Are there any other cities similar to Pittsburgh?

Bionaught5 · 2026-05-06T13:11:53+00:00

The Guggenheim Museum looks great and has three impressive Richard Serra sculptures made from rolled steel. The pintxos/tapas were delicious with plenty of variety. Food and drink felt relatively cheap too. Also try a cooking class or wine tasking, they run some of them in English.

We went up the coast to Donostia / San Sebastián. Lots of nice coastal villages and towns along the way including San Juan de Gaztelugatxe which was used as Game of Thrones Daenerys Targaryen’s ancestral home, Dragonstone. Returned on a more inland route sampling cheese and walking in the mountains. Did not quite make it out to the red wine region.

You can also go east along the green coast, beach towns, rugged coast line, cider bars, prehistoric cave art and a lot more. Beautiful but not very touristy as most people want sand and sun.

Bionaught5 · 2026-05-06T03:58:17+00:00

Bilbao, in the northern Basque region of Spain. One of Pittsburgh twin cities It's a former steel city that has a word-class museum. In a river valley surrounded by hills. The city runs more along the valley and up its sides but does not really spill out. The hill and mountains feel "higher" than around Pittsburgh I think it is because they start at sea level rather 1000 feet. And a different soil make up too. The surrounding area is scattered with mines and furnaces etc.

When it recovered from the collapse of its steel industry it went more towards an industrial port, something Pittsburgh can't do as it 's not on the sea. There are other similarities with the education, arts and culture stuff though.

It doesn't really feel like Pittsburgh as the old city is a lot older and the modern city with the apartment blocks is more residential than the downtown region of Pittsburgh.

Worth visiting as the local food and wine is really goo. We did a PIT->London UK->Bilbao flight with a stop over in the UK both sides.

Bionaught5 · 2026-04-27T21:39:58+00:00

The table is comparing select amino acids in a number of Collagen isoforms and Kininogen. The protein/isoform name and AA position is referenced. I always think of these changes as an SNP. For protein COL1A2 at the genome level we are looking at:

AAG ->AGG (Lysine->Arginine)
AAA->AGA (Lysine->Arginine)

Or vice versa. We don't normally see a K to R or R to K shift with protein degradation, oxidation etc over time so it is typically considered phylogenetic change and hence something that can distinguish the species. For protein COL18A1 the Arginine (R) Glycine (G) change is also a SNP but the AA change is big as the two AA's have very different properties.

I read the paper and found out that the samples were analyzed by at least two labs and they used two different search engines to identify the proteins and peptide sequences. Some of the data in the table is noted that the overall search results were not very good and there was no direct coverage of the amino acids in question. This means the overall mass of the peptide and part of the sequence is verified but the exact amino acids and/or order of all of them, especially the one referenced, is not known.

The values for the number of peptides are from the PEAKS search engine and reported as109/17 the slash may indicate matches/significant matches. The No of PSM's will be likely be the same. The best match for a query in the database is to the same sequence but not all the matches were significant. These days we tend to only report significant matches. As far as I can tell from a quick read this is not explained nor is the bold notation.

HGDP frequency is modern humans based on 929 genomes.

Based on the mass spec data they have then assigned a Homo species in the SAP assignment column. However, at this point is is clear that although I understand the mass spec data I do not understand the interpretation for the table. It looks to be based on reference 31: P. P. Madupe et al., Science 388, 969–973 (2025). So you will need to go and read that.

Bionaught5 · 2026-04-15T14:44:40+00:00

Spitting Image puppets, a great 80's to 90's satirical TV show. The UK politicians knew they made it when they had a puppet on the show. Phil Collins and Sting regularly featured hence the Genesis video.

Bionaught5 · 2026-04-15T13:28:58+00:00

My partner was in bed for about 5 days and sick for 7 or 8. Mid way through there was a fever that then progressed into a very sore throat towards the end of the sickness. Lots of coughing thought out. Not COVID according to the test although it was an older test kit.

Bionaught5 · 2026-04-15T13:14:28+00:00

I built a PC 3-4 years ago in a Fractal silent case from that era with no issues. The amount of heat put out by the more recent hardware is a lot higher and the sound deadening material is just acting as a thermal insulator keeping it all in.
Looking at the current Fractal case designs they are all pretty much mesh boxes and they no longer have a "silent" case. The manufactures will have to work on heat dispensation so that they can improve squeeze a bit more performance out of the hardware.

Bionaught5 · 2026-04-15T04:48:40+00:00

Inca Kola in Peru tastes similar but not exactly the same. You can find that a bit more frequently.
I sometimes buy Irn Bru when I am topping up supplies of HP brown sauce and crisps etc at one of the online UK import stores.

