jkh1

6 ms·

1.
by jkh1 6mo ago
Most of the time in bio-related fields, we need high-throughput computing not high-performance computing.
2.
Worker cooperative for open source tech related to scientific image data(image.coop)
1 points by jkh1 7mo ago|0 comments
3.
by jkh1 1y ago
You can track things in live cells with MINFLUX, one of the recent super-resolution techniques coming from Stefan Hell's lab. Edit: add MINFLUX review: https://arxiv.org/pdf/2410.15902
4.
by jkh1 1y ago
cell/molecular biology
5.
by jkh1 1y ago
In my field, trying to reproduce results or conclusions from papers happens on a regular basis especially when the outcome matters for projects in the lab. However, whatever the outcome, it can't be published because either it confirms
6.
by jkh1 2y ago
> There's no good alternatives on Linux Maybe I misunderstand what this refers to but there are RDP software for Linux. I've used remmina [1] on Linux for a few years (now I am using VMWare Horizon at work). [1] https:/
7.
by jkh1 2y ago
Running locally is sometimes necessary, e.g. you don't want to send sensitive data to any random third party server.
8.
by jkh1 2y ago
Another benchmark: https://www.biorxiv.org/content/10.1101/2024.04.19.590278v2....
9.
Benchmarking Large Language Models for Bio-Image Analysis Code Generation(biorxiv.org)
1 points by jkh1 2y ago|0 comments
10.
by jkh1 3y ago
How many workflow management systems do we need? Over 300[1]. If that's not reinventing the wheel. [1] https://github.com/common-workflow-language/common-workflow-...
11.
by jkh1 3y ago
The problem is that ISO standards are not open.
12.
by jkh1 3y ago
What seems to help in the life sciences is the existence of public repositories. These could be replaced by portals that collect info on data hosted elsewhere. But the main advantages are that they provide clear, well known places to start
13.
by jkh1 3y ago
In the life sciences there are dedicated structured repositories. These are searchable by keywords and often crossreference each other. They are the goto places for finding data.
14.
by jkh1 3y ago
In biology we now routinely produce datasets in the multiple terrabytes range. It can easily be n = 3 x 10 TB such as for example imaging 3 fly embryos by light sheet microscopy.
15.
by jkh1 3y ago
Can I put my 25 TB microscopy image data set on GitHub? Will they host it for free indefinitely? In the life sciences, there are dedicated public repositories (databases) where the data is hosted (free to the researcher), catalogued, standa
16.
by jkh1 3y ago
> A lot of researchers are bad at writing code, but they can audit it. Can they really? It seems to me that users of this would be those that can't write the code they need. How would they be in a position to audit what they get?
17.
by jkh1 4y ago
Historically much of computational biology was driven by people with no wet lab experience and no access to a wet lab so hypotheses went untested because nobody wanted to bet their grant on someone else's work they didn't understa
18.
by jkh1 4y ago
Of course there are more than that. Look at any comprehensive guide book on edible/foreageable plants and you'll definitely find more than a couple hundreds. For example, the plants for a future database ( https://pfaf.o
19.
by jkh1 4y ago
Once published, it's not new anymore. It would cost a few millions just to repeat the work on a few hundred proteins and unless something new or interesting surfaces, it won't be publishable in a high-visibility place. Also it mig
20.
by jkh1 4y ago
For those interested, we did something similar a few years ago but for proteins in dividing cells where we could quantify how much of a protein is where in the cell over time during cell division [0]. Data [1], code [2] and web-based visual
21.
by jkh1 4y ago
Perl was the first language I used professionally and I used it almost exclusively for years. I don't understand all the negative comments about its use of sigils, I find them useful and I never got the impression that they made the co
22.
by jkh1 4y ago
I've been working from home using a RPi 4B hooked up to a large monitor as a thin client for the last two years, first using Remmina and now mostly running VMWare Horizon client. The only thing I am not using it for is video conferenci
23.
by jkh1 5y ago
Works fine for me. Must have been a temporary glitch.
24.
by jkh1 5y ago
Didn't see this post so posted it also. Also relevant: https://www.embl.org/news/science/alphafold-potential-impact...
25.
by jkh1 5y ago
See also https://www.embl.org/news/science/alphafold-potential-impact...
26.
AlphaFold protein structures publicly available(alphafold.ebi.ac.uk)
3 points by jkh1 5y ago|1 comments
27.
by jkh1 5y ago
This brings back memories. My first Z80 assembly program was a jetpac game for the Sinclair ZX80 around 1984 because I couldn't get a ZX Spectrum to play it. I don't think any written copy still exists but there's still a cop
28.
by jkh1 6y ago
I've been working from home for almost a year using a Pi4B running remmina. The other end is a Dell workstation running x11vnc on Ubuntu 16.04. I've only experienced occasional hiccups that I've narrowed down to things interf
29.
by jkh1 6y ago
> whether there are also potential users who would have been perfectly happy with javascript/python/R bindings and a good tutorial If you think people in some communities would benefit then you should be proactive in advertisin
30.
by jkh1 6y ago
There are tools to generate realistic patient data, for example Synthea: https://synthetichealth.github.io/synthea/

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