How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Fisher Scientific UVP LM-26E Benchtop 2UV Transilluminator by 
Ciro Santilli 40 Updated 2025-07-16
Ciro Santilli 40 Updated 2025-07-16www.bidspotter.com/en-us/auction-catalogues/bscsur/catalogue-id-bscsur10011/lot-c6605b41-1a14-40e5-a255-a5c5000866e0 (archive) Cannot exact same product on official website, but here is a similar one: www.fishersci.co.uk/shop/products/lm-26-2uv-transilluminator/12382038 (archive).
The algorithmically minded will have noticed that paging requires associative array (like Java
Map of Python dict()) abstract data structure where:The single level paging scheme uses a simple array implementation of the associative array:and in C pseudo-code it looks like this:
- the keys are the array index
- this implementation is very fast in time
- but it is too inefficient in memory
linear_address[0] = physical_address_0
linear_address[1] = physical_address_1
linear_address[2] = physical_address_2
...
linear_address[2^20-1] = physical_address_NBut there another simple associative array implementation that overcomes the memory problem: an (unbalanced) k-ary tree.
Using a K-ary tree instead of an array implementation has the following trade-offs:
In C-pseudo code, a 2-level K-ary tree with and we have the following arrays:
K = 2^10 looks like this:level0[0] = &level1_0[0]
level1_0[0] = physical_address_0_0
level1_0[1] = physical_address_0_1
...
level1_0[2^10-1] = physical_address_0_N
level0[1] = &level1_1[0]
level1_1[0] = physical_address_1_0
level1_1[1] = physical_address_1_1
...
level1_1[2^10-1] = physical_address_1_N
...
level0[N] = &level1_N[0]
level1_N[0] = physical_address_N_0
level1_N[1] = physical_address_N_1
...
level1_N[2^10-1] = physical_address_N_Nand it still contains
2^10 * 2^10 = 2^20 possible keys.K-ary trees can save up a lot of space, because if we only have one key, then we only need the following arrays:
Man-made virus!
TODO: if we had cheap de novo DNA synthesis, how hard would it be to bootstrap a virus culture from that? github.com/cirosantilli/cirosantilli.github.io/issues/60
Is it easy to transfect a cell with the synthesized DNA, and get it to generate full infectious viral particles?
If so, then de novo DNA synthesis would be very similar to 3D printed guns: en.wikipedia.org/wiki/3D_printed_firearms.
It might already be possible to order dissimulated sequences online:
DNA replication is a key limiting factor of bacterial replication time by Ciro Santilli 40 Updated 2025-07-16
Ciro Santilli 40 Updated 2025-07-16TODO confirm, but looks like it, e.g. E. Coli starts DNA replication before the previous one finished.
The weird one, not directly coded in the genetic code.
Design software for synthetic biological circuit.
The input is in Verilog! Overkill?
Grouping their mouse brain projcts here.
Tutorial: Allen Developing Mouse Brain by Allen Institute (2014)
Source. "De novo" means "starting from scratch", that is: you type the desired sequence into a computer, and the synthesize it.
The "de novo" part is important, because it distinguishes this from the already well solved problem of duplicating DNA from an existing DNA template, which is what all our cells do daily, and which can already be done very efficiently in vitro with polymerase chain reaction.
Notably, the dream of most of those companies is to have a machine that sits on a lab bench, which synthesises whatever you want.
The initial main applications are likely going to be:but the real pipe dream is building and bootstraping entire artificial chromosomes
- polymerase chain reaction primers (determine which region will be amplified
- creating a custom sequence to be inserted in a plasmid, i.e. artificial gene synthesis
News coverage:
Nuclera eDNA enzymatic de novo DNA synthesis explanatory animation (2021)
Source. The video shows nicely how Nuclera's enzymatic DNA synthesis works:- they provide blocked nucleotides of a single type
- add them with the enzyme. They use a werid DNA polymerase called terminal deoxynucleotidyl transferase that adds a base at a time to a single stranded DNA strand rather than copying from a template
- wash everything
- do deblocking reaction
- and then repeat until done
It is quite mind blowing when you think about it, that the huge majority of your body's cells is essentially just there to support a tiny ammount of germline, which are the only cells that can actually pass on! It is fun to imagine the cell type tree for this, with a huge branching of somatic cells, and only a few germline going forward.
- www.quora.com/How-is-a-voice-transmitted-from-one-phone-to-another
- www.quora.com/How-many-wires-does-a-telephone-use/answer/Peter-Yardley-1
Basic analogue phones connected to the public exchange use two wires mainly arranged as a twisted pair to reduce noise. The voice signal is differential (the voltage in one wire equal and opposite to the other) biased above ground by 48V. Using a twisted pair reduces induced noise because the noise signal will induce an equal voltage in each wire and because the signal is transmitted as the difference the effect of the induced noise will be dramatically reduced.
Phone Intercom by Make (2014)
Source. This video illustrates will the incredible simplicity of the connection of a telephone system. Compare that to the relative complexity of wireless communication, which requires modulation.www.wholecellviz.org/viz.php awesome visualization of simtk, paper: www.ncbi.nlm.nih.gov/pmc/articles/PMC3413483/ A Whole-Cell Computational Model Predicts Phenotype from Genotype - 2013 - Jonathan R. Karr.
Followed up by the E. Coli Whole Cell Model by Covert Lab.
But one thing you should really know, as often mentioned in Power, Sex, Suicide by Nick Lane (2006): they are all eukaryotes.
Because prokaryotes are fundamentally unable to do phagocytosis, because they have a rigid cell wall. Changing cell shape at will requires a cytoskeleton.
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