On Ubuntu 20.10 PostgreSQL 12.6, login with
psql
on my default username without sudo fails with: stackoverflow.com/questions/11919391/postgresql-error-fatal-role-username-does-not-existThis is the one that worked on Ubuntu 21.04: stackoverflow.com/questions/11919391/postgresql-error-fatal-role-username-does-not-exist/38444152#38444152Explanation:
sudo -u postgres createuser -s $(whoami)
createdb $(whoami)
You can now run shows that peer authentication is available to all users apparently:
psql
without any password. This works without password due to peer authentication:sudo cat /etc/postgresql/12/main/pg_hba.conf
local all postgres peer
# TYPE DATABASE USER ADDRESS METHOD
# "local" is for Unix domain socket connections only
local all all peer
List users:output:
psql -c '\du'
List of roles
Role name | Attributes | Member of
-------------+------------------------------------------------------------+-----------
ciro | Superuser, Create role, Create DB | {}
owning_user | | {}
postgres | Superuser, Create role, Create DB, Replication, Bypass RLS | {}
Delete user later on:
psql -c 'DROP USER username;'
Help toplevel:
help
List supported SQL commands:
\h
Show syntax for one type of command:
\h SELECT
List all databases:which shows:
psql -c '\l'
Name | Owner | Encoding | Collate | Ctype | Access privileges
-------------+----------+----------+-------------+-------------+-----------------------
ciro | postgres | UTF8 | en_GB.UTF-8 | en_GB.UTF-8 |
postgres | postgres | UTF8 | en_GB.UTF-8 | en_GB.UTF-8 |
template0 | postgres | UTF8 | en_GB.UTF-8 | en_GB.UTF-8 | =c/postgres +
| | | | | postgres=CTc/postgres
template1 | postgres | UTF8 | en_GB.UTF-8 | en_GB.UTF-8 | =c/postgres +
| | | | | postgres=CTc/postgres
testdb0 | postgres | UTF8 | en_GB.UTF-8 | en_GB.UTF-8 |
(6 rows)
If you didn't give a database from the command line e.g.:you can do that afterwards with:
psql
\c testdb0
Let's create a table and test that it is working:
psql testdb0 -c 'CREATE TABLE table0 (int0 INT, char0 CHAR(16));'
List tables, no special tables:gives:
psql testdb0 -c '\dt'
List of relations
Schema | Name | Type | Owner
--------+--------+-------+-------
public | table0 | table | ciro
(1 row)
View table schema: stackoverflow.com/questions/109325/postgresql-describe-tableoutput:
psql testdb0 -c '\d+ table0'
Table "public.table0"
Column | Type | Collation | Nullable | Default | Storage | Stats target | Description
--------+---------------+-----------+----------+---------+----------+--------------+-------------
int0 | integer | | | | plain | |
char0 | character(16) | | | | extended | |
Insert some data into it and get the data out:output:
psql testdb0 -c "INSERT INTO table0 (int0, char0) VALUES (2, 'two'), (3, 'three'), (5, 'five'), (7, 'seven');"
psql testdb0 -c 'SELECT * FROM table0;'
int0 | char0
------+------------------
2 | two
3 | three
5 | five
7 | seven
(4 rows)
Delete the table:
psql testdb0 -c 'DROP TABLE table0;'
An optical multiplexer!
This section discusses the pre-photon understanding of the polarization of light. For the photon one see: photon polarization.
People were a bit confused when experiments started to show that light might be polarized. How could a wave that propages through a 3D homgenous material like luminiferous aether have polarization?? Light would presumably be understood to be analogous to a sound wave in 3D medium, which cannot have polarization. This was before Maxwell's equations, in the early 19th century, so there was no way to know.
Who are the developers that are making the most money through GitHub sponsors? by
Ciro Santilli 35 Updated 2025-04-18 +Created 1970-01-01
Got it working as mentioned at: github.com/cirosantilli/feathers-chat/tree/sequelize-pg
Bibliography:
There's also a
heroku
branch at: github.com/feathersjs/feathers-chat/tree/heroku, but it also seems to use NeDB? So you can have a filesystem in Heroku? Doesn't seem so: stackoverflow.com/questions/42775418/heroku-local-persistent-storagegothinkster/realworld implementations based on Express.js.
