Neutron star Updated 2025-10-14
Neutron stars are cool. What weird objects!
Newton dot notation Updated 2025-07-16
Nintendo 64 Updated 2025-07-16
This is the one that hit Ciro Santilli the hardest, coming in at the point in which he started to discern between games and the real world a little better. His parents bought it for him during a trip to Disney World in Florida in 1996 (?), since electronics were much cheaper in the USA.
So as Ciro became older, and turned into a software engineer, he started to become more and more morbidly curious about "N64 internals": tool-assisted speedrun, how the devkit looks like, how games were developed for it, hardware leaks, etc.
Luckily Ciro's mind is not interested enough by that useless shit for Ciro to seriously study it himself. But that's what YouTube is for, right? Why do useless stuff when other more useless people can do it for you?
E. Coli K-12 MG1655 gene thrL Updated 2025-07-16
The first gene in the E. Coli K-12 MG1655 genome. Remember however that bacterial chromosome is circular, so being the first doesn't mean much, how the choice was made: Section "E. Coli genome starting point".
Part of E. Coli K-12 MG1655 operon thrLABC.
At only 65 bp, this gene is quite small and boring. For a more interesting gene, have a look at the next gene, e. Coli K-12 MG1655 gene thrA.
Does something to do with threonine.
This is the first in the sequence thrL, thrA, thrB, thrC. This type of naming convention is quite common on related adjacent proteins, all of which must be getting transcribed into a single RNA by the same promoter. As mentioned in the analysis of the KEGG entry for e. Coli K-12 MG1655 gene thrA, those A, B and C are actually directly functionally linked in a direct metabolic pathway.
We can see that thrL, A, B, and C are in the same transcription unit by browsing the list of promoter at: biocyc.org/group?id=:ALL-PROMOTERS&orgid=ECOLI. By finding the first one by position we reach; biocyc.org/ECOLI/NEW-IMAGE?object=TU0-42486.
E. Coli K-12 MG1655 operon thrLABC Updated 2025-07-16
Contains the genes: e. Coli K-12 MG1655 gene thrL, e. Coli K-12 MG1655 gene thrA, e. Coli K-12 MG1655 gene thrB and e. Coli K-12 MG1655 gene thrC, all of which have directly linked functionality.
We can find it by searching for the species in the BioCyc promoter database. This leads to: biocyc.org/group?id=:ALL-PROMOTERS&orgid=ECOLI.
That page lists several components of the promoter, which we should try to understand!
Some of the transcription factors are proteins:
After the first gene in the codon, thrL, there is a rho-independent termination. By comparing:we understand that the presence of threonine or isoleucine variants, L-threonyl and L-isoleucyl, makes the rho-independent termination become more efficient, so the control loop is quite direct! Not sure why it cares about isoleucine as well though.
E. Coli Whole Cell Model by Covert Lab Default run variant Updated 2025-07-16
The default run variant, if you don't pass any options, just has the minimal growth conditions set. What this means can be seen at condition.
Notably, this implies a growth medium that includes glucose and salt. It also includes oxygen, which is not strictly required, but greatly benefits cell growth, and is of course easier to have than not have as it is part of the atmosphere!
But the medium does not include amino acids, which the bacteria will have to produce by itself.
NIST Atomic Spectra Database Updated 2025-07-16
Searching for "H" for hydrogen leads to: physics.nist.gov/cgi-bin/ASD/lines1.pl?spectra=H&limits_type=0&low_w=&upp_w=&unit=1&submit=Retrieve+Data&de=0&format=0&line_out=0&en_unit=0&output=0&bibrefs=1&page_size=15&show_obs_wl=1&show_calc_wl=1&unc_out=1&order_out=0&max_low_enrg=&show_av=2&max_upp_enrg=&tsb_value=0&min_str=&A_out=0&intens_out=on&max_str=&allowed_out=1&forbid_out=1&min_accur=&min_intens=&conf_out=on&term_out=on&enrg_out=on&J_out=on
NIST Post-Quantum Cryptography Standardization Updated 2025-07-16
It was mind blowing when in 2022, after several years of selection, one of the 7 finalists was broken on a classical computer, not even in a quantum computer! news.ycombinator.com/item?id=30466063 | eprint.iacr.org/2022/214 Breaking Rainbow Takes a Weekend on a Laptop by Ward Beullens. Dude announced he had a break a few days before submission: twitter.com/WardBeullens/status/1492780462028300290 On Twitter. He's so young. Epic.
