Episodes of the life of Blaise Pascal.
BLAST is a sequence alignment.
The NCBI free-to-use BLAST server: blast.ncbi.nlm.nih.gov/Blast.cgi. Having a centralized query server is fundamental, because the gain of sequence alignment really comes from having one huge database to link information together, which is best centralized.
- www.cell.com/cell/fulltext/S0092-8674(15)00568-1 2015. Using Genome-scale Models to Predict Biological Capabilities. Edward J. O'Brien, Jonathan M. Monk, Bernhard O. Palsson.
- www.quora.com/What-are-some-good-books-on-Escherichia-Coli-E-Coli
Size: 1-2 micrometers long and about 0.25 micrometer in diameter, so:
2 * 0.5 * 0.5 * 10e-18 and thus 0.5 micrometer square.Reference strain: E. Coli K-12 MG1655.
Genome:
- 4k genes
- 5 Mbps
- www.ncbi.nlm.nih.gov/genome/167
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/005/845/GCF_000005845.2_ASM584v2/GCF_000005845.2_ASM584v2_genomic.fna.gzwget -O NC_000913.3.fasta 'https://www.ncbi.nlm.nih.gov/search/api/sequence/NC_000913.3/?report=fasta'
Synthesis project: www.sciencemag.org/news/2016/08/biologists-are-close-reinventing-genetic-code-life
Omics modeling: www.ncbi.nlm.nih.gov/pmc/articles/PMC5611438/ Tools for Genomic and Transcriptomic Analysis of Microbes at Single-Cell Level Zixi Chen, Lei Chen, Weiwen Zhang.
This dude has done well.
Their crash system does not have an amazing user interface.
Tested on Ubuntu 21.10.
After something crashes, look under
/var/crash for a crash file, which helps to determine which package to report under on Launchpad.E.g. a file
/var/crash/_usr_sbin_gdm3.0.crash makes you want to file the bug under gdm at: bugs.launchpad.net/ubuntu/+source/gdm/+filebugThen, while reporting the bug, you want to give the developpers access to that Ubuntu's crash report system has already uploaded the
.crash file. But you can't publicly upload it because it contains memory dumps and could contain secret information. The way to do it is to look at the ID under:sudo cat /var/crash/_usr_sbin_gdm3.0.uploaded.crash for you, so you just have to confirm it and give the ID on the ticket.You can view a list of all your uploaded errors at:and each of those contain a link to:which you yourself cannot see.
xdg-open https://errors.ubuntu.com/user/$(sudo cat /var/lib/whoopsie/whoopsie-id)https://errors.ubuntu.com/oops/<.uloaded error id>askubuntu.com/questions/434431/how-can-i-read-a-crash-file-from-var-crash asks how to read the
.crash files.Running:splits it up into a few files, but does not make any major improvements.
sudo apport-unpack /var/crash/_usr_sbin_gdm3.0.crash /tmp/appapport-retracesudo apt install apport-retrace
sudo chmod 666 /var/crash/_usr_sbin_gdm3.0.crash
apport-retrace -g /var/crash/_usr_sbin_gdm3.0.crashTried:but then
echo "deb http://ddebs.ubuntu.com $(lsb_release -cs) main restricted universe multiverse" | sudo tee -a /etc/apt/sources.list.d/ddebs.list
echo -e "deb http://ddebs.ubuntu.com $(lsb_release -cs)-updates main restricted universe multiverse\ndeb http://ddebs.ubuntu.com $(lsb_release -cs)-proposed main restricted universe multiverse" | sudo tee -a /etc/apt/sources.list.d/ddebs.list
sudo apt install ubuntu-dbgsym-keyringsudo apt update fails with:E: The repository 'http://ddebs.ubuntu.com impish-security Release' does not have a Release file. Who are the developers that are making the most money through GitHub sponsors? Updated 2025-01-10 +Created 1970-01-01
Year 1 of the physics course of the University of Oxford Updated 2025-01-10 +Created 1970-01-01
This is something worth investigating!