History of the electromagnetic theory of light by
Ciro Santilli 35 Updated 2025-04-18 +Created 1970-01-01
reconstruction/ecoli/flat/condition/nutrient/minimal.tsv
contains the nutrients in a minimal environment in which the cell survives:If we compare that to"molecule id" "lower bound (units.mmol / units.g / units.h)" "upper bound (units.mmol / units.g / units.h)" "ADP[c]" 3.15 3.15 "PI[c]" 3.15 3.15 "PROTON[c]" 3.15 3.15 "GLC[p]" NaN 20 "OXYGEN-MOLECULE[p]" NaN NaN "AMMONIUM[c]" NaN NaN "PI[p]" NaN NaN "K+[p]" NaN NaN "SULFATE[p]" NaN NaN "FE+2[p]" NaN NaN "CA+2[p]" NaN NaN "CL-[p]" NaN NaN "CO+2[p]" NaN NaN "MG+2[p]" NaN NaN "MN+2[p]" NaN NaN "NI+2[p]" NaN NaN "ZN+2[p]" NaN NaN "WATER[p]" NaN NaN "CARBON-DIOXIDE[p]" NaN NaN "CPD0-1958[p]" NaN NaN "L-SELENOCYSTEINE[c]" NaN NaN "GLC-D-LACTONE[c]" NaN NaN "CYTOSINE[c]" NaN NaN
reconstruction/ecoli/flat/condition/nutrient/minimal_plus_amino_acids.tsv
, we see that it adds the 20 amino acids on top of the minimal condition:so we guess that"L-ALPHA-ALANINE[p]" NaN NaN "ARG[p]" NaN NaN "ASN[p]" NaN NaN "L-ASPARTATE[p]" NaN NaN "CYS[p]" NaN NaN "GLT[p]" NaN NaN "GLN[p]" NaN NaN "GLY[p]" NaN NaN "HIS[p]" NaN NaN "ILE[p]" NaN NaN "LEU[p]" NaN NaN "LYS[p]" NaN NaN "MET[p]" NaN NaN "PHE[p]" NaN NaN "PRO[p]" NaN NaN "SER[p]" NaN NaN "THR[p]" NaN NaN "TRP[p]" NaN NaN "TYR[p]" NaN NaN "L-SELENOCYSTEINE[c]" NaN NaN "VAL[p]" NaN NaN
NaN
in theupper mound
likely means infinite.We can try to understand the less obvious ones:ADP
: TODOPI
: TODOPROTON[c]
: presumably a measure of pHGLC[p]
: glucose, this can be seen by comparingminimal.tsv
withminimal_no_glucose.tsv
AMMONIUM
: ammonium. This appears to be the primary source of nitrogen atoms for producing amino acids.CYTOSINE[c]
: hmmm, why is external cytosine needed? Weird.
reconstruction/ecoli/flat/reconstruction/ecoli/flat/condition/timeseries/
contains sequences of conditions for each time. For example:reconstruction/ecoli/flat/reconstruction/ecoli/flat/condition/timeseries/000000_basal.tsv
contains:which means just using"time (units.s)" "nutrients" 0 "minimal"
reconstruction/ecoli/flat/condition/nutrient/minimal.tsv
until infinity. That is the default one used byrunSim.py
, as can be seen from./out/manual/wildtype_000000/000000/generation_000000/000000/simOut/Environment/attributes/nutrientTimeSeriesLabel
which contains just000000_basal
.reconstruction/ecoli/flat/reconstruction/ecoli/flat/condition/timeseries/000001_cut_glucose.tsv
is more interesting and contains:so we see that this will shift the conditions half-way to a condition that will eventually kill the bacteria because it will run out of glucose and thus energy!"time (units.s)" "nutrients" 0 "minimal" 1200 "minimal_no_glucose"
Timeseries can be selected with--variant nutrientTimeSeries X Y
, see also: run variants.We can use that variant with:VARIANT="condition" FIRST_VARIANT_INDEX=1 LAST_VARIANT_INDEX=1 python runscripts/manual/runSim.py
reconstruction/ecoli/flat/condition/condition_defs.tsv
contains lines of form:"condition" "nutrients" "genotype perturbations" "doubling time (units.min)" "active TFs" "basal" "minimal" {} 44.0 [] "no_oxygen" "minimal_minus_oxygen" {} 100.0 [] "with_aa" "minimal_plus_amino_acids" {} 25.0 ["CPLX-125", "MONOMER0-162", "CPLX0-7671", "CPLX0-228", "MONOMER0-155"]
condition
refers to entries inreconstruction/ecoli/flat/condition/condition_defs.tsv
nutrients
refers to entries underreconstruction/ecoli/flat/condition/nutrient/
, e.g.reconstruction/ecoli/flat/condition/nutrient/minimal.tsv
orreconstruction/ecoli/flat/condition/nutrient/minimal_plus_amino_acids.tsv
genotype perturbations
: there aren't any in the file, but this suggests that genotype modifications can also be incorporated heredoubling time
: TODO experimental data? Because this should be a simulation output, right? Or do they cheat and fix doubling by time?active TFs
: this suggests that they are cheating transcription factors here, as those would ideally be functions of other more basic inputs
Ciro Santilli really likes this dude, because Ciro really likes simulation.
If you pass parallel light.
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