Topics (119k) Articles (119k) Users (287) Discussions (237) Comments (383) Files (715) New article
Contains the path to the dynamic loader, i.e.
/lib64/ld-linux-x86-64.so.2 in Ubuntu 18.10. Explained at: stackoverflow.com/questions/8040631/checking-if-a-binary-compiled-with-static/55664341#55664341Contains a lot of different flag masks.
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/contains sequences of conditions for each time. For example:reconstruction/ecoli/flat/reconstruction/ecoli/flat/condition/timeseries/000000_basal.tsvcontains:which means just using"time (units.s)" "nutrients" 0 "minimal"reconstruction/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.pyreconstruction/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
The default run variant, if you don't pass any options, just has the minimal growth conditions set. What this means can be seen at condition.
Notably, this implies a growth medium that includes glucose and salt. It also includes oxygen, which is not strictly required, but greatly benefits cell growth, and is of course easier to have than not have as it is part of the atmosphere!
But the medium does not include amino acids, which the bacteria will have to produce by itself.
E. Coli Whole Cell Model by Covert Lab Time series run variant by 
Ciro Santilli 40 Updated 2025-07-16
Ciro Santilli 40 Updated 2025-07-16To 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.
Note that this is not the conventional starting point for gene numbering: Section "E. Coli genome starting point".
As of 2021, last updated 2016, and python 3.5 appears to be mandatory or else:which apparently broke in 3.6: stackoverflow.com/questions/41343263/provide-classcell-example-for-python-3-6-metaclass and
RuntimeError: __class__ not set defining 'AbstractBaseUser' as <class 'django.contrib.auth.base_user.AbstractBaseUser'>. Was __classcell__ propagated to type.__new__?pyenv install fails on Ubuntu 20.10, so... fuck. Workarounds at:but am I in the mood considering that the ancient Django version would require an immediate port anyways? Repo is at Django 1.0, while newest is now already Django 3. The Rails one is broken for the same reason. Fuck 2.
Ciro Santilli really likes this dude, because Ciro really likes simulation.
Cool data embedded in the Bitcoin blockchain ILoveYouMore.jpg by Ciro Santilli 40 Updated 2026-04-05
Ciro Santilli 40 Updated 2026-04-05This 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.org/root/5bfd6eab2df2eb615dd72172408e02e07fddba2f00fed9b80cd66c0b115ee03d/index.htm "Found on Mady's camera", EMBII wearing a funny red suit and drinking orange juice
Cool data embedded in the Bitcoin blockchain Nelson-Mandela.jpg by Ciro Santilli 40 Updated 2026-04-05
Ciro Santilli 40 Updated 2026-04-05bitfossil.org/root/78f0e6de0ce007f4dd4a09085e649d7e354f70bc7da06d697b167f353f115b8e/ in block 273536 (2013-12-07).
This is one of the earliest AtomSea & EMBII uploads.
Nelson-Mandela.jpg"There is nothing like returning to a place that remains unchanged to find the ways in which you yourself have altered." - Nelson Mandela Nelson Rolihlahla Mandela was a South African anti-apartheid revolutionary, politician and philanthropist who served as President of South Africa from 1994 to 1999. - Wikipedia Born: July 18, 1918, Mvezo, South Africa Died: December 5, 2013.
Often just called collimated light due to the collimator being the main procedure to obtain it.
However, you move very far away from the source, e.g. the Sun, you also get essentially parallel light.
Pinned article: Introduction to the OurBigBook Project
Welcome to the OurBigBook Project! Our goal is to create the perfect publishing platform for STEM subjects, and get university-level students to write the best free STEM tutorials ever.
Everyone is welcome to create an account and play with the site: ourbigbook.com/go/register. We belive that students themselves can write amazing tutorials, but teachers are welcome too. You can write about anything you want, it doesn't have to be STEM or even educational. Silly test content is very welcome and you won't be penalized in any way. Just keep it legal!
Intro to OurBigBook
. Source. We have two killer features:
- topics: topics group articles by different users with the same title, e.g. here is the topic for the "Fundamental Theorem of Calculus" ourbigbook.com/go/topic/fundamental-theorem-of-calculusArticles of different users are sorted by upvote within each article page. This feature is a bit like:
- a Wikipedia where each user can have their own version of each article
- a Q&A website like Stack Overflow, where multiple people can give their views on a given topic, and the best ones are sorted by upvote. Except you don't need to wait for someone to ask first, and any topic goes, no matter how narrow or broad
This feature makes it possible for readers to find better explanations of any topic created by other writers. And it allows writers to create an explanation in a place that readers might actually find it.
Figure 1. Screenshot of the "Derivative" topic page. View it live at: ourbigbook.com/go/topic/derivativeVideo 2. OurBigBook Web topics demo. Source. - local editing: you can store all your personal knowledge base content locally in a plaintext markup format that can be edited locally and published either:This way you can be sure that even if OurBigBook.com were to go down one day (which we have no plans to do as it is quite cheap to host!), your content will still be perfectly readable as a static site.
- to OurBigBook.com to get awesome multi-user features like topics and likes
- as HTML files to a static website, which you can host yourself for free on many external providers like GitHub Pages, and remain in full control
Figure 2. You can publish local OurBigBook lightweight markup files to either OurBigBook.com or as a static website.
Figure 3. Visual Studio Code extension installation.
Figure 5. . You can also edit articles on the Web editor without installing anything locally. Video 3. Edit locally and publish demo. Source. This shows editing OurBigBook Markup and publishing it using the Visual Studio Code extension. 
- Infinitely deep tables of contents:
All our software is open source and hosted at: github.com/ourbigbook/ourbigbook
Further documentation can be found at: docs.ourbigbook.com
Feel free to reach our to us for any help or suggestions: docs.ourbigbook.com/#contact