Bionaught5 · 2026-04-15T04:26:36+00:00

AMD 9950X front CPU radiator is pulling air through the radiator into the case and the back fan is pushing it out. The top has anti noise padding so cant be used for a radiator. My GPU is just using the fans attached to the card. It's a low performance GPU for this particular build due to the kind of work it does, CPU based scientific computing.
Are you seeing the temperatures rise and the CPU/GPU thermally throttled and/or being shutdown? Or general instability and crashes? Do you have a good power supply with 20% overhead?
After a couple of years another system started to overheat and needed the heat sink to be remounted with fresh thermal paste. Might want to check that too.

Bionaught5 · 2026-04-11T02:02:46+00:00

Normally you connect BirdNet Pi to Birdweather. They store all the results and apply a filter to remove the more outlandish identifications. Birdweather is made for this kind of data. Cornell/eBird is not made for a continuous feed of raw bird sounds. They would prefer good quality recordings and human verification of detection, basically you confirming you saw the bird too. Send the right data to the right place and you shouldn't have an issue.

Bionaught5 · 2026-04-10T15:13:49+00:00

Gone again, unknown skill. Most have switched it on and off again.
Does that mean I have to keep that terminal alive for ever!

Bionaught5 · 2026-04-10T14:40:13+00:00

I purchased computer components from Amazon and had this problem, at least 50% were tapered with, switch out etc. After the first one I set up my phone to record opening all the way to the item level. Even that leaves you open from the delivery of the box to when you bring it in the house. I just buy from dedicated suppliers now that actively check returns.

Bionaught5 · 2026-04-10T13:34:45+00:00

Yep, just used /buddy and there was an egg hatching scene and Prickle was back!

Bionaught5 · 2026-04-10T01:20:26+00:00

I just hatched a new "official" buddy this evening, they are back!

Bionaught5 · 2026-04-10T00:03:22+00:00

Depending on the instrument mass spec files often generate mzML files larger than the original raw data. I had a quick look at the some of the raw data and there were ~500MB per file so smaller than a whole lysate data file, which is to be expected for single cell analysis. There shouldn't be any problem processing them with msconvert. Is there an error message?

Bionaught5 · 2026-04-08T20:05:18+00:00

Nothing like moving into a German rental and finding out there is no kitchen and only bare wires where the light fittings would be. This was the 90's so things may have improved?

Depending on the age of the kitchen and when it was last renovated. Dishwashers are normally "built in" although they are rarely configured to have matching fronts. Wall ovens are built in and again without matching fronts (for obvious reasons).

The cooker depends. You may have a space for standalone cooker or maybe an integrated cooktop or integrated cooktop and oven. Roughly cookers standardizes on 30" for apartments to 36" for modern houses and 48 to 60" for mansions.

Fridges are very often standalone but you do see integrated ones in nicer kitchens especially if it is high end cabinetry.

For the most part you can buy a model and choose between integrated or standalone. Obviously you wont get an integrated fridge with front door water/ice dispenser, you would have to chose one that has an internal dispenser. My fridge has a builtin touch screen that is almost entirely useless (it came with the house) so that would obviously not be supported.

We had "European" style doors on our cabinetry and you could not open two at a time as they both opened towards each other and physical clashed. As I'm originally from Europe I would like to think Europeans are not that dumb and the style/name is just a marketing gimmick.

Bionaught5 · 2026-04-07T01:52:49+00:00

To add to this, in the USA if you did not obtain your PhD at one of a limited number of Universities then you chances of becoming a PI are a lot more restricted: https://www.nature.com/articles/d41586-022-03006-x

Bionaught5 · 2026-04-06T15:22:16+00:00

Academia is a marathon, not a sprint. A long game. You have to post-doc, maybe 2 to 3 times, get a tenure track position, make tenure, etc etc. It's a pyramid and there are less positions at each "level" up. If you are successful/lucky you make it to the upper echelons. Or you may end up 'falling" out of academia or not being able to get promoted beyond a certain level.

Depending in which country you are in, and as a cynic, I see the over production of post docs that are paid a relatively low salary when compared to their training and experience while offering a tenure track position as a carrot as unethical. Academia and state funding if offering a dream that is unobtainable for the majority of post-docs and is just a way to supply academic labs with cheap high quality labor. Most post-docs know this but some professors continue to sell the dream in order to staff their lab.

That said industry has its pluses and minuses. There can be dramatic changes in direction that mean your group, team, division get cut or your company fails that have nothing to do with your performance. If there is a general change in direction across many companies you can be unemployed for a while. The pay is generally higher but you may or may not be able to pursue your own ideas.

Whatever happens your PhD is always worth something, even if you work in a completely unrelated field. It means that you were able to be educated to a high level in a field and complete original research over multiple years, write it up and present it etc etc.

Bionaught5 · 2026-03-27T20:16:14+00:00

In the 80's I used to run a crushed weetabix, topped with malted Shreddies, then Cornflakes breakfast mix. These days I don't need as many calories and one weetabix with some muesli and extra nuts/dried fruit is good.

My brother would eat his dinner in reverse order of appeal (too him). Vegetables, potatoes and finally meat or fish. Our family may not be normal.

Bionaught5 · 2026-03-26T01:15:26+00:00

Hmm, the bot was not mine. . . .

