David Eccles 🌻🇵🇸7x🩹🛡️

@gringene.org

1741 Followers 1288 Following

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

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",...
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.
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." """
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.
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.
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.
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]
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).
Image of Zohran Mamdani and Brad Lander having a *big* laugh. There is a leafy spreading plant in the background, possibly ivy.
- 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.
Nvidia loss $225 B, revenue $478 B, net profit $253 B
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
Response from me to a question in the Nanopore community that has 1 reply in 5 days: "Changing from a P2 Solo to a P2i is not an upgrade" [i.e. my response is the only reply]
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.
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?
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]
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.
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.
REPAVER profile 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, and those elements are excluded from the remaining sequences, leaving a mostly bare plot that indicates where in the first sequence the subsequent sequences can be found.
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.
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.
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.
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.
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.
Screengrab of the bottom of a video about an RNA development platform, showing a tube valve holder attached to the foot of a bench.
A very small (i.e. low resolution) full jacket image from Help The Witch, showing the hare on the back cover, and the tree on the front cover.
Screenshot from the build pipeline for OrcaSlicer, showing where built images can be downloaded from. For example, build_windows -> Build OrcaSlicer -> Upload artifacts Win Zip
Screenshot of the build of my latest 3D honeycomb update, showing a cube with a 3D honeycomb infill at 11% density, filled pattern tops, two outer walls, and 2 multilines.
Sissel Juul shown next to a question from Chris: You have said nothing so far about the planned obsolescience of the P2 Solo, [a response] which is widely reviled by your customer base (146 reples to the community page announcement) - P2i is 10x more expensive to buy and maintain. It's sequencing for a some, in a few places, not anyone anywhere. Reconsider?
Image from the big screen at the Nanopore conference, ass seen in the "LC26 Studio: Where are our hidden secrets in genomics, and why should we care?"
Screenshot from the "Product update: P2" page from the ONT community pages. The banner of the page depicts James Ferguson with a speech bubble thinking "Lol I totally forgot that was on". Highlighted on the page: * the launch of the PromethION 2 range *was* our approach to bring high-output analyses to more people in more environments * PromethION 2 Solo (P2S) - is the most accessible high-output sequencing system on the market
Found Scale #13 at Mishal Park | The Soul of a Fae
Image of Found Scale in Angeline Era at Mishal Park | Baleful Bally Building
PacBio long read input requirements: 500 ng for SPRQ chemistry; 1 ng for Ampli-Fi protocol
Diagram from a PacBio explainer video, demonstrating how PacBio HiFi reads are based on a consensus from multiple reads of a single molecule.
Form Question: "Which ethnic group(s) does your young person identify with? (Tick all that apply) The form is a radio button interface. Multiple selections cannot be chosen. Also, the form includes "Other European", but there's no other "Other".
Technology Connections showing off the Sunbeam Radiant toaster, with a surprised look on their face as the toast rises by itself after the toaster has switched off.
Image of Jenna Lynch showing a picture on her cellphone to Chris Hipkins. They are standing inside parliament, with slightly curved cream walls and red carpet below them.
Screen grab from the video, showing a MinION Mk1b next to two PromethION P2 Solo sequencers. Both of these types of devices are on the chopping block for ONT.
Highlighted: "Ensure patients use a respiratory (e.g. N95, FPP2) during the transfer."
UN Sustainable Development goals, as they were in 2017, with #8 circled: "Decent work and Economic Growth". 1 - No Poverty 2 - Zero Hunger 3 - Good Health and Well-being 4 - Quality Education 5 - Gender Equality 6 - Clean Water and Sanitation 7 - Affordable and Clean Energy 8 - Decent Work *and Economic Growth* 9 - Reduced Inequalities 11 - Sustainable Cities and Communities 12 - Responsible Consumption and Production 13 - Climate Action 14 - Life Below Water 15 - Life On Land 16 - Peace, Justice and Strong Institutions 17 - Partnerships For The Goals
Petrol -- days of supply (latest data 06 May). Most recent data (6th May) shows in-country 34 days; on-water 15.3 days.
Figure: Limited consensus of marine viral diversity observed across techniques. In sub-figure A of this plot, PacBio HiFi shows both lower species proportions and lower genus proportions (normalised to Mbp assembled in contigs over 10 kb) than all other methods. Original figure legend: Proportion of species (blue) and genera (orange) recovered by each method, normalized by the number of base pairs (Mbp) assembled in contigs over 10 kb. (A) All species and genera detected by each method. (B) Species and genera with only one recovered member (singletons) detected by each method.
"In response to part 6 of your request Health NZ has not provided the Office with any reports... your request for information is refused... as this document... cannot be found."
Java code for a Global variable class that stores an integer value. When I was writing my Java code for a Sudoku game, I needed a way for different classes to share a global idea of settings, and this is what I came up with: public class GlobalVar { private final String varLabel; private int value = 0; public GlobalVar() { varLabel = ""; } public GlobalVar(String tLabel){ varLabel = tLabel; } /** * Retrieves the current label for this global variable. * @return The label associated with this global variable class */ public String getLabel() { return varLabel; } ...
