Quantum systems engineering Research group of the University of Oxford by 
Ciro Santilli 34 Updated 2024-12-15 +Created 1970-01-01
Ciro Santilli 34 Updated 2024-12-15 +Created 1970-01-01 Program the Raspberry Pi Pico W with MicroPython from Thonny by Ciro Santilli 34 Updated 2024-12-15 +Created 1970-01-01
Ciro Santilli 34 Updated 2024-12-15 +Created 1970-01-01With 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.
Scientific Industries Inc. Vortex-Genie 2 by Ciro Santilli 34 Updated 2024-12-15 +Created 1970-01-01
Ciro Santilli 34 Updated 2024-12-15 +Created 1970-01-01 Fisher Scientific UVP LM-26E Benchtop 2UV Transilluminator by Ciro Santilli 34 Updated 2024-12-15 +Created 1970-01-01
Ciro Santilli 34 Updated 2024-12-15 +Created 1970-01-01www.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).
Apparently, DC current comes in, and microwaves come out.
TODO: sample power efficiently of this conversion and output spectrum of this conversion on some cheap device we can buy today.
Device that Won WW2 by Curious Droid
. Source. Exist because double bonds don't rotate freely. Have different properties of course, unlike enantiomer.
Contains the genes: e. Coli K-12 MG1655 gene thrL, e. Coli K-12 MG1655 gene thrA, e. Coli K-12 MG1655 gene thrB and e. Coli K-12 MG1655 gene thrC, all of which have directly linked functionality.
We can find it by searching for the species in the BioCyc promoter database. This leads to: biocyc.org/group?id=:ALL-PROMOTERS&orgid=ECOLI.
By finding the first operon by position we reach: biocyc.org/ECOLI/NEW-IMAGE?object=TU0-42486.
That page lists several components of the promoter, which we should try to understand!
Some of the transcription factors are proteins:
After the first gene in the codon, thrL, there is a rho-independent termination. By comparing:we understand that the presence of threonine or isoleucine variants, L-threonyl and L-isoleucyl, makes the rho-independent termination become more efficient, so the control loop is quite direct! Not sure why it cares about isoleucine as well though.
TODO which factor is actually specific to that DNA region?
sigoden/node-express-realworld-example-app by Ciro Santilli 34 Updated 2024-12-15 +Created 1970-01-01
Ciro Santilli 34 Updated 2024-12-15 +Created 1970-01-01Appears to be a port of gothinkster/node-express-realworld-example-app to Sequelize.
Seemed to just work at 68bbadfd77f679f0df0fcd0de5bceb9c37b1144a Ubuntu 20.10, was forked from parent project in 2018.
- www.raspberrypi.com/documentation/microcontrollers/c_sdk.html
- github.com/raspberrypi/pico-sdk
- github.com/raspberrypi/pico-examples The key hello world examples are:
Ubuntu 22.04 build just worked, nice! Much feels much cleaner than the Micro Bit C setup:
sudo apt install cmake gcc-arm-none-eabi libnewlib-arm-none-eabi libstdc++-arm-none-eabi-newlib
git clone https://github.com/raspberrypi/pico-sdk
cd pico-sdk
git checkout 2e6142b15b8a75c1227dd3edbe839193b2bf9041
cd ..
git clone https://github.com/raspberrypi/pico-examples
cd pico-examples
git checkout a7ad17156bf60842ee55c8f86cd39e9cd7427c1d
cd ..
export PICO_SDK_PATH="$(pwd)/pico-sdk"
cd pico-exampes
mkdir build
cd build
# Board selection.
# https://www.raspberrypi.com/documentation/microcontrollers/c_sdk.html also says you can give wifi ID and password here for W.
cmake -DPICO_BOARD=pico_w ..
make -jThen we install the programs just like any other UF2 but plugging it in with BOOTSEL pressed and copying the UF2 over, e.g.:Note that there is a separate example for the W and non W LED, for non-W it is:
cp pico_w/blink/picow_blink.uf2 /media/$USER/RPI-RP2/cp blink/blink.uf2 /media/$USER/RPI-RP2/Also tested the UART over USB example:You can then see the UART messages with:
cp hello_world/usb/hello_usb.uf2 /media/$USER/RPI-RP2/screen /dev/ttyACM0 115200TODO understand the proper debug setup, and a flash setup that doesn't require us to plug out and replug the thing every two seconds. www.electronicshub.org/programming-raspberry-pi-pico-with-swd/ appears to describe it, with SWD to do both debug and flash. To do it, you seem need another board with GPIO, e.g. a Raspberry Pi, the laptop alone is not enough.
Matches the quantum superposition probability proportional to the square law. Poor Étienne-Louis Malus, who died so much before this was found.
The first thing we had to do with the sample was to extract the DNA present in the water in a pure form for the PCR.
We did that with a Qiagen DNeasy PowerWater Kit.
As you would expect, this consists of a purification procedure with several steps.
In each step we take a physical or chemical action on the sample, which splits it into two parts: the one with the DNA and the one without.
We then take the part with the DNA, and throw away the one without the DNA.
The first steps are coarser, and finer and finer splits are done as we move forward.
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