Ciro Santilli (@cirosantilli) - Newly followed articles

ELF Hello World Tutorial / .rel.text by

Ciro Santilli 37  Updated 2025-07-01  +Created 1970-01-01

Besides sh_type == SHT_RELA, there also exists SHT_REL, which would have section name .text.rel (not present in this object file).

Those represent the same struct, but without the addend, e.g.:

typedef struct {
    Elf64_Addr  r_offset;
    Elf64_Xword r_info;
} Elf64_Rela;

The ELF standard says that in many cases the both can be used, and it is just a matter of convenience.

 Read the full article

Continent by

Ciro Santilli 37  Updated 2025-07-01  +Created 1970-01-01

 Read the full article

E. Coli Whole Cell Model by Covert Lab / Time series run variant by

Ciro Santilli 37  Updated 2025-07-01  +Created 1970-01-01

 View more

To modify the nutrients as a function of time, with To select a time series we can use something like:

python runscripts/manual/runSim.py --variant nutrientTimeSeries 25 25

As mentioned in python runscripts/manual/runSim.py --help, nutrientTimeSeries is one of the choices from github.com/CovertLab/WholeCellEcoliRelease/blob/7e4cc9e57de76752df0f4e32eca95fb653ea64e4/models/ecoli/sim/variants/__init__.py#L57

25 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 reconstruction/ecoli/flat/condition/timeseries/000025_cut_aa.tsv and contains

"time (units.s)" "nutrients"
0 "minimal_plus_amino_acids"
1200 "minimal"

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.

nutrients likely means condition in that file however, see bug report with 1 1 failing: github.com/CovertLab/WholeCellEcoliRelease/issues/24

When we do this the simulation ends in:

Simulation finished:
 - Length: 0:34:23
 - Runtime: 0:08:03

so we see that the doubling time was faster than the one with minimal conditions of 0:42:49, 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 25

We 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 same out/ folder, wildtype_000000 and nutrientTimeSeries_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.
Then, at 20 minutes, which is about 0.3 hours, we see that the cell starts growing a bit less fast as the slope of the curve decreases a bit, because we removed that free amino acid supply.
Figure 1.
Minimal condition vs amino acid cut mass fraction plot
. Source. From file out/manual/plotOut/svg_plots/massFractionSummary.svg.

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

Figure 2.
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

Figure 3.
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.
For PHE however, the flux is at all times, except shortly after the cut. Why? And why there was no excretion on the default conditions?

Figure 4.
Evaluation time
. Source. `evaluationTime.svg`: this has nothing to do with biology, but it is rather a profile of the program runtime. We can see that the simulation gets slower and slower as time passes, presumably because there are more and more molecules to simulate.

Figure 5.
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.
and
In E. coli, EF-Tu is encoded by two genes, tufA and tufB
. What they seem to mean is that tufA and tufB are two similar molecules, either of which can make up the EF-Tu of the E. Coli, which is an important part of translation.

Figure 6.
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.

 Read the full article

E. Coli K-12 MG1655 promoter by

Ciro Santilli 37  Updated 2025-07-01  +Created 1970-01-01

 View more

biocyc.org/group?id=:ALL-PROMOTERS&orgid=ECOLI

From this we see that there is a convention of naming promoters as protein name + p, e.g. the first gene in E. Coli K-12 MG1655 promoter thrLp encodes protein thrL.

It is also possible to add numbers after the p, e.g. at biocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=PM0-45989 we see that the protein zur has two promoters:

zurp6
zurp7

TODO why 6 and 7? There don't appear to be 1, 2, etc.

 Read the full article

Cool data embedded in the Bitcoin blockchain / ILoveYouMore.jpg by

Ciro Santilli 37  Updated 2025-07-01  +Created 1970-01-01

 View more

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.

Figure 1.
`ILoveYouMore.jpg`
. Source.
Message:
My Dearest Chiharu....I Love you more. <3 Eric
Note that she's Japanese and not really bond, it's hair dye.
tx affbac1bfde690c1fabd60812d046c911b2882038a42b18a4d2e7cb50e989604, block 272593 (2013-12-02)

Figure 2.
`OurWedding.jpg`
. Source.
Message:
My Dearest Chiharu, I will love you forever. Taken Aug 6th 2014 in Ipswich, SD.
393f4d3b3b0ac018b6483f58390ac0d56adf5f70f68e846af7d745359ca14bf9, block 314482 (2014-08-07)

Figure 3.
`MadyBobbyOffToCollege.jpg`
. Source.
Associated messages:
A #father could not ask for more perfect daughters. I #Love you both so much!! <3 Pa
My oldest daugher moves into the dorms tomorrow morning. Dear Mady, You are forever my baby. <3 Pa
EMBII's daughter, Maddy Bobby, (presumably not with Chiharu) is going off to college! Sadface.
tx 937f70bf641ccabaf623772367df64bd867ad44c53fd227d01f2662e74aeacbf (2016-01-28)

Figure 4.
`Chiharu EMBII and The Atom Sea say Happy Halloween.jpg`
. Source.
Message:
#Chiharu #embii & the #AtomSea #Fargo #ND
so their location was: en.wikipedia.org/wiki/Fargo,_North_Dakota
tx 966e090d19172b6a6f988b1f1d32141492349279cedd2a436d7a2143c67d7af4, block 401592 (2016-03-07)

Figure 5.
`Chiharu.jpg`
. Source.
Messages:
mini camera test #Wilson #Chiharu #embii #Broadway #Fargo #ND
and:
"Trip to Italy" Mini Digital Camera N. Broadway, Fargo, ND 49°F
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.
tx 366bfe5b135ffc52894f67f53936ec2ec693cad61c64e52f1624ef22815d4de7, block 401592 (2016-03-07)

Figure 6.
`Loraine.jpg`
. Source.
"Loraine" on tx b4b8fe752a258f95b191b8c5426319ee0e8d41d5db53ea2ae18beed141cbb9bd, block 448352 (2017-01-15).
Photographer unknown, but presumably EMBII's father or another close family member.
Message:
In loving memory of Loraine Elizabeth White
EMBII's mum died :-(
Cost: ~0.001 BTC ~ $0.80 at the time.

