David Eccles 🌻🇵🇸7x🩹🛡️

@gringene

Neurodivergent freelance bioinformatician, cuddler of data, and theoretical geneticist, with a love for Free Software and the hacking thereof. Rangitāne o Wairau. He/they. Website:

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David Eccles 🌻🇵🇸7x🩹🛡️@gringene· 17d

* pulling hair out * A fail on that check was meant to be impossible!

A spatial programming task, trying to create a program that sorts a list, using little men that can only hold two things at once, and have a counter in their backback that they can't read.

In this case, one of the little men has crashed into a wall, because the return value from a check was incorrect, because I sent a data packet before I sent a metadata packet.

David Eccles 🌻🇵🇸7x🩹🛡️@gringene· 17d

#icfp2026 Rank 100 at some point in the contest; I don't think I'll be able to manage much better than that. It has been a fun contest, and I've done better than some previous years, but I think I've pretty much reached my limit for spatial programming involving little men with tiny backpacks.

Ranks 90-106 (scores 6.71 to 5.76 respectively), with me at rank 100 with a score of 6.02.

I might be able to manage another couple of points from sorting and plotting, but I doubt I'll get more than that.

David Eccles 🌻🇵🇸7x🩹🛡️@gringene· 17d

I got to rank 98 of 200 before the standings were frozen. I did my "mad rush to just get something done" about an hour ago. Currently getting distracted by plotting; I doubt I'll be finished before the lightning round is done.

Standings table for ranks 94-102, with GrinGene at a score of 4.65 (rank 94 score is 4.88, rank 102 score is 4.49)

David Eccles 🌻🇵🇸7x🩹🛡️@gringene· 18d

#icfp2026 I really appreciate when the creators of the programming contests have designed a UI to allow things to be done manually. It makes getting on board and doing the fun stuff so much easier and quicker.

David Eccles 🌻🇵🇸7x🩹🛡️@gringene· 19d

Wow, amazing! I'll be sure to send this stunning achievement about my Data: Figure S4: Location maps (from OpenStreetmap) with inset Pavian images to all my friends, so they can read it as well.

Congratulations, David!
Your data reached 20 reads
Achieved on July 23, 2026
Data: Figure S4: Location maps (from OpenStreetmap) with inset Pavian images

David Eccles 🌻🇵🇸7x🩹🛡️@gringene· 20d

I'm not a fan of obfuscated code:

$JavaScript code seen from 'view' source, one of two such functions, starting with: var _0x3de9=["\x70\x6F\x77","\x72\x6F\x75\x6E\x64","\x20\x50\x75\x72\x72\x73\x20\x50\x65\x72\x20\x4D\x69\x6E\x75\x74\x65","\x25",...$

David Eccles 🌻🇵🇸7x🩹🛡️@gringene· 22d

#REPAVER No telomeric sequence, numerous sequence breaks, and lots of sequence breaks that occur within repetitive regions. While there are tandem repeat arrays that span distances greater than 10kb, the longest is not even 300kb, so I wouldn't call this assembly "chromosome-level".

REPAVER plot of chromosome 1 (k=51) showing about 20 numerous N-stretch sequence breaks (represented by vertical lines). Many of these breaks occur within repetitive sequences.

David Eccles 🌻🇵🇸7x🩹🛡️@gringene· 24d

Post from Pooklebinky:

"""
Every day Mamdani comes out and is like "hey guys, I turned off the orphan-crushing machine. Literally just had to flip a switch. Took less than 5 minutes."
"""

David Eccles 🌻🇵🇸7x🩹🛡️@gringene· 28d

Why are you asking the question if you won't let us answer "No"?

Should WCC merge with other Councils? | Brooklyn and Bunny St connections
Kia ora koutou,

Amalgamation – join the conversation

Should WCC merge with other councils in the region? Fill out our amalgamation survey by this Sunday, 19 July or come along and talk to councillors at a public forum on 29 or 30 July.

David Eccles 🌻🇵🇸7x🩹🛡️@gringene· 29d

TFW the production server is down, and you'd rather finish off your squishy head thing than try to find workarounds for problems that other people have created.

