Python is a shockingly slow language. A test on a raspberry pi of simply “turn this pin on and off as fast as you can” gave the results below.
| System | Library | Speed |
|---|---|---|
| Shell | /proc/mem access | 2.8 kHz |
| Shell / gpio utility | WiringPi gpio utility | 40 Hz |
| Python | RPI.GPIO | 70 kHz |
| Python | wiringPi2 bindings | 28 kHz |
| Ruby | wiringPi bindings | 21 kHz |
| C | Native library | 22 MHz |
| C | BCM 2835 | 5.4 MHz |
| C | wiringPi | 4.1 – 4.6 MHz |
| Perl | BCM 2835 | 48 kHz |
Node-RED is an, open-source, visual programming tool that lets you wire together hardware (such as sensors), APIs (such as REST/POST) and custom functions. However, its custom functions aren’t simply the JavaScript you write, they can also be containers!
This can provide an intuitive front-end to otherwise difficult software. For example, you’ve written your magnum opus, you’ve even documented it (though no-one will ever read it) and to ensure maximum compatibility for the widest possible audience, you’ve containerised it. But it’s still a command-line driven application. Using node-RED you can make this accessible to an inexperienced audience.
Out of the box, node-RED’s quite pretty, you can string together nodes to perform functions that are useful. In this case, it’s for monitoring a log file, if the log doesn’t grow, something’s gone wrong, so email me to take a look at it.
The New York Times Spelling Bee is a free online word game, where players must construct as many words as possible using the letters provided in the Bee’s grid, always including the middle letter. Bonus points for using all the letters and creating a pangram.
However, this is the kind of thing which computers are very good at. If you’ve become frustrated trying to decipher the abstruse ways of the bee, let the command line help.
tl;dr:
grep -iP "^[adlokec]{6,}$" /usr/share/dict/words |grep a | awk '{ print length, $0 }' |sort -n |cut -f2 -d" "
Continue reading Using an ESP8266 and some DS18B20 one-wire temperature sensors, I have been automatically recording temperature data from various parts of my pond, to see how it fluctuated with air temperature, depth and filter configuration.
Despite the help I was receiving from the feline fish monitor, I was getting a bit irked at the quality of the graphs I was getting using matplotlib.
Matplotlib has been around since 2003, more than 20 years now. It’s arguably the defacto method of producing graphs in python and it’s not going away. However, it’s also a pain to use and by default produces some quite ugly plots unless you put in the mileage. In fact, when attempting to quickly explore data, Michael L. Waskom’s frustrations with matplotlib were directly related to the production of the seaborn library. “By producing complete graphics from a single function call with minimal
arguments, seaborn facilitates rapid prototyping and exploratory data analysis.”
Seaborn makes use of matplotlib and integrates tightly with pandas provide a neat wrapper for matplotlib functions, allowing you to avoid a lot of the data herding needed to view a graph.
You may think “OK, so seaborn finally tames matplotlib, why should I use anything else?” In short, interactivity. Seaborn and Matplotlib may produce graphs, but a graph alone doesn’t really let you explore the data. If you look at a graph you’re limited to the scale the author thought made sense, you can’t zoom in or out and if one line is behind another, you’re kind of stuck.
Where plotly really shines is with just two lines you can generate your figure and then either save it as the image below, or as an interactive HTML graph such as this.
This week (2024-08-07) instead of our usual group meeting, OPIG took to the high seas. The OPIGlets pooled our resources and procured punts from many different berths. Organised by Admiral Nele, we departed from the Cherwell boathouse and shipped out the 0.5 nautical miles (3.28801867e-6 light seconds for those playing along in metric) upriver to the Vicky Arms.
Despite visiting the odd bush on the way, scurvy scallywags one and all were herded in a generally upstream direction with Matt and Eoin leading the way. With the first two punts having safely reached dry land and refuelled their ethanol fuel cells, the question remained where on earth everyone had got to. Sagely concluding they’d probably all sunk another pint was had in their honour.
For various reasons we might need to convert files from one format to another, for instance from lossless FLAC to MP3. For example:
ffmpeg -i lossless-audio.flac -acodec libmp3lame -ab 128k compressed-audio.mp3
This could be any conversion, but it implies that the input file and the output file are in the same directory. What if we have a carefully curated directory structure and we want to convert (or rename) every file within that structure?
find . -name “*.whateveryouneed” -exec somecommand {} \; is the tool for you.
Continue readingPrion are both fascinating and terrifying. They occur naturally and have a purpose, but what that purpose is we’re still not entirely sure. Gene-knockout mice which no longer code for the prion protein do live, but they ain’t born typical.
The endogenous form of the prion protein (PrPC) can, through currently unknown mechanisms, take a different conformation, the pathogenic PrPSc. PrPSc is responsible for fatal, rapidly progressing neurodegenerative disorders which in many cases can jump species.
At OPIG, we recently discussed a remarkably rigorous series of experiments outlined in the paper “A Protein Misfolding Shaking Amplification-based method for the spontaneous generation of hundreds of bona fide prions” Whilst deliberately creating new pathogenic prions may seem and odd thing to wish to achieve, the authors aimed to determine if there was a golden thread linking “infectivity determinants, interspecies transmission barriers or the structural influence of specific amino acids”.
Continue readingOne of the nice things about OPIG, is that you can talk about something which is outside of your wheelhouse without feeling that the specialists in the group are going to eat your lunch. Last week, I gave an overview of the Hubbell group‘s Nature paper Synthetically glycosylated antigens for the antigen-specific suppression of established immune responses. I am not an immunologist by any stretch of the imagination, but sometimes you come across a piece of really interesting science and just want to say to people: Have you seen this, look at this, it’s really clever!
Continue readingWe’ve all had things go wrong with computers, however when they go catastrophically wrong, there’s often little you can do other than to be physically on site to reinstall. This doesn’t have to be the case though. Most PCs have a tiny secondary processor which can allow full remote control of a computer that’s crashed, unresponsive or even switched off.
Continue readingLucubration – The action or occupation of intensive study originally by candle or lamplight.
Gaslighting – Psychological abuse in which a person or group causes someone to question their own sanity, memories, or perception.
I was recently having a play with Google Bard. Bard, unlike ChatGPT has access to live data. It also undergoes live feedback and quality control. I was hoping to see if it would find me any journals with articles on prion research which I’d previously overlooked.
Me: Please show me some recent articles about prion research.
(Because always be polite to our AI overlords, they’ll remember!)