Edit: and then, after the third round, things were a bit unclear, so they made a fourth round with 4 choices out of the 7 from round 3, and in August 2022 one of the four was broken again on a classic CPU!!! OMG: arstechnica.com/information-technology/2022/08/sike-once-a-post-quantum-encryption-contender-is-koed-in-nist-smackdown/
NLab Updated 2025-07-16
Decent encyclopedia of mathematics. Not much motivation, mostly statements though.
Created by:
Nobel disease Updated 2025-09-11
The Eighth Day of Creation has a related quote:
In a conversation a few weeks earlier at the faculty club of the Massachusetts Institute of Technology, a couple of biologists had speculated whether Pauling, whose recent popular book on the benefits to health and sanity of massive doses of vitamin C was stacked in display near the entrance of the M.I.T. bookstore, was showing signs of what one of the men called "old scientist's disease" - which they defined as what happens to great men when they grow beyond the psychological reach of the salutary system by which scientists blow the whistle on one another's mistakes.
The Nobel Prize Winners With Crazy Theories by Qxir
. Source. E. Coli Whole Cell Model by Covert Lab Publications Updated 2025-07-16
Unfortunately, due to lack of one page to rule them all, the on-Git tree publication list is meager, some of the most relevant ones seems to be:
- 2021 open access review paper: journals.asm.org/doi/full/10.1128/ecosalplus.ESP-0001-2020 "The E. coli Whole-Cell Modeling Project". They should just past that stuff in a README :-) The article mentions that it is a follow up to the previous M. genitalium whole cell model by Covert lab. Only 43% of known genes modelled at this point however, a shame.
- 2020 under Science paywall: www.science.org/doi/10.1126/science.aav3751 "Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation"
E. Coli Whole Cell Model by Covert Lab Run variants Updated 2025-07-16
It would be boring if we could only simulate the same condition all the time, so let's have a look at the different boundary conditions that we can apply to the cell!
We are able to alter things like the composition of the external medium, and the genome of the bacteria, which will make the bacteria behave differently.
The variant selection is a bit cumbersome as we have to use indexes instead of names, but one you know what you are doing, it is fine.
Of course, genetic modification is limited only to experimentally known protein interactions due to the intractability of computational protein folding and computational chemistry in general, solving those would bsai.
Edge (graph) Updated 2025-07-16
Edit war Updated 2025-07-16
Bitcoin block Updated 2025-07-16
Bitcoin miner inscription Updated 2025-07-16
Secure Shell Updated 2025-07-16
HTTP Updated 2025-07-16
Ciro Santilli's hardware Lenovo ThinkPad P14s gen4 amd Updated 2025-07-16
Bought: November 2023 during Black Friday sale for £1,323.00 to be Ciro Santilli's main personal laptop.
Six years after, and we are 2x on every key spec (except processor Hz ;-) at about 1/2 the price and 1/2 the weight (though smaller 14" screen for greater portability), so not bad! Customized to max out each hardware spec:
Specs:
- Processor: AMD Ryzen 7 PRO 7840U Processor (3.30 GHz up to 5.10 GHz)
- Graphic Card: Integrated GraphicsThe Ubuntu 23.10 "About system GUI describes its graphics as: Radeon 780M Graphics × 16, which e.g. www.techpowerup.com/gpu-specs/radeon-780m.c4020 documents as running the RDNA 3 microarchitecture.
