iiinova — where your digital self keeps evolving

Rob Beynon @originalastacus.bsky.social · 15/08/2025

One for the scientists My site for calculation of recipes for thermodynamically correct pH buffers has data about the buffers that are made. phbuffers.org/BuffferCalc/... Analysis of about 40,000 buffers. -> lot of the five most common buffer species. Anyone care to guess what these top 5 are?

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Rob Beynon @originalastacus.bsky.social · 11/07/2025

As a welshman, I appreciate the Dylan Thomas, albeit mutated :)

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Rob Beynon @originalastacus.bsky.social · 11/07/2025

Many of you (say, about one million) have used my buffer site to calculate thermodynamically correct buffers. Well, today, I upgraded the site with added security, becuase it was stopping soem people connecting. Should all be fine now. https rather than http. Enjoy! phbuffers.org/BuffferCalc/...

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Rob Beynon @originalastacus.bsky.social · 07/07/2025

Just before the Beynfest! Claude continues to impress. I asked it to write a simple protein dotplot tool to explain to a PhD student how two sequences are related, and 20 minutes later: phbuffers.org/Claude/DotPl... Free for all to use...

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Rob Beynon @originalastacus.bsky.social · 06/07/2025

Slight ambarassed to be at the ’Putting Beynon out to pasture’ celebration at @ukbspr.bsky.social tomorrow. Thanks to the organisers…

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Rob Beynon @originalastacus.bsky.social · 25/06/2025

I asked Claude to writ ethe annotation guide, and it built in features I did not ask for, and did not know about! I hope this will actually be of use.. phbuffers.org/Claude/pepti...

phbuffers.org

PeptideMapper Annotation Syntax Guide

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Rob Beynon @originalastacus.bsky.social · 25/06/2025

yes, me too. frequent saves, and 'start over' with that version. The dialogue with Claude, from the tool, actually talked about protein chemistry! I, and I suspect you, and the future generation will learn to give clear instructions.

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Rob Beynon @originalastacus.bsky.social · 25/06/2025

Here's the annotation language for peptidemapper phbuffers.org/Claude/pepti...

phbuffers.org

PeptideMapper Annotation Syntax Guide

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Rob Beynon @originalastacus.bsky.social · 25/06/2025

BTW, 1600 lines of code. SO impressed phbuffers.org/Claude/pepti...

phbuffers.org

PeptideMapper by Rob Beynon

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Rob Beynon @originalastacus.bsky.social · 25/06/2025

"I Claudiused" - tragic tale. My tool is now silly. (haven't quite made a mess-alina of it though!). Has a flexible annotation language, which was not easy to get right. But "P14 sequence blue out above L1" means "Label P14 with its sequence in blue outside the map" @catfranco.bsky.social

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Rob Beynon @originalastacus.bsky.social · 24/06/2025

Oh yes, the URL of the peptide mapper: phbuffers.org/Claude/pepti...

phbuffers.org

PeptideMapper by Rob Beynon

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Rob Beynon @originalastacus.bsky.social · 24/06/2025

So, I rewrote my little peptide mapping tool And, in conversation with @catfranco.bsky.social she suggested a feature - so, in 5 minutes, it was implemented.with an annotation language K fill cyan C circle yellow in V diamond green out below P45 fill orange Fun!

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Rob Beynon @originalastacus.bsky.social · 24/06/2025

And here it is. OK, there is no doubt that writing the original taught me how to specify the task, and there is less functionality in some areas, but more in others, yet, within about 6h, here it is! phbuffers.org/Claude/pepti...

phbuffers.org

PeptideMapper by Rob Beynon

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Rob Beynon @originalastacus.bsky.social · 23/06/2025

I wrote a neat little tool to draw peptide maps a long time (In Livecode/Hypercard) and in 4h have had Claude create a near identical web app...when it works well I'll share a hyperlink. @catfranco.bsky.social

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Rob Beynon @originalastacus.bsky.social · 21/06/2025

I asked it to ‘prettify’ my buffer program.. made a total mess of it over and over again…so not perfect

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Rob Beynon @originalastacus.bsky.social · 21/06/2025

Neat tool though… and it can always be improved . In fact hard to leave alone..

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Rob Beynon @originalastacus.bsky.social · 21/06/2025

Loved it.. now you know where ‘MEERCAT’ came from…

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Rob Beynon @originalastacus.bsky.social · 21/06/2025

Loved it! We are still looking for marilin- watch this space! Fantastic interview! Will see Kathryn in the BSPR meeting in Liverpool in July, www.bspr.org/annual-meeti... when there is a ‘putting Beynon out to pasture’ session! Payback for the embarassment!

bspr.org

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Rob Beynon @originalastacus.bsky.social · 19/06/2025

capsaicin? Cathepsin is a cysteine proteinase e.g. papain, bromelain, so maybe in papaya and pineapple? :)

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Rob Beynon @originalastacus.bsky.social · 19/06/2025

Any other stories like this? end/ Anyone used Ai to code scientific applications? I do think the main limitation is in specifying the parameters of the tools that I want to make. That is on me. end/

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Rob Beynon @originalastacus.bsky.social · 19/06/2025

But, for ordinary, inept folk like me, this makes simple tasks completely within reach. e.g. I asked Claude for an SVG viewer for my peptide mapper programme -easy. Of course, I will now rewrite the entire tool as a web app.. so much more user friendly. 8/ (phbuffers.org/Research/Pma...)