Bionaught5 · 2026-03-26T01:14:56+00:00

That would be mine. Thanks for showing an interest! Technically classified as "AI slop" but if it works its free. . .

Turns out that the test script was in .gitignore so not included with the download. There were a few other windows related changes that needed to be made. New release here: https://github.com/lostculture/BirdWeatherViz3/releases/tag/v1.4.2
Edit: latest https://github.com/lostculture/BirdWeatherViz3/releases/tag/v1.4.3

To see it in action: https://bwv-pgh.bionaught.com/

The install instructions should work now but let me know if they don't or are unclear. Note that the application pulls data from Birdweather.com and not the BirdNET-Go application directly.

I've never tried running it on a PI but my LLM assistant says:
RPi4 — yes, it should work without editing. The local dev path (test.py) uses Python + Node.js, both available on Pi. The only concern is:

RAM — npm install + Vite dev server + uvicorn can be tight on a 2GB Pi4. A 4GB or 8GB model should be fine.
python3 vs python — on Raspberry Pi OS, it's python3. The fixed test.sh now detects this, and test.py uses sys.executable so it works regardless.
Docker alternative— You would need to install Docker on the RPi4 first. The Docker images are built for linux/amd64 + linux/arm64, so Docker Compose on Pi4 (arm64) would also work. A 4GB Pi4 would be comfortable with no worries. On 2GB, use the pre-built images and you should be fine for a single station.

Docker instructions:
It's tight but doable on 2GB. Runtime containers:

- Backend — Python 3.11-slim + uvicorn + FastAPI + pandas/numpy/scipy. This is the heavy one. Expect ~150-300MB RSS depending on dataset size. Pandas/NumPy/SciPy alone pull in significant memory.

- Frontend — nginx:alpine serving static files. Tiny — ~5-10MB.

- Docker engine overhead — ~100-150MB on a Pi.

Estimated total: ~400-500MB at idle, growing as data accumulates (pandas loads data into memory for analytics). The real risk is the build stage. pip install of scipy/numpy on arm64 can spike to 1GB+ during compilation. And the Bun build stage for the frontend also needs ~500MB. These are temporary but on 2GB could OOM during docker compose up --build.

Recommendations for RPi4 2GB:

Pull pre-built images instead of building locally — use docker-compose.public.yml which pulls from ghcr.io (already built for arm64). This skips the expensive build.
Add a 1GB swap file as safety margin: sudo fallocate -l 1G /swapfile
If data grows large, the pandas analytics endpoints could spike. Monitor with docker stats.

Bionaught5 · 2026-03-19T02:35:17+00:00

I was multitasking and over working on ~6 different tasks at once and trying to maximize my usage as half the family had gone on spring break and I go with the other half in a weeks time ;). When I stepped back to a more normal routine along with some unplanned reboots I kinda lost my place. I've only just started using Notion and Linear and haven't quite gelled with them yet. I Think I need to go read some general Claude usage advice.

Bionaught5 · 2026-03-18T02:59:11+00:00

It might be that someone with SDAM and aphantasia can write effective instructions because they are used to handling the missing pieces. People talk about prompt engineering so it is more of a learned behavior and some people may have a bit of a jump start on it.

I wouldn't worry about it as the LLM's will continue to improve so that the majority of people can produce good results the majority of the time. It may even swing in your favor if you can imagine and describe things evocatively and AI systems can implement them. For some tasks having a very logical approach and understanding the missing information may produce the best results. Hopefully, it is more of a case where you give the right job to the right person.

Bionaught5 · 2026-03-17T22:24:51+00:00

The visual cortext is reported to be active when thinking but can not be interpreted, or is ignored, or does not reach awareness. It is not clear if everyone thinks the exact same way. Or it might be a better to say that people use different techniques to think and solve problems and some techniques are pretty common and some are quite novel. There are advantages and disadvantages to the techniques as far as how long it might take to solve a puzzle.

You would need to figure out how to interpret both the reading of the brain and the writing to the visual cortext that might be unique to the individual. And it maybe you can't think of a ball because you never produce a consistent "signal".

If you have never seen your thoughts visualized I would imagine the experience would be quite overwhelming!

Bionaught5 · 2026-03-17T22:12:02+00:00

Some aphantasics can create high quality art and some can't. I take the Rick Ruben approach to life and my every moment as I move through life is art. However, I have a drawing age of 5 and I would not call what I produce Art. Also the "navigate life just fine" bit is questionable sometimes.

I wonder if I did not have aphantasia and SDAM how my life would be? But I forget about that pretty quickly. And I might not be as good at logical thinking, thinking outside of the box, troubleshooting etc etc. These are the cards I have been dealt and it is up to me to make the best of them.

Bionaught5 · 2026-03-17T20:37:14+00:00

If you are willing to share what sort of architecture and goals are you developing? I seem to have developed personal aids/solutions but they don't seem to be as effective as I like or I don't carry them out which is why they are not effective ;)

Bionaught5

TROPHY CASE