A squishy foam head thingy to protect my head from getting squished by the top of my Jabra headphones, about half-way through its construction. Created by attaching a piece of foam to the top of the headphones with some loose red string, then crocheting a tube around it.

This image shows the headphones (with orange cord), the crochet hook, the half-completed squishy thingy, and the ball of cotton that the half-finished crochet is attached to.

A squishy foam head thingy to protect my head from getting squished by the top of my Jabra headphones, after finishing its construction. Created by attaching a piece of foam to the top of the headphones with some loose red string, then crocheting a tube around it.

This image shows the headphones and the finished squishy thingy: a squishy crochet tube attached to the top of headphones, with a couple of dangly bits of thread at the ends.

David Eccles 🌻🇵🇸7x🩹🛡️@gringene· Jul 10

Ooh, paper accepted!

July 9, 2026

Title: "Engineering antigenic breadth against SARS-CoV-2 by pairing divergent RBDs within a single mRNA immunogen"
Tracking #: <redacted>
Authors: Montgomerie et al.

Dear Dr. Eccles,

We are pleased to inform you that <redacted> has given provisional approval of your article for publication. <redacted> conducted the initial review of your manuscript, will also be informed of the decision.

David Eccles 🌻🇵🇸7x🩹🛡️@gringene· Jun 26

Missed a golden opportunity for calling it PosterioR. For those curious about the hex image:

a swooping ribbon in a 3D 'S' shape (in a white / dark blue colouring) which sweeps from the bottom left corner of the hex to the top right hand corner of the hex. The hex has a steel blue background, and has the text "mc-stan.org" adorning the bottom right edge.

[this appears to be a generic image for mc-stan, rather than a specific image for the Posterior package]

David Eccles 🌻🇵🇸7x🩹🛡️@gringene· Jun 25

What the AI? How many milliseconds did you spend checking this for technical accuracy?

Bullshit sequencing technology at a glance, showing [inaccurately] that Sanger has longer reads than PacBio and Nanopore, with an unannotated scale that ranges from 1 (High) through 3 (Medium), and all the way to 5 (High).

David Eccles 🌻🇵🇸7x🩹🛡️@gringene· Jun 25

""" [Winston Peters and Ryan Bridge] went on to discuss the Middle East situation and the UK's apparent revolving door of prime ministers, during which Peters - who first entered Parliament in the late 1970s - derided 'career politicians' """

Image of Zohran Mamdani and Brad Lander having a *big* laugh.

There is a leafy spreading plant in the background, possibly ivy.

David Eccles 🌻🇵🇸7x🩹🛡️@gringene· Jun 25

Iconic

- Senior House Dem, asked if members are worried: "Yes they are"

Image of Zohran Mamdani and Brad Lander having a *big* laugh.

There is a leafy spreading plant in the background, possibly ivy.

David Eccles 🌻🇵🇸7x🩹🛡️@gringene· Jun 24

The pick and shovel business is making a profit. Remember, when everybody is digging for gold, it’s good to be in the pick and shovel business.

Nvidia loss $225 B, revenue $478 B, net profit $253 B

David Eccles 🌻🇵🇸7x🩹🛡️@gringene· Jun 23

Public Service Announcement

Do not plant bamboo near data centers

Bamboo can spread rapidly through underground rhizomes and can be extremely difficult to remove

Please choose responsible landscaping alternatives

Thank you for your cooperation

This message has been reviewed by absolutely nobody

Posted in r/ColoradoSprings

David Eccles 🌻🇵🇸7x🩹🛡️@gringene· Jun 15

#NanoporeCommunity 🦗🦗🦗

David Eccles 🌻🇵🇸7x🩹🛡️@gringene· Jun 13

This is a pretty clear example of sexism:

Assume [all the men selected for the NASA mission are] more qualified [than all the women astronauts who didn't get picked], unless contrary specific evidence.

b/c when less qualified chosen, Bad Things' chances skyrocket. That lesson learned already.

& consider crew chemistry issue. Unknown for us both.

