In order to create a test user with password instead of peer authentication, let's create test user:
createuser -P user0
createdb user0-P makes it prompt for the users password.Alternatively, to create the password non-interactively stackoverflow.com/questions/42419559/postgres-createuser-with-password-from-terminal:Can't find a way using the
psql -c "create role NewRole with login password 'secret'"createuser helper.We can then login with that password with:which asks for the password we've just set, because the
psql -U user0 -h localhost-h option turns off peer authentication, and turns off password authentication.The password can be given non-interactively as shown at stackoverflow.com/questions/6405127/how-do-i-specify-a-password-to-psql-non-interactively with the
PGPASSWORD environment variable:PGPASSWORD=a psql -U user0 -h localhostNow let's create a test database which
user0 can access with an existing superuser account:createdb user0db0
psql -c 'GRANT ALL PRIVILEGES ON DATABASE user0db0 TO user0'We can check this permission with:which now contains:The permission letters are explained at:
psql -c '\l' List of databases
Name | Owner | Encoding | Collate | Ctype | Access privileges
-----------+----------+----------+-------------+-------------+-----------------------
user0db0 | ciro | UTF8 | en_GB.UTF-8 | en_GB.UTF-8 | =Tc/ciro +
| | | | | ciro=CTc/ciro +
| | | | | user0=CTc/cirouser0 can now do the usual table operations on that table:PGPASSWORD=a psql -U user0 -h localhost user0db0 -c 'CREATE TABLE table0 (int0 INT, char0 CHAR(16));'
PGPASSWORD=a psql -U user0 -h localhost user0db0 -c "INSERT INTO table0 (int0, char0) VALUES (2, 'two'), (3, 'three'), (5, 'five'), (7, 'seven');"
PGPASSWORD=a psql -U user0 -h localhost user0db0 -c 'SELECT * FROM table0;'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.
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.
Some glaring issues are listed at the horrors of Sequelize.
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:
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.
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.
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.
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.
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.jpg
MadyBobbyOffToCollege.jpg
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.jpgMessages:and:TODO actual Italy? Or some place named Italy in the US? One of the photos is from the First Lutheran church in Fargo, Nort Dacota.
Loraine.jpg"Loraine" on tx b4b8fe752a258f95b191b8c5426319ee0e8d41d5db53ea2ae18beed141cbb9bd, block 448352 (2017-01-15).
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
OpenWorm Sibernetic demo by Mike Vella (2013)
Source. Sibernetic adds a fluid dynamics solver for brain-in-the-loop simulation of C. elegans. Unlisted articles are being shown, click here to show only listed articles.