Cirists,

No closed form solution, but good approximation that can be calculated by hand with the Hartree-Fock method, see hartree-Fock method for the helium atom.

Bibliography:

With all this ready, we opened the Nanopore flow cell, which is the 500 dollar consumable piece that goes in the sequencer.

We then had to pipette the final golden Eppendorf into the flow cell. My anxiety levels were going through the roof: Figure 4. "Oxford nanopore MinION flow cell pipette loading.".

At this point bio people start telling lab horror stories of expensive solutions being spilled and people having to recover them from fridge walls, or of how people threw away golden Eppendorfs and had to pick them out of trash bins with hundreds of others looking exactly the same etc. (but also how some discoveries were made like this). This reminded Ciro of: youtu.be/89UNPdNtOoE?t=919 Alfred Maddock's plutonium spill horror story.

Luckily this time, it worked out!

We then just had to connect the MinION to the computer, and wait for 2 days.

During this time, the DNA would be sucked through the pores.

As can be seen from Video 1. "Oxford Nanopore MinION software channels pannel on Mac." the software tells us which pores are still working.

Pores go bad sooner or later randomly, until there are none left, at which point we can stop the process and throw the flow cell away.

48 hours was expected to be a reasonable time until all pores went bad, and so we called it a day, and waited for an email from the PuntSeq team telling us how things went.

We reached a yield of 16 billion base pairs out of the 30Gbp nominal maximum, which the bio people said was not bad.

KCNK2, also known as K2P2.1 or TREK-1, is a gene that encodes for a member of the two-pore domain potassium channel family. This channel plays a significant role in regulating the electrical activity of neurons and other cells by allowing potassium ions to flow across the cell membrane, which is crucial for maintaining the resting membrane potential and contributing to the repolarization phase of action potentials.

Because Ciro's a software engineer, and he's done enough staring in computers for a lifetime already, and he believes in the power of Git, he didn't pay much attention to this part ;-)

According to the eLife paper, the code appears to have been uploaded to: github.com/d-j-k/puntseq. TODO at least mention the key algorithms used more precisely.

Ciro can however see that it does present interesting problems!

Because it was necessary to wait for 2 days to get our data, the workshop first reused sample data from previous collections done earlier in the year to illustrate the software.

First there is some signal processing/machine learning required to do the base calling, which is not trivial in the Oxford Nanopore, since neighbouring bases can affect the signal of each other. This is mostly handled by Oxford Nanopore itself, or by hardcore programmers in the field however.

After the base calling was done, the data was analyzed using computer programs that match the sequenced 16S sequences to a database of known sequenced species.

This is of course not just a simple direct string matching problem, since like any in experiment, the DNA reads have some errors, so the program has to find the best match even though it is not exact.

The PuntSeq team would later upload the data to well known open databases so that it will be preserved forever! When ready, a link to the data would be uploaded to: www.puntseq.co.uk/data

Protocols are the biologist term for "recipe".

I found that a lot of biology comes down to this: get the right recipe, follow it well even though you don't understand all the proprietary details, and pray.

The Ainu creation myth is part of the indigenous Ainu culture of Japan, particularly associated with the northern regions such as Hokkaido. The Ainu have a rich oral tradition, and their mythological stories illustrate their understanding of the world, nature, and their relationship with the divine. In Ainu creation myths, the world is often described as being formed from the sea. One notable myth starts with the god of the sea, who created the first land.

The Aircraft Reactor Experiment (ARE) was a project developed by the United States in the late 1950s to explore the feasibility of using nuclear power for aircraft propulsion. Conducted by the Los Alamos National Laboratory and the Atomic Energy Commission, the primary objective of the experiment was to determine if a nuclear reactor could be designed for use in an aircraft engine and if it could provide sufficient thrust and power for sustained flight.

An intransitive game is a type of game or sport where the relationship between the players or strategies does not follow a simple transitive order. In a transitive game, if Player A defeats Player B and Player B defeats Player C, then Player A is expected to defeat Player C. However, in an intransitive game, this pattern does not hold; the outcomes can be cyclical or non-linear.

Gelenbevi Ismail Efendi, also known as Gelenbevi Ismail or simply Ismail Efendi, was a prominent figure in the late Ottoman Empire, particularly noted for his contributions to the field of education, especially in relation to modernizing and reforming the educational system in Turkey. He is particularly associated with the title of "Gelenbevi," which refers to his origins in the town of Gelenbe in present-day Turkey.

The Atiyah conjecture on configurations is a mathematical statement concerning the representation theory of algebraic structures, specifically related to bundles of vector spaces over topological spaces. It is named after the British mathematician Michael Atiyah, who has made significant contributions to several areas of mathematics, including topology, geometry, and mathematical physics.

Fractional-order control refers to a control strategy that utilizes fractional-order calculus, which extends traditional integer-order calculus to non-integer (fractional) orders. This approach allows engineers and control theorists to model and control dynamic systems with a greater degree of flexibility and complexity than traditional integer-order controllers.

A function tree is a visual representation that illustrates how various functions or components of a system relate to one another. It is often used in project management, software development, and organizational contexts to break down complex tasks, processes, or systems into simpler components or functions.

Highly Optimized Tolerance (HOT) is a theoretical framework related to complex systems, particularly in the fields of statistical physics and complex networks. The concept refers to systems that exhibit a balance between stability and adaptability, allowing them to endure a high degree of variability and external perturbations while maintaining their core functionalities. In HOT systems, a high level of tolerance to flaws, errors, or disruptions is achieved through optimization of the underlying structures or processes.

Hyperstability is a concept often discussed in control theory and dynamical systems, primarily in the context of system stability and robustness. It generally refers to a system's ability to maintain stable behavior under a wider set of conditions than traditional stability concepts would account for. In mathematical terms, hyperstability typically implies that a system can tolerate certain types of perturbations or variations in parameters while still returning to a stable equilibrium.

L-stability is a concept related to numerical analysis, particularly in the context of solving ordinary differential equations (ODEs) and partial differential equations (PDEs) using numerical methods. It is a property of a numerical method that ensures stable behavior when applied to stiff problems. In essence, L-stability refers to the ability of a numerical method to dampen apparent oscillations or instabilities that arise from stiff components of the solution, particularly as the step size tends to zero.

The Monodomain model is a mathematical representation used in cardiac electrophysiology to simulate the electrical activity of heart tissue. It simplifies the complex, three-dimensional structures of cardiac cells and tissues into a more manageable framework. In the Monodomain model, the heart tissue is treated as a continuous medium through which electrical impulses can propagate. Key features of the Monodomain model include: 1. **Continuity**: Cardiac tissue is treated as a continuous medium rather than a collection of discrete cells.