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Rob Beynon @originalastacus.bsky.social · 19/06/2025

Scarily, Claude not only correctly interpreted the Python code but also intimated that if I had the exe file, it could probably reverse engineer that too. 7/

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Rob Beynon @originalastacus.bsky.social · 19/06/2025

And bingo, a web app that replaces an exe file with a fast and pretty, user-friendly flexible web app. I did no coding at all, and it took me less than a day of intermittent access. The decoding is instantaneous for large files. 6/

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Rob Beynon @originalastacus.bsky.social · 19/06/2025

Breakthrough. A very clever research in our group had previously decoded the data, and we found the old Python code to do that. Showed this to Claude and bingo! Immediate result. After that, long dialogue about making it pretty, export options, tooltips and an explanation of the coding method 5/

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Rob Beynon @originalastacus.bsky.social · 19/06/2025

So, Claude tried to build a lookup table to reverse engineer the time from known examples. Many days of data, at very high time resolution, was never going to happen, as it required just too many data points, and even then, no guarantee all possibilities would be covered. 4/

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Rob Beynon @originalastacus.bsky.social · 19/06/2025

But we hit an interesting sticking point. Claude correctly identified which bytes encoded the timebase, but could not unpack the highly compressed format (it involved a variable number of sixteenths of a second increments) 3/

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Rob Beynon @originalastacus.bsky.social · 19/06/2025

The first attempt was poor, and with a bit of inspection, I was able to let Claude know what the EOF and EOR markers were, as well as indication what the columns of data were when unpacked. Second attempt - so much better. 2/

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Rob Beynon @originalastacus.bsky.social · 19/06/2025

OK, I have been playing with AI for coding (Claude) and I am stunned. This was to develop a web app for decoding a highly compressed/efficient data logger, binary file and unpack into human useable form. I gave Claude the original binary file and the decoded output. 1/

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Rob Beynon @originalastacus.bsky.social · 19/06/2025

Not all of them are complex - and of course, taste is largely olfaction.. so mapping the tasteome is an n by m matrix where all combinations and permutations are possible, and n and m are both (in UK parlance) ginormous! But, AI..? (see my next post)

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Rob Beynon @originalastacus.bsky.social · 08/06/2025

Sad to hear of death of Bill Atkinson, inventor of Hypercard.. the first home for my buffer calculator ..now at phbuffers.org ( no fee, no adds, no cookies) @benneely.com

phbuffers.org

Professor Rob Beynon

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Rob Beynon @originalastacus.bsky.social · 03/06/2025

Pleased to see this very nice paper out by an excellent team. Mass spec where you do not know what you are measuring - this is the sort of area where AI can make a difference.. to be seen. All data sets are public, so lots of opportunity. Open access, of course. www.nature.com/articles/s41...

nature.com

Rapid evaporative ionisation mass spectrometry can age field caught Anopheles gambiae malaria vectors - Scientific Reports

Scientific Reports - Rapid evaporative ionisation mass spectrometry can age field caught Anopheles gambiae malaria vectors

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Rob Beynon @originalastacus.bsky.social · 13/05/2025

The original buffer program was in Hypercard Beynon RJ. A Macintosh Hypercard stack for calculation of thermodynamically-corrected buffer recipes. Comput Appl Biosci. 1988 Nov;4(4):487-90. doi: 10.1093/bioinformatics/4.4.487. PMID: 3208185.

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Rob Beynon @originalastacus.bsky.social · 11/03/2025

Nice, but horrible fixing brackets!

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Reposted by Rob Beynon

Supertanskiii @supertanskiiii.bsky.social · 29/01/2025

Sky News CONTINUING to refer to the chancellor as ‘Rachel from Accounts’, would they have referred to a male chancellor by an insulting nickname? Of course not. It’s misogynistic and they’re repeating it.

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Rob Beynon @originalastacus.bsky.social · 30/01/2025

I let an AI write about Zwitter (phbuffers.org). I'm actually quite impressed with what it produced after a bit of coaching.

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Rob Beynon @originalastacus.bsky.social · 30/01/2025

Dear Research Fish, I'm retired for five years, and am not pushing out streams of outputs anymore, apart from bird photographs and vegetables. Since these are not reportable, please let me off the hook. In any case, I am not going to take part this year, except at my usual consultancy rates.😀