rbartelme

8 ms·

1.
by rbartelme 2mo ago
As a bioinformatics person that's spent time in and out of industry/academia, I agree with some of the article's thesis. While I don't think LLMs or AI are going away, I do think it will allow people in academia to pump
2.
by rbartelme 3mo ago
Yeah, I definitely do something similar with my personal projects. I come from more of a hardware & environmental engineering background and we were always taught that projects were iteratively built via Design, Build, Test, Learn cycle
3.
by rbartelme 7mo ago
I wonder if the same thing happened with--or is happening at--NSF? I know researchers that did not get funding for quantitative ecology fellowships or grants. After back channeling with program managers, it seems that using "diversity&
4.
Optimizing sparse and skew hashing: faster k-mer dictionaries(biorxiv.org)
3 points by rbartelme 8mo ago|1 comments
5.
by rbartelme 8mo ago
Pretty cool bioinformatics algorithm to speed up what was traditionally a dynamic Burrows-Wheeler Transform. Interested to see where this gets implemented outside of benchmarking in the next few years!
6.
by rbartelme 8mo ago
Thanks for the perspective. This makes me think I was a bit quick to judge their methodologies.
7.
by rbartelme 8mo ago
It's somewhat interesting, but the authors' conclusions are a bit odd given their data. They acknowledge that fame is potentially confounding: Risk factors (impulsivity, substance use, etc.) -> Fame achievement | Risk factors -
8.
by rbartelme 10mo ago
Might be coming soon based on this: https://docs.rustfs.com/features/replication/
9.
by rbartelme 10mo ago
Outside bioconductor or the tidyverse in R can be just as unstable due to CRAN's package requirements.
10.
by rbartelme 10mo ago
This is a non-issue with Polars dataframes to_pandas() method. You get all the performance of Polars for cleaning large datasets, and to_pandas() gives you backwards compatibility with other libraries. However, plotnine is completely compat
11.
by rbartelme 10mo ago
> Life's two most fundamental properties are homeostasis and reproduction. > The loss of these two combined with its parasitic nature makes this cell a form on non-life. This is a decidedly Eukaryote-centric take. Homeostasis in
12.
by rbartelme 10mo ago
For all the folks saying, "Isn't this just a virus?" The actual paper states that the genome encodes transfer RNA's and ribosomal RNA's. I think that's a really important biological distinction missing from the
13.
by rbartelme 10mo ago
If you're interested in this topic, I'd highly recommend checking out Michigan State's E coli Long-term Evolution Experiment: https://lenski.mmg.msu.edu/ecoli/index.html
14.
by rbartelme 11mo ago
Yeah I think this is definitely the future. Recently, I too have spent considerable time on probabilistic hyper-graph models in certain domains of science. Maybe it _is_ the next big thing.
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by rbartelme 11mo ago
Sometimes I miss the benchwork, but moving into bioinformatics/data science full-time has been much better for my physical and mental health.
16.
by rbartelme 11mo ago
Countable is a relative term in microbiology. I like that the author stuck to the phrase "countable colonies", since colony forming units are not really "countable as cells". Allan Konopka does a good deep dive into &quo
17.
MemMachine(memmachine.ai)
2 points by rbartelme 11mo ago|1 comments
18.
by rbartelme 11mo ago
> Meet MemMachine, an open-source memory layer for advanced AI agents. It enables AI-powered applications to learn, store, and recall data and preferences from past sessions to enrich future interactions. MemMachine's memory layer p
19.
by rbartelme 11mo ago
>The replication crisis is a growing concern. This! The amount of clinicians I know who simply read the abstract of a case study, with no real statistical interpretation of results, is a non-zero number. Whenever I see some hyped up popu
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by rbartelme 1y ago
I agree with all of this. I've worked in optical engineering, bioinformatics, and data science writ large for over a decade, knowing the data collection process is foundational to statistical process control and statistical design of e
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by rbartelme 1y ago
This MCP agent still doesn't defend the statistically illiterate from themselves.
22.
by rbartelme 4y ago
This professor was, quite literally, on a teaching only contract.
23.
by rbartelme 4y ago
I recently made the transition from academia to industry (also a PhD holder). I would echo a lot of what other commenters said about learning python and the associated data science tooling. Coming from an R heavy scientific discipline (quan
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by rbartelme 5y ago
"Grant Applications: Very specific academic "skill" which is intimately tied to the bureaucracy of the university system of your particular country or region. It also has a lot to do with things that aren't even in the a
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by rbartelme 5y ago
> Any PhD worth their salt would know that a much more likely reason why their hard skills were valuable had nothing to do with PhDs and everything to do with them as a person being able to complete a PhD. I often equate my Ph.D. with th
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by rbartelme 5y ago
Cost/benefit analysis may dictate that, as other posters suggested, you'd be better served to get raw fastq files from a sequencing lab. Even better if you can send the lab a sample and they'll process the extractions for ext
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by rbartelme 5y ago
I think it might depend on whether or not U.S. insurance companies are involved. If so HIPAA is a real liability as a company. For example, a former colleague worked at a high profile private research facility that had their HIPAA firewall
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by rbartelme 5y ago
https://archive.md/pog41
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by rbartelme 5y ago
This is an extreme example of what can happen in a "company town". https://en.wikipedia.org/wiki/Bay_View_massacre
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by rbartelme 5y ago
Running a Hidden Markov Model against shotgun metagenomic datasets != culturing microorganisms that can "do the thing". Link to actual journal article: https://journals.asm.org/doi/10.1128/mBio.02155-21

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