A device that modifies photon polarization.
As mentioned at Video "Quantum Mechanics 9b - Photon Spin and Schrodinger's Cat II by ViaScience (2013)", it can be modelled as a bra.
Source code: github.com/sequelize/sequelize
Some usage examples under: Section "Sequelize example".
As of 2021, this library is extremely painful to use. It does feel semi-mature, but there are just too much horrible things going on;
- the documentation is a bit messy and misses a lot of stuff. The examples are often too short, and it is hard to understand what specific options they are talking about do because they lack clear input/expected output pairs. Examples:
- the implementation has several inelegant/unintuitive annoyances/requirements of code repetition that drive you mad.The association API feels notably bad, it took a few days for Ciro Santilli to learn to do what he considers "basic" association operations, knowledge which he dumped to: stackoverflow.com/questions/22958683/how-to-implement-many-to-many-association-in-sequelize/67973948#67973948See also: how to decide if an ORM is good?.
- bugs are piling up. It appears that many key devs left, and current maintainers are just not being able to keep up.And they have setup a stupid bot that closes every thread automatically after a few days, what's the point... valid bugs are being closed due to this, and it is impossible to distinguish what is solved and what isn't since everything gets closed.
Some glaring issues are listed at the horrors of Sequelize.
Present in chormosome 4.
Good video showing what appears to be the adenine nucleotide translocator. although they don't use that name, instead saying ADP/ATP carrier.
The video also briefly depicts the ATP synthase and the mitochondrial phosphate carrier protein.
essential metabolism for a minimal cell (2019) mentions:
- NCBI: www.ncbi.nlm.nih.gov/nuccore/CP014940.1
- 473 genes
phenomena.nationalgeographic.com/2016/04/21/we-built-the-worlds-simplest-cell-but-dunno-how-it-works/ likely talks about it.
Stuff built on top:
This is a good read: quantumai.google/hardware/datasheet/weber.pdf May 14, 2021. Their topology is so weird, not just a rectangle, one wonders why! You get different error rates in different qubits, it's mad.
Google Sycamore Weber quantum computer connectivity graph
. Weber is a specific processor of the Sycamore family. From this we see it clearly that qubits are connected to at most 4 other qubits, and that the full topology is not just a simple rectangle.Besides
sh_type == SHT_RELA, there also exists SHT_REL, which would have section name .text.rel (not present in this object file).Those represent the same
struct, but without the addend, e.g.:typedef struct {
Elf64_Addr r_offset;
Elf64_Xword r_info;
} Elf64_Rela;The ELF standard says that in many cases the both can be used, and it is just a matter of convenience.
To modify the nutrients as a function of time, with To select a time series we can use something like:As mentioned in
python runscripts/manual/runSim.py --variant nutrientTimeSeries 25 25python runscripts/manual/runSim.py --help, nutrientTimeSeries is one of the choices from github.com/CovertLab/WholeCellEcoliRelease/blob/7e4cc9e57de76752df0f4e32eca95fb653ea64e4/models/ecoli/sim/variants/__init__.py#L5725 25 means to start from index 25 and also end at 25, so running just one simulation. 25 27 would run 25 then 26 and then 27 for example.The timeseries with index 25 is so we understand that it starts with extra amino acids in the medium, which benefit the cell, and half way through those are removed at time 1200s = 20 minutes. We would therefore expect the cell to start expressing amino acid production genes exactly at that point.
reconstruction/ecoli/flat/condition/timeseries/000025_cut_aa.tsv and contains"time (units.s)" "nutrients"
0 "minimal_plus_amino_acids"
1200 "minimal"nutrients likely means condition in that file however, see bug report with 1 1 failing: github.com/CovertLab/WholeCellEcoliRelease/issues/24When we do this the simulation ends in:so we see that the doubling time was faster than the one with minimal conditions of
Simulation finished:
- Length: 0:34:23
- Runtime: 0:08:030:42:49, which makes sense, since during the first 20 minutes the cell had extra amino acid nutrients at its disposal.The output directory now contains simulation output data under
out/manual/nutrientTimeSeries_000025/. Let's run analysis and plots for that:python runscripts/manual/analysisVariant.py &&
python runscripts/manual/analysisCohort.py --variant 25 &&
python runscripts/manual/analysisMultigen.py --variant 25 &&
python runscripts/manual/analysisSingle.py --variant 25We can now compare the outputs of this run to the default
wildtype_000000 run from Section "Install and first run".out/manual/plotOut/svg_plots/massFractionSummary.svg: because we now have two variants in the sameout/folder,wildtype_000000andnutrientTimeSeries_000025, we now see a side by side comparision of both on the same graph!The run variant where we started with amino acids initially grows faster as expected, because the cell didn't have to make it's own amino acids, so growth is a bit more efficient.Then, at 20 minutes, which is about 0.3 hours, we see that the cell starts growing a bit less fast as the slope of the curve decreases a bit, because we removed that free amino acid supply.
Figure 1. Minimal condition vs amino acid cut mass fraction plot. Source. From fileout/manual/plotOut/svg_plots/massFractionSummary.svg.