You're right re inspiration! But lower priority than competence.

Thx for good engagement.

David Eccles 🌻🇵🇸7x🩹🛡️@gringene· Jun 9

* taps sign * The internet has become less interested in insight, and more interested in stealing attention. Unfortunately, it seems we're creating a society of loud oblivion.

Two Lines on Everything; entry from 2019-Feb-23:

My prediction: we are heading towards a world in which there are no experts. This is the disruptive form of an open society.

Warning: scatter-brained thoughts

Consider the Curse of The Traveler, or the Curse of The Bioinformatician. Every new area explored opens up new areas to be explored.

This is happening in music, where the most voted-on songs are old songs, because the music space for recent music is so large that the idea of popular music starts to lose meaning. If you want to listen to a particular style of music, it's there for the listening. If it's not there, then the vacuum can be filled by anything that loosely matches the style. In the words of Betty Campbell, "If it's worth doing, it's worth doing badly." People outside the clique may not even notice how good (or bad) it is. A world-class violinist can play what they consider to be the most difficult piece in the world, but if they're doing it while busking at a train station, it'll still be rubbished by a passer-by that doesn't appreciate the challenge or magnificence.

This is probably also happening in science. We understand the Dunning-Kruger effect, where novice people tend to overestimate their abilities, and experts tend to underestimate their abilities. For anyone who is not well-versed in the particular niche of research, it is difficult to distinguish profound wisdom from profound bullshit. When it would take years to research and prove (or refute) an off-the-cuff statement made in a few minutes, how can anyone expect anyone to have the experience to be an expert in all but the most specific area of research?

The flip-side of this is that we can all become experts in our own world. We have a unique perspective to offer that cannot be completely refuted. Will the world learn how to listen to everyone, or will it forget how to listen to anyone?

David Eccles 🌻🇵🇸7x🩹🛡️@gringene· Jun 7

With a little bit of a perspective shift, this billboard seems a whole lot more reasonable.

Billboard going up and endorsed by Simeon Brown MP, altered with a perspective transform to make it more readable, replacing "Your" with "Simeon's".

Text panels read:
* Tax Simeon's house [Go with Labour]
* Tax Simeon's wealth [Get the Greens]
* Tax Simeon's business [And Te Pāti Māori]

David Eccles 🌻🇵🇸7x🩹🛡️@gringene· Jun 7

A little bit of cleanup to get rid of unnecessary comparisons for the dotplot view:

REPAVER dotplot plot (k=50) showing one sequence about 14 Mb in length, followed by 14 x 1 Mb sequences that tile across the first sequence in a random order. The repetitive elements of the first sequence are shown in the left of the plot, and those elements are excluded from the remaining sequences, leaving a mostly bare plot that indicates on the right hand side where in the first sequence the subsequent sequences can be found.

David Eccles 🌻🇵🇸7x🩹🛡️@gringene· Jun 6

What I want to use this for is to help me understand how assembled contigs can be mapped onto an existing - more contiguous - backbone, ideally in an automated fashion.

REPAVER dotplot (k=125 bp) from the kākāpō genome, showing a primary backbone sequence that is being compared to three other sequences. The first other sequence has an additional tandem repeat array that isn't present in the primary sequence. The second other sequence maps essentially exactly to the tandem repeat array in the primary sequence (with a few scattered novel kmers). The third other sequence maps in a reverse-complement orientation to the non-tandem bits of the primary sequence.

David Eccles 🌻🇵🇸7x🩹🛡️@gringene· Jun 6

Here's an update of the comparison mode plot, which gets much closer to the sort of information I want to know: Which bits in the additional sequences don't match internally-repetitive kmers, and can therefore be used for reliably anchoring the additional sequences onto the first sequence?

David Eccles 🌻🇵🇸7x🩹🛡️@gringene· Jun 5

Why are you using generative images and not checking them for simple mistakes?