Figure 7.
`SatoFamily.jpg`
. Source.
94ba41330b7bfb1e6528497e3b1dd21018c63a7f163e0bc9281c21cc1071462e, block 450516 (2017-01-29)
This one gives Chiharu's full identity with picture basically. Message:
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!!
so presumably Chiharu's full name is Chiharu Sato.
More from their vacation:
bitfossil.com/fa15ac78927bf9a4a99c259f554b4c24715f69e548aeea8a8f5552b0215ce028/ yellowstone.jpg

More EMBII social media:

bitfossil.com/5bfd6eab2df2eb615dd72172408e02e07fddba2f00fed9b80cd66c0b115ee03d/index.htm "Found on Mady's camera", EMBII wearing a funny red suit and drinking orange juice

 Read the full article

Ionic bond by

Ciro Santilli 37  Updated 2025-07-01  +Created 1970-01-01

 Read the full article

OpenWorm by

Ciro Santilli 37  Updated 2025-07-01  +Created 1970-01-01

 View more

openworm.org

Whole organism simulation of C. elegans.

High level simulation only, no way to get from DNA to worm! :-) Includes:

nervous system
muscle system

3D body viewer at: browser.openworm.org/ TODO can you click on a cell to get its name?

Video 1.

OpenWorm Sibernetic demo by Mike Vella (2013)

Source. Sibernetic adds a fluid dynamics solver for brain-in-the-loop simulation of C. elegans.

 Read the full article

f-orbital by

Ciro Santilli 37  Updated 2025-07-01  +Created 1970-01-01

 Read the full article

Fermentation by

Ciro Santilli 37  Updated 2025-07-01  +Created 1970-01-01

 Read the full article

x86 Paging Tutorial / TLB replacement policy by

Ciro Santilli 37  Updated 2025-07-01  +Created 1970-01-01

 View more

When TLB is filled up, older addresses are overwritten. Just like CPU cache, the replacement policy is a potentially complex operation, but a simple and reasonable heuristic is to remove the least recently used entry (LRU).

With LRU, starting from state:

  valid  linear  physical
  -----  ------  --------
> 1      00003   00005
  1      00007   00009
  1      00009   00001
  1      0000B   00003

adding 0000D -> 0000A would give:

  valid  linear  physical
  -----  ------  --------
  1      0000D   0000A
> 1      00007   00009
  1      00009   00001
  1      0000B   00003

 Read the full article

x86 Paging Tutorial / Kernel vs process memory layout by

Ciro Santilli 37  Updated 2025-07-01  +Created 1970-01-01

 View more

The Linux Kernel reserves two zones of virtual memory:

one for kernel memory
one for programs

The exact split is configured by CONFIG_VMSPLIT_.... By default:

on 32-bit:

the bottom 3/4 is program space: 00000000 to BFFFFFFF

the top 1/4 is kernel memory: C0000000 to FFFFFFFF, like this:

------------------ FFFFFFFF
Kernel
------------------ C0000000
------------------ BFFFFFFF


Process


------------------ 00000000

on 64-bit: currently only 48-bits are actually used, split into two equally sized disjoint spaces. The Linux kernel just assigns:
- the bottom part to processes 00000000 00000000 to 008FFFFF FFFFFFFF
- the top part to the kernel: FFFF8000 00000000 to FFFFFFFF FFFFFFFF, like this:
  ------------------ FFFFFFFF Kernel ------------------ C0000000 (not addressable) ------------------ BFFFFFFF Process ------------------ 00000000

Kernel memory is also paged.

In previous versions, the paging was continuous, but with HIGHMEM this changed.

There is no clear physical memory split: stackoverflow.com/questions/30471742/physical-memory-userspace-kernel-split-on-linux-x86-64

 Read the full article

x86 Paging Tutorial / Identity mapping by

Ciro Santilli 37  Updated 2025-07-01  +Created 1970-01-01

 View more

FFFFF 000 points to its own physical address FFFFF 000. This kind of translation is called an "identity mapping", and can be very convenient for OS-level debugging.

 Read the full article

x86 Paging Tutorial / Why not a balanced tree by

Ciro Santilli 37  Updated 2025-07-01  +Created 1970-01-01

 View more

Learned readers will ask themselves: so why use an unbalanced tree instead of balanced one, which offers better asymptotic times en.wikipedia.org/wiki/Self-balancing_binary_search_tree?

Likely:

the maximum number of entries is small enough due to memory size limitations, that we won't waste too much memory with the root directory entry
different entries would have different levels, and thus different access times
tree rotations would likely make caching more complicated

 Read the full article

Electromagnetic radiation by