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.
There is value in tutorials written by early pioneers of the field by Ciro Santilli 40 Updated 2025-07-16
Ciro Santilli 40 Updated 2025-07-16Everyone is beginner when the field is new, and there is value in tutorials written by beginners.
For example, Ciro Santilli felt it shocking how direct and satisfying Richard Feynman's scientific vulgarization of quantum electrodynamics were, e.g. at: Richard Feynman Quantum Electrodynamics Lecture at University of Auckland (1979), and that if he had just assumed minimal knowledge of mathematics, he was about to give a full satisfactory picture in just a few hours.
Other supporters of this:
- Ron Maimon: the same also applies to early original papers of the field, not just tutorials
- Dean Kamen: quick mention at: fi.edu/en/awards/laureates/dean-kamen, but a better longer mention on Dreamer (2020), nearby section from trailer: youtu.be/Cj2VKVJKf1I?t=16
And most important of all: you should not start learning phenomena by reading the from first principles derivation.
Instead, you should see what happens in experiments, and how matches some known formula (which hopefully has been derived from first principles).
Only open the boxes (understand from first principles derivation) if the need is felt!
E.g.:
- you don't need to understand everything about why SQUID devices have their specific I-V curve curve. You have to first of all learn what the I-V curve would be in an experiment!
- you don't need to understand the fine details of how cavity magnetrons work. What you need to understand first is what kind of microwave you get from what kind of input (DC current), and how that compares to other sources of microwaves
- lasers: same
Physics is all about predicting the future. If you can predict the future with an end result, that's already predicting the future, and valid.
Starting in the 2019 redefinition of the SI base units, the elementary charge is assigned a fixed number, and the Ampere is based on it and on the second, which is beautiful.
This choice is not because we attempt to count individual electrons going through a wire, as it would be far too many to count!
Rather, it is because because there are two crazy quantum mechanical effects that give us macroscopic measures that are directly related to the electron charge. www.nist.gov/si-redefinition/ampere/ampere-quantum-metrology-triangle by the NIST explains that the two effects are:
- quantum Hall effect, which has discrete resistances of type:for integer values of .
- Josephson effect, used in the Josephson voltage standard. With the Inverse AC Josephson effect we are able to produce:per Josephson junction. This is about 2 microvolt / GHz, where GHz is a practical input frequency. Video "The evolution of voltage metrology to the latest generation of JVSs by Alain Rüfenacht" mentions that a typical operating frequency is 20 GHz.But this is possible to implement in a single chip with existing micro fabrication techniques, and is exactly what the Josephson voltage standard does!
Those effect work because they also involve dividing by the Planck constant, the fundamental constant of quantum mechanics, which is also tiny, and thus brings values into a much more measurable order of size.
The Roland GR-300 is a guitar synthesizer that was introduced in the late 1970s. It is notable for its ability to convert guitar signal into control voltages to synthesize sound, allowing guitarists to produce a wide range of tones and effects that are typically associated with synthesizers, rather than traditional guitar sounds.
A speaker terminal is a connector or binding point on a speaker where audio cables are attached to enable the transmission of sound signals from an amplifier or audio source to the speaker. Speaker terminals can vary in design and type, but they generally fall into a few common categories: 1. **Binding Posts**: These are typically found on higher-end speakers and allow the use of banana plugs, spade connectors, or bare wire. They offer a secure and reliable connection.
Bernie Krause is a prominent American musician, bioacoustician, and soundscape ecologist known for his work in the field of natural sound and the acoustic environment. He has been a pioneer in recording and studying the sounds of various ecosystems, including forests, wetlands, and oceans. Through his work, Krause has emphasized the importance of natural soundscapes and their role in understanding biodiversity and environmental health.
South African bioinformaticians are scientists and researchers who specialize in the field of bioinformatics within South Africa. Bioinformatics is an interdisciplinary field that combines biology, computer science, mathematics, and statistics to analyze and interpret biological data, particularly genetic and genomic information. In South Africa, bioinformaticians may work in various sectors, including academic institutions, research organizations, healthcare, agriculture, and biotechnology companies.
South African statisticians refer to individuals engaged in the field of statistics within South Africa. They may work in various sectors such as academia, government, healthcare, finance, and private industry, utilizing statistical methods to collect, analyze, interpret, and present data. South Africa has a vibrant community of statisticians, with various institutions and organizations dedicated to the advancement of statistical science. The South African Statistical Association (SASA) is one example, serving as a professional body for statisticians in the country.
Speck Electronics is a company known for designing and manufacturing various electronic devices and accessories. While they are particularly recognized for their mobile phone cases and protective accessories, they may also produce other types of consumer electronics. Their products typically focus on combining functionality with style, offering consumers choices that cater to both aesthetic and practical needs. For the most accurate and up-to-date information, it's advisable to visit the official Speck Electronics website or check recent news sources.
Spectral Band Replication (SBR) is a technique used in audio coding and compression, particularly in the context of lossy compression formats like AAC (Advanced Audio Codec). The primary goal of SBR is to enhance the perceived audio quality while keeping the file size relatively small. ### How it Works: 1. **High-Frequency Extension**: SBR is primarily used to reconstruct high-frequency content that can be difficult to encode at lower bit rates.
Variable-Rate Multimode Wideband (VR-MMWB) is a communication technology concept used in various high-speed data transmission applications, including wireless communications and optical networks. The term can encompass a range of techniques and methodologies designed to enhance the capabilities of multimode (MM) transmission systems to adaptively adjust data rates based on current network conditions or user requirements.
The Zeppelin is a line of speaker systems designed by Bowers & Wilkins, known for their high-quality audio equipment. The Zeppelin speakers are particularly notable for their distinctive design and performance, catering specifically to iPod and iPhone users. The original model was released in 2007, featuring a unique oval shape and a dock for Apple devices, which allowed users to play music directly from their iPods or iPhones.
Soviet computer scientists refers to individuals involved in the field of computer science and computing technologies during the Soviet Union era (1922-1991). This group includes a variety of researchers, engineers, and academics who contributed to the development of theoretical foundations of computer science, programming languages, computer architecture, and various applications of computing.
As of my last knowledge update in October 2021, there is no widely known concept, theory, or person specifically referred to as "Denis Higgs." It might refer to a lesser-known individual or be a misspelling or variation of "Higgs," which is often associated with the Higgs boson—a particle in physics that is part of the Standard Model and was discovered in 2012.
Donald Livingstone is a mathematician known for his work in various areas of mathematics, particularly in connection to mathematical logic, set theory, and related fields. He has made contributions to the understanding of mathematical structures and has been involved in teaching and research activities. Specific details about his work might also include publications and his role in mathematical education.
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 3. Visual Studio Code extension installation.
Figure 4. Visual Studio Code extension tree navigation.
Figure 5. Web editor. 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.Video 4. OurBigBook Visual Studio Code extension editing and navigation demo. Source. 
- 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