Bibliography:
- 2023 www.uktech.news/foodtech/investors-lab-grown-meat-startups-regulation-20230216 mentions the company Ivy Farm
Paging makes it easier to compile and run two programs or threads at the same time on a single computer.
For example, when you compile two programs, the compiler does not know if they are going to be running at the same time or not.
So nothing prevents it from using the same RAM address, say,
0x1234, to store a global variable.And thread stacks, that must be contiguous and keep growing down until they overwrite each other, are an even bigger issue!
But if two programs use the same address and run at the same time, this is obviously going to break them!
Paging solves this problem beautifully by adding one degree of indirection:
(logical) ------------> (physical)
pagingWhere:
- logical addresses are what userland programs see, e.g. the contents of
rsiinmov eax, [rsi].They are often called "virtual" addresses as well. - physical addresses can be though of the values that go to physical RAM index wires.But keep in mind that this is not 100% true because of further indirections such as:
Compilers don't need to worry about other programs: they just use simple logical addresses.
As far as programs are concerned, they think they can use any address between 0 and 4GiB (2^32,
FFFFFFFF) on 32-bit systems.The OS then sets up paging so that identical logical addresses will go into different physical addresses and not overwrite each other.
This makes it much simpler to compile programs and run them at the same time.
Paging achieves that goal, and in addition:
- the switch between programs is very fast, because it is implemented by hardware
- the memory of both programs can grow and shrink as needed without too much fragmentation
- one program can never access the memory of another program, even if it wanted to.This is good both for security, and to prevent bugs in one program from crashing other programs.
Or if you like non-funny jokes:
Comparison between the Linux kernel userland memory virtualization and The Matrix
. Source. Is this RAM real?
If either PAE and PSE are active, different paging level schemes are used:
- no PAE and no PSE:
10 | 10 | 12 - no PAE and PSE:
10 | 22.22 is the offset within the 4Mb page, since 22 bits address 4Mb. - PAE and no PSE:
2 | 9 | 9 | 12The design reason why 9 is used twice instead of 10 is that now entries cannot fit anymore into 32 bits, which were all filled up by 20 address bits and 12 meaningful or reserved flag bits.The reason is that 20 bits are not enough anymore to represent the address of page tables: 24 bits are now needed because of the 4 extra wires added to the processor.Therefore, the designers decided to increase entry size to 64 bits, and to make them fit into a single page table it is necessary reduce the number of entries to 2^9 instead of 2^10.The starting 2 is a new Page level called Page Directory Pointer Table (PDPT), since it _points_ to page directories and fill in the 32 bit linear address. PDPTs are also 64 bits wide.cr3now points to PDPTs which must be on the fist four 4GB of memory and aligned on 32 bit multiples for addressing efficiency. This means that nowcr3has 27 significative bits instead of 20: 2^5 for the 32 multiples * 2^27 to complete the 2^32 of the first 4GB. - PAE and PSE:
2 | 9 | 21Designers decided to keep a 9 bit wide field to make it fit into a single page.This leaves 23 bits. Leaving 2 for the PDPT to keep things uniform with the PAE case without PSE leaves 21 for offset, meaning that pages are 2M wide instead of 4M.
Generalization of AlphaGo Zero that plays Go, Chess and shogi.
- www.science.org/doi/10.1126/science.aar6404 A general reinforcement learning algorithm that masters Chess, Shogi, and Go through self-play by Silver et al. (2018), published without source code
- www.quora.com/Is-there-an-Open-Source-version-of-AlphaZero-specifically-the-generic-game-learning-tool-distinct-from-AlphaGo
www.quora.com/Which-chess-engine-would-be-stronger-Alpha-Zero-or-Stockfish-12/answer/Felix-Zaslavskiy explains that it beat Stockfish 8. But then Stockfish was developed further and would start to beat it. We know this because although AlphaZero was closed source, they released the trained artificial neural network, so it was possible to replay AlphaZero at its particular stage of training.
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