Star system Updated 2025-07-16
American university Updated 2025-07-16
Cascading Style Sheets Updated 2025-07-16
- css/code-block.html
- css/img-table-vertical-center.html
- css/viewport-height.html: a div that is a tall as the viewport, and does not generate a toplevel scrollbar
- css/responsive-image-max-height.html: here we try to create an image that is never wider than the screen. If the screen is less wide than the image, then the image scales down proportionally. Otherwise, the image has a user determined fixed by the CSS or the HTML
heightproperty. Related:TODO I'm unable to do this....... stackoverflow.com/questions/69964332/how-to-set-the-default-height-of-responsive-images-when-screen-is-wide-and-have The objective was to implement: github.com/ourbigbook/ourbigbook/issues/168 - css/top-navigation.html
OsmAnd Updated 2025-07-16
Ortholog Updated 2025-07-16
Origins of Precision by Machine Thinking (2017) Updated 2025-07-16
Great overview of the earlier history of unit standardization.
Gives particular emphasis to the invention of gauge blocks.
Origin of replication Updated 2025-07-16
oriC = Origin of Chromosomal replication.
Organization developing quantum hardware Updated 2025-07-16
Organization developing photonic quantum computer Updated 2025-07-16
Organizationally unique identifier Updated 2025-07-16
Organism model Updated 2025-09-09
Organ (anatomy) Updated 2025-07-16
Orange Papers Updated 2025-07-16
Oracle Database Updated 2025-07-16
Optical microscope Updated 2025-07-16
Operon vs transcription unit Updated 2025-07-16
Consider the E. Coli K-12 MG1655 operon thrLABC.
That single operon can produce two different mRNA transcription units:
- thrL only, the transcription unit is also called thrL: biocyc.org/ECOLI/NEW-IMAGE?object=TU0-42486
- thrL + thrA + thrB + thrC all together, the transcription unit is called thrLABC: biocyc.org/ECOLI/NEW-IMAGE?type=OPERON&object=TU00178
The reason for this appears to be that there is a rho-independent termination region after thrL. But then under certain conditions, that must get innactivated, and then the thrLABC is produced instead.
Open X-Embodiment Updated 2025-07-16
Terrible name, but very interesting dataset:
GitHub describes the input quite well:
The model takes as input a RGB image from the robot workspace camera and a task string describing the task that the robot is supposed to perform.What task the model should perform is communicated to the model purely through the task string. The image communicates to the model the current state of the world, i.e. assuming the model runs at three hertz, every 333 milliseconds, we feed the latest RGB image from a robot workspace camera into the model to obtain the next action to take.
TODO: how is the scenario specified?
TODO: any simulation integration to it?
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Overview of the experiment Updated 2025-07-16
For those that know biology and just want to do the thing, see: Section "Protocols used".
The PuntSeq team uses an Oxford Nanopore MinION DNA sequencer made by Oxford Nanopore Technologies to sequence the 16S region of bacterial DNA, which is about 1500 nucleotides long.
This kind of "decode everything from the sample to see what species are present approach" is called "metagenomics".
This is how the MinION looks like: Figure 1. "Oxford Nanopore MinION top".
Oxford Nanopore MinION top open
. Source. 
Before sequencing the DNA, we will do a PCR with primers that fit just before and just after the 16S DNA, in well conserved regions expected to be present in all bacteria.
The PCR replicates only the DNA region between our two selected primers a gazillion times so that only those regions will actually get picked up by the sequencing step in practice.
Eukaryotes also have an analogous ribosome part, the 18S region, but the PCR primers are selected for targets around the 16S region which are only present in prokaryotes.
This way, we amplify only the 16S region of bacteria, excluding other parts of bacterial genome, and excluding eukaryotes entirely.
Despite coding such a fundamental piece of RNA, there is still surprisingly variability in the 16S region across different bacteria, and it is those differences will allow us to identify which bacteria are present in the river.
The variability exists because certain base pairs are not fundamental for the function of the 16S region. This variability happens mostly on RNA loops as opposed to stems, i.e. parts of the RNA that don't base pair with other RNA in the RNA secondary structure as shown at: Code 1. "RNA stem-loop structure".
This is how the 16S RNA secondary structure looks like in its full glory: Figure 5. "16S RNA secondary structure".
Since loops don't base pair, they are less crucial in the determination of the secondary structure of the RNA.
The variability is such that it is possible to identify individual species apart if full sequences are known with certainty.
With the experimental limitations of experiment however, we would only be able to obtain family or genus level breakdowns.
Open source software Updated 2025-07-16
What happens when the underdogs get together and try to factor out their efforts to beat some evil dominant power, sometimes victoriously.
Or when startups use the cheapest stuff available and randomly become the next big thing, and decide to keep maintaining the open stuff to get features for free from other companies, or because they are forced by the Holy GPL.
Open source frees employees. When you change jobs, a large part of the specific knowledge you acquired about closed source a project with your blood and tears goes to the trash. When companies get bought, projects get shut down, and closed source code goes to the trash. What sane non desperate person would sell their life energy into such closed source projects that could die at any moment? Working on open source is the single most important non money perk a company can have to attract the best employees.
Open source is worth more than the mere pragmatic financial value of not having to pay for software or the ability to freely add new features.
Its greatest value is perhaps the fact that it allows people study it, to appreciate the beauty of the code, and feel empowered by being able to add the features that they want.
And "can reverse engineer the undocumented GPU hardware APIs", Ciro would add.
While software is the most developed open source technology available in the 2010's, due to the "zero cost" of copying it over the Internet, Ciro also believes that the world would benefit enormously from open source knowledge in all areas on science and engineering, for the same reasons as open source.
Open source AlphaGo implementation Updated 2025-07-16
- www.quora.com/Will-Google-open-source-AlphaGo Will Google open source AlphaGo?
- www.nature.com/articles/nature16961 Mastering the game of Go with deep neural networks and tree search by Silver et al. (2016), published without source code
There are unlisted articles, also show them or only show them.