVG Tank Wars game field with a modal MIRV selection dialog over the top of it. The dialog includes 5 different splitting styles (plus, cross, horizontal, vertical, random) and three different detonation styles (impact, simultaneous, none). The MIRV currently doesn't split, but it does change explosion effects and sound depending on whether the detonation is set to "none".
November 3, 2025 at 12:07 PM
gringene.org
#SVGTank pew, pew!

This looks almost identical to my last screenshot from a couple of days ago, but there have been lots of bug fixes and enhancements under the hood. The laser now has a sound, and will bore through a greater distance if it's fired at the same spot multiple times.
A dark green hilly landscape with four tanks / turrets placed on top of it. The purple turret, Zahra, is firing a laser that is bouncing off the upper wall and in the process of boring into a large hill on the left. The laser colour is greenish-yellow, indicating that it is about 1/3 of the way through using up all its energy.
November 2, 2025 at 9:27 AM
gringene.org
* shudder *
An image that is described in a video as "genes"; represented as a spikey laddery double helix formed from bubbly green foamy stuff. Well... at least it's a right-handed twist.
November 2, 2025 at 8:38 AM
gringene.org
PacBio-only assemblies often lead to gaps, especially in highly-repetitive regions. PacBio reads are often supplemented by Hi-C mapping, which can help stitch some adjacent regions together, but can lead to gaps and misassemblies where the stitching isn't perfect.

bsky.app/profile/grin...
Cartoon image of dark defoliated trees in a purple mist, from PacBio's animation. Text reads "Fragmented Reads That Creep in the Dark... HiFi sequencing delivers complete, accurate data". Purple circles highlight breaks in branches and legs that are joined together.
November 1, 2025 at 1:29 AM
gringene.org
As part of the process of creating proteins, DNA is transcribed into RNA, and adapted post-transcription to add additional chemical modifications. The sample preparation used by almost all sequencing platforms (where RNA is converted back to DNA) means that these RNA variants are hidden from view.
Image from PacBio's animation, "Missing Variants That Vanish Like Ghosts... HiFi reads catch every detail." The image shows dark trees with ghosts in the background.
November 1, 2025 at 1:17 AM
gringene.org
A common data error in sequencing is drops in coverage, where issues with amplification, polymerisation, sequencing, or repeat structure lead to a loss of map to a region. It's like taking a picture of a tree, and seeing branches all over the place that get thinner closer to the trunk.
Image from PacBio's video "Don't let data errors haunt you this Halloween" with a few drops in coverage highlighted, where branches have been drawn thinner than what would make sense for a tree.
November 1, 2025 at 1:09 AM
gringene.org
I rolled over a button on my work jacket yesterday, breaking it in half. I decided it was an excellent opportunity to fetch some scrap cherry wood I had lying around for making another button.
Wooden cherry button on a black and black alternating diagonal vertical pin-striped jacket. The button is striated in multiple places, showing the grain of the wood, and has a raised edge. It has been sanded then oiled with walnut oil. The button is sewn onto the jacket using a brown/white tie-died thread to approximately match the colour of the grain. The other non-broken black button of the jacket is visible at the top of the image, out of focus.
October 31, 2025 at 7:15 AM
gringene.org
I had an insight about the lasers in SVGTank that I could just declare them as projectiles that weren't under the influence of gravity. This allowed me to use a lot of existing projectile code to deal with collisions and wall interaction operations.
Screenshot from the game SVGTank, showing a profile of a green hilly landscape with straight bouncing blue lines over it. Where the blue lines intersect with the green landscape, the green bits have random scattered holes, indicating a burrowing effect with some collateral damage.
October 30, 2025 at 10:32 AM
gringene.org
Another attempt, with completely flat shading for the DNA.
An orthographic sepia map of the world, with a faded 3D DNA molecule above it, hovering over west Africa and Europe. The DNA molecule has no shading, but the crossover points are erased so that it's obvious that it is a right-handed molecule.
October 29, 2025 at 10:31 AM
gringene.org
My initial attempt, without any paper effect, created using Blender's Toon shader.
An orthographic sepia map of the world, with a faded 3D DNA molecule above it, hovering over west Africa and Europe.
October 29, 2025 at 10:19 AM
gringene.org
Hi, I think I'm in the Zoom meeting; is anyone else there?
Image of small room with a small TV monitor and window, with lots of blood smeared everywhere. Text at the bottom of the image reads "Caption this with the 2nd to last text you sent"
October 27, 2025 at 4:39 AM
gringene.org
My attempt at quickly whipping up a similar image, using a more chemically-correct version of DNA
Perseverance rover image of Mars, acquired on June 2, 2023 (Sol 812) at the local mean solar time of 10:19:24. This shows a rocky outcrop with hills in the background, and a bit of sky showing. Along the bottom of the image (as an overlay) is an array of short blue DNA molecules. There are some cheap-looking god beams that have been shoddily added to the image.
October 24, 2025 at 10:15 PM
gringene.org
Ooh, my new mousepad just arrived; that was much quicker than I had expected!

bsky.app/profile/grin...
A hand pointing at a 3D DNA model on a mousepad, which has a wireless black "rapoo" mouse on top of it. Mousepad image: Coloured glass DNA, with A = green, C=blue, G=gold, T=salmon, and a purple / magenta backbone. There are a few bubble-like things floating around the image, which has a pale chartreuse background. When interpreted as gene codons and translated into single-letter amino acid codes, the DNA spells *DAVID*ECCLES*.
October 20, 2025 at 7:49 AM
gringene.org
My sign insert design has now been printed and installed, with plenty of time to spare; check it out the next time you're passing through Island Bay!
Sign advertising Island Bay Presbyterian Church (standing in front of said church), with a replaceable insert region, currently filled with a burnt orange Halloween poster showing "Halloween Garden of memories Here Oct 31". The poster includes some bunting, a church illuminating the path in front of it, seven kākā silhouettes, a balanced rock formation, a gate, a silhouette of a defoliated pōhutukawa tree, and a few scattered gravestones.
October 20, 2025 at 7:36 AM
gringene.org
No changes in elected Wellington councillors since the preliminary results:
Profile images of the elected 2025 Wellington City Councillors (final results): Andrew_Little (Koromatua) Diane_Calvert (Wharangi) Rebecca_Matthews (Wharangi) Ray_Chung (Wharangi) Geordie_Rogers (Pukehīnau) Nicola_Young (Pukehīnau) Afnan_Al-Rubayee (Pukehīnau) Karl_Tiefenbacher (Motukairangi) Sam_O'Brien (Motukairangi) Jonny_Osborne (Motukairangi) Ben_McNulty (Takapū) Tony_Randle (Takapū) Andrea_Compton (Takapū) Nureddin_Abdurahman (Paekawakawa) Laurie_Foon (Paekawakawa) Matthew_Reweti (Te_Whanganui-a-Tara)
October 18, 2025 at 3:40 AM