Star wars Anakin meme - Anakin: We're using AI instead of biased humans Padme (smile): What did you train the AI on? Anakin: Emotionless face Padme (concerned look): What did you train the AI on?
Chrome: Which website would you like to see User: I don't want you to know Chrome: <holds up puppet> What about telling Mr. Incognito? User: Okay! [image credit: skeletonclaw.com]
UK energy generation graphs, showing 24.3 GW renewable, 5 GW nuclear, 0.9 GW fossil fuels, 4 GW imports, 0.8 GW biomass, 0.45 GW other.
Three orthographic images of the world, with the central image centred on the Strait of Hormuz, the left image 120° west (showing the Americas), and the right image 120° east (showing the Pacific). Oil route flow lines / arrows and delay times have been added, using data included in the JP Morgan image.
Three orthographic images of the world, with the central image centred on the Strait of Hormuz, the left image 120° west (showing the Americas), and the right image 120° east (showing the Pacific). These images will be used as a base for an oil flow map that I will create, using data included in the JP Morgan image.
Petrol vessel TBD: 4.2 days ETA, 5.1 days NZ supply. No other supplies visible on that track, but +31.7 days is claimed by MBIE. ... but it's apparently "Created with Perplexity Computer", so I'm not sure whether these numbers and/or predictions are valid.
The back of a Phantexs Evolv X case, with the SSD tray flipped down, showing two SSDs, one labeled 2022 musculus root (ADATA 480 GB SSD), and the other labeled 2026 musculus /home (SAMSUNG 2 TB SSD).
Section 134 of the 1961 NZ Crimes Act. Highlighted text: "It is a defence to a charge under section 134 if the person charged proves that... at the time of the act concerned, he or she believed on reasonable grounds that the young person was of or over the age of 16 years" 134 Sexual conduct with young person under 16 (1) Every one who has sexual connection with a young person is liable to imprisonment for a term not exceeding 10 years. (2) Every one who attempts to have sexual connection with a young person is liable to imprisonment for a term not exceeding 10 years. (3) Every one who does an indecent act on a young person is liable to imprisonment for a term not exceeding 7 years. (4) ... (5) The young person in respect of whom an offence against this section was committed cannot be charged as a party to the offence if the person who committed the offence was of or over the age of 16 years when the offence was committed. (6) In this section,— (a) young person means a person under the age of 16 years; and (b) doing an indecent act on a young person includes indecently assaulting the young person. 134A Defence to charge under section 134 (1) It is a defence to a charge under section 134 if the person charged proves that,— (a) before the time of the act concerned, he or she had taken reasonable steps to find out whether the young person concerned was of or over the age of 16 years; and (b) at the time of the act concerned, he or she believed on reasonable grounds that the young person was of or over the age of 16 years; and (c) the young person consented. (2) Except to the extent provided in subsection (1),— (a) it is not a defence to a charge under section 134 that the young person concerned consented; and (b) it is not a defence to a charge under section 134 that the person charged believed that the young person concerned was of or over the age of 16 years.
Demonstrative COBOL code: OPEN INPUT sales, OUTPUT report-out INITIATE sales-report PERFORM UNTIL 1 <> 1 READ sales AT END EXIT PERFORM END-READ VALIDATE sales-record IF valid-record GENERATE sales-on-day ELSE GENERATE invalid-sales END-IF END-PERFORM TERMINATE sales-report CLOSE sales, report-out
Store device pricing for nanoporetech.com: * MinION Mk1D - $3,150.00 * GridION - Price on request * PromethION 24 - Price on request * PromethION 2 Integrated - Price on request * PromethION 2 Solo - Price on request
Time-ordered skeets from Walter Plinge over the past two weeks (with speculation non-statements, links, and quotes removed), split into direct statements from the thread I replied to, and other statements (which are also discussing the same topic about sex testing for Olympic Games). It was unclear to me what specifically Walter Plinge was referring to when they made the statement, "I misspoke", but given that their statements were centered around the same theme, I could imagine that falsifying any one of them would cause the whole house of cards to crash down into a pile of nonsense. As a generous interpretation about "I misspoke", Walter could be said to be walking back the statement that there is no sex-based discrimination for "men's" events at the Olympic games. However, if that walking back is correct, then they would also need to walk back their statement that the sex testing for "women's" events at the Olympic games is not discriminatory. And if it is a valid proposition that the sex testing *is* discriminatory (i.e. sexist), then other statements presented by Walter (like the supposedly science-based reasons behind the asymmetry of testing) fall flat. TLDR: Walter appears to be arguing for trans exclusion, without explicitly saying that they're excluding trans people, and getting tied up in knots when they're called out on it.
Repaver plot (k=12 bp) for Lumpy skin disease virus isolate Oman_2009, complete genome. There is a lot of noise in the repeat structure at 12bp density (somewhat typical for viral genomes), but both the inverted repeats at the ends and the 39bp terminal tandem repeat arrays can be seen.
Key exchange (requiring a lot of training and explanation about how it works and how it protects privacy) so that an evaluator can carry out the black box functions provided by a modeler to do analysis of the data of a client. VS A modeler who travels to the client to predict PRS using their own computer. OR A modeler who teaches the client how to predict PRS, using public datasets for the teaching.
Multiple intersecting waves representing focused energy that creates a particle. Points at the edges of a circle create waves that spread, expanding out to interfere and intersect with each other, growing until they combine at the centre of the circle, forming a focused hot spot. The underlying texture forms and expands at the focused hot spot. The waves keep travelling, eventually fading out to a bulbous shape and disappearing. The texture expands with the expanding wavefront, until it reaches its full size.