tdido

6 ms·

1.
by tdido 15d ago
Spanish National Cancer Research Centre (CNIO) | Madrid, Spain | HYBRID | Senior Scientific Computing Engineer | Full-time CNIO is one of Europe's leading cancer research centres. We're looking for a senior scientific computing en
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by tdido 5mo ago
You can go a very long way just mapping your DNA reads to a reference genome [0]. This reference will have associated annotations of different types, e.g. mutations, which automatically give you relevant information about your own genome by
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by tdido 1y ago
See here for updates: https://bsky.app/profile/matrix.org/post/3lxuslbzjuc2t
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by tdido 1y ago
That's actually pretty much what Andrej Karpathy mentions as a mitigation for hallucinations here: https://m.youtube.com/watch?v=7xTGNNLPyMI&t=5400s
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by tdido 1y ago
Spanish National Cancer Research Centre (CNIO) | Madrid, Spain | HYBRID (2d/week on-site) | HPC Engineer | Full-time We're looking for an HPC engineer to join us at the Bioinformatics Unit to help us boost the scientific computing
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by tdido 4y ago
https://arxiv.org/abs/2301.12670
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by tdido 4y ago
https://news.ycombinator.com/item?id=34830936
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by tdido 4y ago
Having a 3D printer available, I've been using these two projects to set up my modest workshop and it's worked out great. https://github.com/jeffbarr/gridfinity-catalog https://github.com/ader
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by tdido 4y ago
Very much so. As a bioinformatician, for me conda has become a central part of my workflow as a generic package manager through the conda-forge and bioconda channels. I know a few university HPC clusters that use it to handle software inste
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by tdido 4y ago
I sync my journal directory using syncthing and it works reasonably well.
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by tdido 4y ago
This is used in both bwa [1] and bowtie [2], two of the most popular DNA sequence aligners. [1] https://github.com/lh3/bwa [2] https://github.com/BenLangmead/bowtie
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by tdido 4y ago
I would easily expect even worse than that any day during peak hour in any of the larger stations here in Madrid.
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by tdido 4y ago
It won't be perfect, but you will have a fair amount of places where it can and will be implemented. Our research centre has central A/C and they announced the change a few days ago.
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by tdido 4y ago
Both more powerful and less glamorous than Mare Nostrum 4, which is located inside a former chapel: https://www.silicon.es/wp-content/uploads/2017/06/2017_BSC_S...
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by tdido 4y ago
You can use "-i" for in-place password generation, which will just replace the first line.
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by tdido 4y ago
El Diablo and Murcielago were also fighting bulls.
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by tdido 4y ago
Not paid well at all, so compensation can't be a driver. That doesn't mean you can't find decent wages, but the average is low. If you're still interested feel free to email me and I'll be happy give you some pointe
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by tdido 4y ago
Certainly not because of compensantion, but I switched to academia after 10 years as a consultant by doing a PhD in bioinformatics. I now work in a cancer research centre. There is a serious lack of people with computational background in t
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by tdido 5y ago
I use https://www.mkdocs.org/ , which is markdown-based. It's simple to get started and customizable enough if needed.
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by tdido 5y ago
Seems like there's a conda package in the works: https://github.com/bioconda/bioconda-recipes/pull/29660
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Seq – A programming language for computational genomics and bioinformatics(github.com)
116 points by tdido 5y ago|59 comments
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by tdido 5y ago
See also: https://dl.acm.org/doi/pdf/10.1145/3360551 https://www.nature.com/articles/s41587-021-00985-6 (paywalled)
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by tdido 5y ago
Actually, for the use case of genome assemblies you can compensate for the error rate with depth of coverage. Long reads are already the state-of-the-art for assembling genomes and are allowing us to get information that is simply invisible
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by tdido 6y ago
They seem to be under the FCA: https://transferwise.com/help/articles/2932699/what-is-the-f... Do you mean they don't subscribe to the 80k protection or something like that?
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by tdido 6y ago
Ah, sorry about that. I'm not getting a paywall for whatever reason.
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by tdido 6y ago
We're certainly already there with food related companies: https://www.businessinsider.com/10-companies-control-the-foo...
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by tdido 6y ago
Actually, one of the main features of this tech apart from the obvious size-factor is that it's a streaming process. You can analyse data on the fly and decide when to stop the run. Wash the flowcell, and use it for another sample. Eve
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by tdido 6y ago
Nope. You're working with kmers. I think it's 6mers in the current models. It's good because you get redundancy as you move, but coupled with the fact that you can't control dwelling time it makes repetition hard to hand
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by tdido 6y ago
Still, some of the errors can be compensated for with more coverage. So if you can manage 20-30X you're left with the homopolymer problem (nanopores can't tell how long a stretch of the same repeated nucleotide is, because you can
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by tdido 6y ago
I don't think you need the Qubit with the rapid prep.

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