- Operating System: No Operating System selected upgrade
- Operating System Language: No Operating System Languag eselected upgrade
- Microsoft Productivity Software: None
- Memory: 64 GB LPDDR5X-6400MHz (Soldered)selected upgrade. Specs at: www.lenovo.com/gb/en/p/accessories-and-software/memory-and-storage/memory-and-storage-hard-drives/4xb1d04758 quotes "64 Gbps", i.e. 8 GB/s.
dd count=1M if=/dev/zero of=tmpgives only 255 MB/s however. - Solid State Drive: 2 TB SSD M.2 2280 PCIe Gen4 Performance TLC Opalselected upgrade
- Display: 14" WUXGA (1920 x 1200), IPS, Anti-Glare, Touch, 45%NTSC, 300 nits, 60Hz
- Camera: 1080P FHD RGB/IR Hybrid with Microphone
- Color: Thunder Black
- Factory Color Calibration: No Factory Color Calibration
- Wireless: Qualcomm Wi-Fi 6E NFA725A 2x2 AX & Bluetooth® 5.1 or above
- Integrated Mobile Broadband: No Wireless WAN
- Ethernet: Wired Ethernet
- Near Field Communication: No NFC
- Fingerprint Reader: Fingerprint Reader
- Keyboard: Black - English (EU)selected upgrade
- Battery: 4 Cell Li-Polymer 52.5Whselected upgrade
- Power Cord: 65W USB-C Slim 90% PCC 3pin AC Adapter - UKselected upgrade
- Electronic Privacy Filter: No ePrivacy Filter
- Adobe Elements: None
- Adobe Acrobat: None
- Adobe Creative Cloud: None
- Security Software: None
- Cloud Security Software: No Cloud Security Software
- Warranty: 3 Year Courier or Carry-in
Identifiers:
- Ethernet MAC address: fc:5c:ee:24:fb:b4
- Wi-Fi MAC address: 04:7b:cb:cc:1b:10
Upon arrival:
Buy research:
- www.phoronix.com/review/thinkpad-p14s-gen4 says Ubuntu running fine
- Intel vs amd: the Intel ones could come with a discrete rtx A500 GPU. GPU likely makes laptop heavier and less power efficient. And both have basically the same benchmark which is crazy:So the only downside is not being able to run CUDA.
- thought about Yoga or other Ultrabook options, but 2x price at same specs, so nah...
Log:
2024-01-17: firmware update:Actually fixed performance mode: askubuntu.com/questions/604720/setting-to-high-performance/1343879#1343879
Vendor: LENOVO
Version: R2FET36W (1.16 )
Release Date: 10/24/2023 FFmpeg filter graph Updated 2025-07-16
Filter graphs are a thing of great beauty. What an amazingly obscure domain-specific language, but which can produce striking results with very little!!!
A quick example from stackoverflow.com/questions/59551013/how-to-generate-stereo-sine-wave-using-ffmpeg-with-different-frequencies-for-eac/77730492#77730492 illustrates some of the fundamentals:
ffplay -autoexit -nodisp -f lavfi -i '
sine=frequency=500[a];
sine=frequency=1000[b];
[a][b]amerge, atrim=end=2
' +--------+
[sine=frequency=500]--->[a]-->| |
| amerge |-->[atrim]-->[output]
[sine=frequency=1000]-->[b]-->| |
+--------+So we see the following syntax patterns:
sine,amergeandatrimare filterssine=frequency=500: the first=says "araguments follow";: separates statements[a],[b]: sets the name of an edge,: creates unnamed edge between filters that have one input and one output
A list of all filters can be obtained ith:and parameters for a single filter can be obtained with:Related question: stackoverflow.com/questions/69251087/in-ffmpeg-command-line-how-to-show-all-filter-settings-and-their-parameters-bef
ffmpeg -filtersffmpeg --help filter=sineTODO dump graph to ASCII art? trac.ffmpeg.org/wiki/FilteringGuide#Visualizingfilters mentions a
-dumpgraph option, but haven't managed to use it yet.Bibliography:
- ffmpeg.org/ffmpeg-filters.html official documentation
- trac.ffmpeg.org/wiki/FilteringGuide some handy tips from the FFMpeg Wiki
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