A portion of the image with text on it, "DATSET BLOCK". The portion appears to depict objects that I would usually expect to be fashioned out of metal, but in this case they appear to be wood: conveyor belt, gears top paneling, tiled flooring. There are a few glowing panels with stuff that looks like it might be text, but doesn't match expected text forms. A screen with a glowing "R" is prominent, but it's not the R language's R, it's just a random sans-serif font.

David Eccles 🌻🇵🇸7x🩹🛡️@gringene· May 30

That particular example was a bit of a toy; not very interesting because it was a sequence essentially being compared to itself. Quick to test, and I knew roughly what it should look like. Here are 5 chromosomes from that same organism being compared to each other, covering about 63 Mb in total.

REPAVER plot of the concatenation of the 5 longest chromosomes of the Woolly bottlebrush (Greyia radlkoferi), showing a complement backbone (which is probably the result of STRs that have the same sequence.

David Eccles 🌻🇵🇸7x🩹🛡️@gringene· May 30

I have *finally* added a feature to compare kmer locations for two or more different sequences using my hashasher backend, which is the start of work to stitch sequences onto a backbone, ignoring repetitive sequences. The append code in hashasher needed a bit of tweaking, but it seems to work now.

REPAVER output (k=51 bp) for one 13.8 Mb sequence with 14 1 Mb consecutive and overlapping subsequences taken from the 13.8 Mb sequence that have been shuffled around. The gaps delineating the different sequences are indicated by vertical lines.

The subsequence nature of the 1 Mb sequences shown on the right-hand side of the plot is visualised as horizontal purple and maroon lines.

David Eccles 🌻🇵🇸7x🩹🛡️@gringene· May 29

These need a bit more workshopping; the longest mahmoudi sequence is missing bits, with 10k banding and lots of N patches; the chili sequence is similar, with more breaks. It's been a while since I've looked at a chromosome larger than a gigabase with REPAVER; seems like it's still working okay.

A REPAVER plot of Chr3A_scaffold_3 from the mahmoudi genome (k=350 bp). Despite claims of it being "chromosome-level", the 1.515 Gb chromosome is split up into dozens of smaller pieces, and shows very obvious repeat banding at the 10kb point, suggesting bias from PacBio's sequence length limit of about 10kb.

Demonstrative output from REPAVER running on a 1.5 Gb chromosome using a repeat length search of at least 350bp (i.e. finding all repeats that are *at least* 350 bases in length). The initial forward repeat search took 266 seconds; the secondary search for reverse, complement, and reverse-complement repeats took 409 seconds; plotting the location and separation distance of these repeats took about 4 seconds.

A REPAVER plot of Chr3B_scaffold_1_part1_of_2 from the chili genome (k=350 bp). Despite claims of it being "chromosome-level", the 1.356 Gb chromosome is split up into hundreds of smaller pieces, and shows very obvious repeat banding at the 10kb point, suggesting bias from PacBio's sequence length limit of about 10kb.

David Eccles 🌻🇵🇸7x🩹🛡️@gringene· May 28

Very nice assemblies, with visible centromeres and no obvious banding; looks like the longest scaffolds are all T2T as well! [There's a 7bp STR with reverse-complement matching at the start and end of the 17 longest scaffolds]

result of running "grep -B 2 -A 2 '^>' sorted_bottle.fasta", showing the first and last 100-200bp of each scaffold; it's all 7bp repeats, and the repeats at the start are the reverse-complement of the repeats at the end. This matches what I expect to see in chromosome-length assemblies with telomeres.

REPAVER plots (k=35bp) for scaffolds 7-12 (sorted by length). End telomeric repeats are visible, and there is a backbone of complementarity [not the usual reverse-complement backbone].

REPAVER plots (k=35bp) for scaffolds 13-17 (sorted by length). End telomeric repeats are visible, and there is a backbone of complementarity [not the usual reverse-complement backbone].

REPAVER plots (k=35bp) for scaffolds 1-6 (sorted by length). End telomeric repeats are visible, and there is a backbone of complementarity [not the usual reverse-complement backbone].

David Eccles 🌻🇵🇸7x🩹🛡️@gringene· May 28

Looks like my old work is still using at least one of my #3DPrinting designs www.printables.com/model/726839...