The following plots from under
out/manual/wildtype_000000/000000/{generation_000000,nutrientTimeSeries_000025}/000000/plotOut/svg_plots have been manually joined side-by-side with:for f in out/manual/wildtype_000000/000000/generation_000000/000000/plotOut/svg_plots/*; do
echo $f
svg_stack.py \
--direction h \
out/manual/wildtype_000000/000000/generation_000000/000000/plotOut/svg_plots/$(basename $f) \
out/manual/nutrientTimeSeries_000025/000000/generation_000000/000000/plotOut/svg_plots/$(basename $f) \
> tmp/$(basename $f)
done
Amino acid counts
. Source. aaCounts.svg:- default: quantities just increase
- amino acid cut: there is an abrupt fall at 20 minutes when we cut off external supply, presumably because it takes some time for the cell to start producing its own
External exchange fluxes of amino acids
. Source. aaExchangeFluxes.svg:- default: no exchanges
- amino acid cut: for all graphs except phenylalanine (PHE), either the cell was intaking the AA (negative flux), and that intake goes to 0 when the supply is cut, or the flux is always 0.For PHE however, the flux is at all times, except shortly after the cut. Why? And why there was no excretion on the default conditions?
mRNA count of highly expressed mRNAs
. Source. From file 
expression_rna_03_high.svg. Each of the entries is a gene using the conventional gene naming convention of xyzW, e.g. here's the BioCyc for the first entry, tufA: biocyc.org/gene?orgid=ECOLI&id=EG11036, which comments Elongation factor Tu (EF-Tu) is the most abundant protein in E. coli.
In E. coli, EF-Tu is encoded by two genes, tufA and tufB
External exchange fluxes
. Source. 
mediaExcange.svg: this one is similar to aaExchangeFluxes.svg, but it also tracks other substances. The color version makes it easier to squeeze more substances in a given space, but you lose the shape of curves a bit. The title seems reversed: red must be excretion, since that's where glucose (GLC) is.The substances are different between the default and amino acid cut graphs, they seem to be the most exchanged substances. On the amino cut graph, first we see the cell intaking most (except phenylalanine, which is excreted for some reason). When we cut amino acids, the uptake of course stops.
From this we see that there is a convention of naming promoters as protein name + p, e.g. the first gene in E. Coli K-12 MG1655 promoter thrLp encodes protein
thrL.It is also possible to add numbers after the TODO why 6 and 7? There don't appear to be 1, 2, etc.
p, e.g. at biocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=PM0-45989 we see that the protein zur has two promoters:zurp6zurp7
This is the first of many love declarations and mentions EMBII makes of his partner Chiharu! This came just one day afte the very first uploads of the system.
ILoveYouMore.jpgMessage:Note that she's Japanese and not really bond, it's hair dye.
My Dearest Chiharu....I Love you more. <3 Eric
OurWedding.jpgMessage:
My Dearest Chiharu, I will love you forever. Taken Aug 6th 2014 in Ipswich, SD.
MadyBobbyOffToCollege.jpgAssociated messages:
A #father could not ask for more perfect daughters. I #Love you both so much!! <3 PaMy oldest daugher moves into the dorms tomorrow morning. Dear Mady, You are forever my baby. <3 PaEMBII's daughter, Maddy Bobby, (presumably not with Chiharu) is going off to college! Sadface.
Chiharu EMBII and The Atom Sea say Happy Halloween.jpgMessage:so their location was: en.wikipedia.org/wiki/Fargo,_North_Dakota
#Chiharu #embii & the #AtomSea #Fargo #ND
Chiharu.jpg
Loraine.jpg"Loraine" on tx b4b8fe752a258f95b191b8c5426319ee0e8d41d5db53ea2ae18beed141cbb9bd, block 448352 (2017-01-15).
Photographer unknown, but presumably EMBII's father or another close family member.
Message:
In loving memory of Loraine Elizabeth WhiteEMBII's mum died :-(
Cost: ~0.001 BTC ~ $0.80 at the time.
SatoFamily.jpgThis one gives Chiharu's full identity with picture basically. Message:so presumably Chiharu's full name is Chiharu Sato.
The Sato Family Arrives from Japan! Taken Aug 2. 2014 in Minneapolis MN. (Keiko, Chiharu, Hideaki, Katsuhiko) Now preparing for the Sato / Bobby Great American Vacation!!
More from their vacation:
More EMBII social media:
- bitfossil.com/5bfd6eab2df2eb615dd72172408e02e07fddba2f00fed9b80cd66c0b115ee03d/index.htm "Found on Mady's camera", EMBII wearing a funny red suit and drinking orange juice
High level simulation only, no way to get from DNA to worm! :-) Includes:
- nervous system
- muscle system
3D body viewer at: browser.openworm.org/ TODO can you click on a cell to get its name?
OpenWorm Sibernetic demo by Mike Vella (2013)
Source. Sibernetic adds a fluid dynamics solver for brain-in-the-loop simulation of C. elegans.When TLB is filled up, older addresses are overwritten. Just like CPU cache, the replacement policy is a potentially complex operation, but a simple and reasonable heuristic is to remove the least recently used entry (LRU).
With LRU, starting from state:adding
valid linear physical
----- ------ --------
> 1 00003 00005
1 00007 00009
1 00009 00001
1 0000B 000030000D -> 0000A would give: valid linear physical
----- ------ --------
1 0000D 0000A
> 1 00007 00009
1 00009 00001
1 0000B 00003 There are unlisted articles, also show them or only show them.