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E. Coli K-12 MG1655 origin of replication by 
Ciro Santilli 35 Updated 2025-01-22 +Created 1970-01-01
Ciro Santilli 35 Updated 2025-01-22 +Created 1970-01-01Note that this is not the conventional starting point for gene numbering: Section "E. Coli genome starting point".
By Tagkopoulos lab at University of California, Davies.
- www.nature.com/articles/ncomms13090 Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli (2016)
- www.sciencedaily.com/releases/2016/10/161027173552.htm
reconstruction/ecoli/flat/condition/nutrient/minimal.tsvcontains 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 NaNreconstruction/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 NaNNaNin theupper moundlikely 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.tsvwithminimal_no_glucose.tsvAMMONIUM: 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/000000_basal.tsv
reconstruction/ecoli/flat/reconstruction/ecoli/flat/condition/timeseries/` contains sequences of conditions for each time. For example: *contains:"time (units.s)" "nutrients" 0 "minimal"which means just usingreconstruction/ecoli/flat/condition/nutrient/minimal.tsvuntil 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/nutrientTimeSeriesLabelwhich contains just000000_basal. *reconstruction/ecoli/flat/reconstruction/ecoli/flat/condition/timeseries/000001_cut_glucose.tsvis 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.tsvcontains 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"]conditionrefers to entries inreconstruction/ecoli/flat/condition/condition_defs.tsvnutrientsrefers to entries underreconstruction/ecoli/flat/condition/nutrient/, e.g.reconstruction/ecoli/flat/condition/nutrient/minimal.tsvorreconstruction/ecoli/flat/condition/nutrient/minimal_plus_amino_acids.tsvgenotype 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
\Include and \x and working on dynamic website by Ciro Santilli 35 Updated 2025-01-22 +Created 1970-01-01This was the major final step of fully integrating the OurBigBook CLI into the dynamic website (besides fixing some nasty bugs that escaped passed by me from the previous newsletter).
The implementation was done by "simply" reusing scopes, e.g.:
cirosantilli's article about mathematics has scope cirosantilli and full ID cirosantilli/mathematics.That on the website is equivalent to a local file structure of:
cirodown/mathematics.bigbThe problem is that a bunch of subdirectory scope operations were broken locally as well, as it simply wasn't a major use case. But now they became a major use case for , so I fixed them.
E. Coli starts DNA replication before the previous one finished by Ciro Santilli 35 Updated 2025-01-22 +Created 1970-01-01
Ciro Santilli 35 Updated 2025-01-22 +Created 1970-01-01 Total Blackout Cassette Roller Blind from Order Blinds Online by Ciro Santilli 35 Updated 2025-01-22 +Created 1970-01-01
Ciro Santilli 35 Updated 2025-01-22 +Created 1970-01-01This is my first working setup, done in a rental friendly way without drilling. I am sure that it is possible to do it cheaper, better and with less work, but it the first one that worked for me, so I will document it.
Cost: 150 Dollars for a relatively large 130 x 158 cm window. They do not sell for windows much larger than that.
Bought from www.orderblinds.co.uk on June 2019.
My window faces East, and in summer the sun rises at around 5AM here, and I am a bit light sensitive and was getting destroyed.
This setup, together with:is good enough to allow me to sleep properly, which is priceless.
- the existing sliding curtains which were not enough on their own
- a cheap and comfortable Figure 2. "GO Travel sleeping mask" from the Pharmacy
Demonstration if everything goes exceptionally well:
How to fit a Total Blackout Cassette Roller Blind by Order Blinds Online (2016)
Source. The actual product name appears to be Bloc Blinds or BlocOut, Order Blinds appears to whitelabel them.However, not all will necessarily be fun and games as in that YouTube video, especially if you are doing it for the first time, and the main point of this article is to make you aware of that.
The first problem is that you may have to remove existing useless "privacy blinds" from the way, which can mean putting effort into learning how they work and, has a risk of damaging the property. So be smart and get a chair and a second person to help you out!
Next, fitting the side rails is not going to be that easy. The thing has to be tight to block the light, right? Careful not to scratch the bottom sill!
Then you will notice that, like in the video at youtu.be/cTVVe7codw4?t=106, you are expected to screw the side rails to the bottom wood / plastic sill of the window, which is not rental acceptable! So I didn't to that, but together with the black tape that I will mention next, it held well enough.
The top part requires hammering nails as shown on the video: youtu.be/cTVVe7codw4?t=24 but this is generally rental acceptable, and you can fill the holes afterwards.
Once you have the setup in place, it is likely that there will be some light gaps still, because it is basically impossible to make such large objects fit perfectly. This was especially true for the top of the window, but also for the sides, so I just used some black tape
So I added some wide (50mm) Figure 4. "Diall PVC repairing black tape" between the blind and the wall to completely seal off the light.
Diall PVC repairing black tape
. Source. This tape made things dark and was durable, but note at Section "Removal wall damage review" that it pulled bits of the plaster out with it during removal. I've since learnt about the existence of "painter’s tape"/masking tape, that might have been a better idea to protect the walls when pulling the tape off. It is worth noting that some of the painter's tape do come with a maximum number of days before you can pull them off, presumably after which wall damage becomes a possibility, e.g. Ciro saw one rateed 14 days.There is still some leakage at the bottom however, which cannot be taped. I mitigated that a bit by putting some black T-shirts on the bottom window sill, and together with the pre-existing rental curtain, it was enough.
Another minor annoyance is that parts of the blind cloth sometimes slip out of the conduit holes in the aluminium side bars. For this reason, I have to always open and close slowly and carefully. But if it does happen, fully opening and closing carefully has solved the problem.
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