PuntSeq is a side project led by a few University of Cambridge PhDs that aims to determine which bacteria are present in the River Cam.
In July 2019, the PuntSeq team got together with the awesome Cambridge Biomakespace, an awesome biology makerspace open to all, to create a two day science outreach activity showing their procedures.
The data collected in this experiment, together with other collection sessions done by the organizers actually led to a publication on eLife: elifesciences.org/articles/61504 "Freshwater monitoring by nanopore sequencing" by Lara Urban et al. (2021), so it is awesome to see that were are actual being part of "real science".
Ciro knows nothing about biology, but since he is very curious about it, he jumped at this opportunity, and decided to document things as well as his limited knowledge would allow.
All participants chipped in some money to help cover the experiment's costs. Ciro suspects that this activity was done partially to help crowdfund the experiment, but it was a worthy investment!
The impressions you get from the experiment as a software engineer will be:
- OMG, this is so labour intensive, why haven't they automated this
- OMG, this is frightening, all the 8 hours of work I've just done are present in that tiny plastic tube
- Amazing! Look at that apparatus! And the bio people are like: I've used this a million times, it's cheap and every lab has one, just work faster and don't break you piece of junk!
This section is about groups of ordinal ruleset inscription that share a theme and were presumably created by a single entity.
Generally, if something is labelled as "e-learning", it's not a good sign, as it implies that it adheres to the "teacher"/"student" separation which Ciro Santilli much despises: E-learning websites must allow students to create learning content.
A detailed list of all transactions is kept at: sponsor/budget.js.
Ciro Santilli use the following accounting for this sponsorship calculations.
For significant one time donations, he takes the final money received in one of his cash GBP accounts, then he checks how much that is in dollars on Google at the time of cash out, and then writes that amount down as the final dollar value which is what ultimately counts. This exposes Ciro to USD/GBP fluctuations, but it simplifies accounting for donors which is more important, so it is likely worth it.
For small regular donations, Ciro just tallies it all up in GBP from time to time and converts it all to dollars in one go as it is not worth spending too much time updating those too often.
Ciro Santilli wants to make sure that you get clear highlights of what your donation money is going into!Sponsors also receive the "Ciro's Edit" email newsletter if desired, which contains similar updates to the above, but delivered directly to their inbox.
- OurBigBook updates: docs.ourbigbook.com/news
- Non-OurBigBook updates: Section "Updates"
- why the square: physics.stackexchange.com/questions/535/why-does-kinetic-energy-increase-quadratically-not-linearly-with-speed on Physics Stack Exchange. Ron Maimon's answer is great, as it relies only on the following staring points:He also offers a symmetry argument considering the case of potential energy.
- why the half: physics.stackexchange.com/questions/27847/why-is-there-a-frac-1-2-in-frac-1-2-mv2 on Physics Stack Exchange
Currently a redirect page on Wikipedia: en.wikipedia.org/?title=Department_of_Statistics,_University_of_Oxford&redirect=no Newbies!
Why is this not part of the Mathematical Institute of the University of Oxford? Who knows!
More generic PCR information at: Section "Polymerase chain reaction".
Because it is considered the less interesting step, and because it takes quite some time, this step was done by the event organizers between the two event days, so participants did not get to take many photos.
PCR protocols are very standard it seems, all that biologists need to know to reproduce is the time and temperature of each step.
We did 35 cycles of:
- 94˚C for 30 seconds
- 60˚C for 30 seconds
- 72˚C for 45 seconds
This process used a Marshal Scientific MJ Research PTC-200 Thermal Cycler:
We added PCR primers for regions that surround the 16S DNA. The primers are just bought from a vendor, and we used well known regions are called 27F and 1492R. Here is a paper that analyzes other choices: academic.oup.com/femsle/article/221/2/299/630719 (archive) "Evaluation of primers and PCR conditions for the analysis of 16S rRNA genes from a natural environment" by Yuichi Hongoh, Hiroe Yuzawa, Moriya Ohkuma, Toshiaki Kudo (2003)
One cool thing about the PCR is that we can also add a known barcode at the end of each primer as shown at Code 1. "PCR diagram".
This means that we bought a few different versions of our 27F/1492R primers, each with a different small DNA tag attached directly to them in addition to the matching sequence.
This way, we were able to:
- use a different barcode for samples collected from different locations. This means we
- did PCR separately for each one of them
- for each PCR run, used a different set of primers, each with a different tag
- the primer is still able to attach, and then the tag just gets amplified with the rest of everything!
- sequence them all in one go
- then just from the sequencing output the barcode to determine where each sequence came from!
Input: Bacterial DNA (a little bit)
... --- 27S --- 16S --- 1492R --- ...
|||
|||
vvv
Output: PCR output (a lot of)
Barcode --- 27S --- 16S --- 1492RCode 1.
PCR diagram
. Finally, after purification, we used the Qiagen QIAquick PCR Purification Kit protocol to purify the generated from unwanted PCR byproducts.
The remedy to cowardice, inattention, censorship and amorality.
Due to Ciro Santilli's campaign for freedom of speech in China, Ciro Santilli maintains information on this at mostly at:
Dan Dascalescu's "Web page archiving" comparison table: web.archive.org/web/20130922192354/http://wiki.dandascalescu.com/reviews/online_services/web_page_archiving
A network interface controller that does more than just the base OSI model protocols, notably in a programmable way.
- www.nextplatform.com/2022/05/11/intel-unrolls-dpu-roadmap-with-a-two-year-cadence/
- www.trentonsystems.com/blog/what-is-a-smartnic
- blogs.nvidia.com/blog/2021/10/29/what-is-a-smartnic/ "Some are using FPGAs which promise flexibility"
- www.servethehome.com/intel-ipu-exotic-answer-to-industry-dpu/ "Intel IPU is an Exotic Answer to the Industry DPU"
- 2022 www.datacenterdynamics.com/en/news/amd-to-buy-smartnic-firm-pensando-for-19-billion/ "AMD to buy SmartNIC firm Pensando for $1.9 billion"
- www.theregister.com/2022/06/14/alibaba_dpu_cloud/ mentions that Alibaba Cloud created their own.
Hyperscalers Lead The Way To The Future With SmartNICs by The Next Platform (2019)
Source. - youtu.be/kwroXmFJJf0?t=599 financial industry is one of the users, notably high-frequency trading
Associated article: www.nextplatform.com/2019/10/31/hypercalers-lead-the-way-to-the-future-with-smartnics/ mentions that:
Google is widely believed to be working on its own design.
Biologists are obsessed with these!
There are unlisted articles, also show them or only show them.