Viewing profile — jkh1

Most of the time in bio-related fields, we need high-throughput computing not high-performance computing.

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/2410.1…

cell/molecular biology

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 ou…

> 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 usi…

Running locally is sometimes necessary, e.g. you don't want to send sensitive data to any random third party server.

Another benchmark: https://www.biorxiv.org/content/10.1101/2024.04.19.590278v2....

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-...

The problem is that ISO standards are not open.

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 advanta…

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.

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.

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…

> 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 wo…

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…

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 plant…

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 p…

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 durin…

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 usef…

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. T…

Works fine for me. Must have been a temporary glitch.

Didn't see this post so posted it also. Also relevant: https://www.embl.org/news/science/alphafold-potential-impact...

See also https://www.embl.org/news/science/alphafold-potential-impact...