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michaelhoffman

5,334 karma · joined December 13, 2011

https://hoffmanlab.org/

https://twitter.com/michaelhoffman

https://github.com/michaelmhoffman

https://hnbadges.netlify.app/?user=michaelhoffman

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michaelhoffman··on Report: Microsoft kills official way to activate Windows 11/10 without internet
I understand why this is bad, but I personally would sign up for a Microsoft account anyway. Mainly, I don't want all my stuff in "C:\Users\micha". Is there a way to set your username?
michaelhoffman··on Removing newlines in FASTA file increases ZSTD compression ratio by 10x
When FASTA was invented in 1985, generally sequencing reads would be about half that.

The simplicity of FASTA seems like a dream compared to the GenBank flat file format used before then. And around the year 2000, less computationally-inclined scientists were storing sequence in Microsoft Word binary .doc files.

A lot of file formats (including bioinformatics formats!) have come and gone in that time period. I don't think many would design it this way today, but it has a lot of nice features like the ones you point out that led to its longevity.

michaelhoffman··on I counted all of the yurts in Mongolia using machine learning
Using machine learning, he counted all of the yurts.

Counting all of the yurts that happen to be using machine learning is a way more difficult problem.

michaelhoffman··on Dividing unsigned 8-bit numbers
> I assume the author means "out of all the ISAs I know"?

Out of all the ISAs where they know whether it provides integer division or not.

michaelhoffman··on My mental model of setf was wrong
This is not "hard-coded" as I would describe it. It is defined in `gv.el`:

    (gv-define-setter buffer-string (store)
  `(insert (prog1 ,store (erase-buffer))))
Unfortunately, it is marked obsolete since 29.1. The NEWS says:

* Many seldom-used generalized variables have been made obsolete. Emacs has a number of rather obscure generalized variables defined, that, for instance, allowed you to say things like:

    (setf (point-min) 4)
These never caught on and have been made obsolete. The form above, for instance, is the same as saying

    (narrow-to-region 4 (point-max))
michaelhoffman··on Avoiding Emacs Bankruptcy
This used to be the case until Emacs 24.1, in 2012.

    Passing a nil argument to a minor mode function call now ENABLES
    the minor mode unconditionally.  This is so that you can write e.g.
    
        (add-hook 'text-mode-hook #'foo-mode)
    
    to enable foo-mode in Text mode buffers, removing the need for
    'turn-on-foo-mode' style functions.  This affects all mode commands
    defined by 'define-minor-mode'.  If called interactively, the mode
    command still toggles the minor mode.
michaelhoffman··on I've stopped using box plots (2021)
Wherever possible, I use sina plots, which provide many of the advantages of violin plots while actually showing the individual data points.

https://en.wikipedia.org/wiki/Sina_plot

https://cran.r-project.org/web/packages/sinaplot/vignettes/S...

Adding on a representation of mean in a different style (like a black bar) can be helpful. So can a boxplot-style indication of variance, in some cases.

michaelhoffman··on Linux Crisis Tools
When would you need to use rdmsr and wrmsr in a crisis?
michaelhoffman··on Performance Analysis of Python's Dict() and {}
I wonder if they swapped the benchmark results somehow. Because on my computer, I get roughly the same times but with {} twice as fast as dict().
michaelhoffman··on Bus Sniffing the IBM 5150
I don't think so, but in 2023 "PC" can refer to a whole bunch of different things, and "5150" is precisely clear about what it refers to.
michaelhoffman··on Paint on Windows is getting layers and transparency support
I hope it keeps its blazing-fast startup. I regularly used Paint instead of Photoshop on a system where I had both because Paint starts instantly but Photoshop took a bit.
michaelhoffman··on California tech transplants unhappy with exodus to Austin, report says
The Bay Area has inadequate public transport for a metro of its size, but its utility is kind of another universe from the Austin's CapMetro.
michaelhoffman··on Show HN: I automated half of my typing
This is super cool. I use Emacs `abbrev-mode` for taking contemporaneous notes but autosuggesting words would be great.
michaelhoffman··on My Caste
It seems like you may be reading some things into my comment that I didn't write? I made no claims about the procedure being fair or unfair—I'm just describing what it is.
michaelhoffman··on My Caste
I am faculty at University of Toronto. As part of the process of considering someone for tenure here, the university solicits six appraisals from relevant experts at other institutions. The candidate will not know who the referees are. Generally, the appraisals are positive; a negative appraisal may severely affect someone's tenure case.

I don't see the concern in this post as one of widespread caste discrimination at University of Toronto, but more that he's worried that a single prejudiced person might upset this, either an external referee, or someone internal involved in the decision-making process. In fact, that is exactly what he says.

https://www.aapm.utoronto.ca/academic-administrative-procedu...

michaelhoffman··on We Don’t Need a New Twitter
Of course, we don't NEED a new Twitter, but many folks WANT a new Twitter.
michaelhoffman··on Advanced Python Mastery
They're in good company—the C standard also has something called an "expression statement" which is similar.
michaelhoffman··on Advanced Python Mastery
> A Python program may contain statements or expressions. Here's a Python program that contains no statements: 42.

According to the Python Language Reference, that is a Python program made of one expression statement:

https://docs.python.org/3/reference/simple_stmts.html#expres...

michaelhoffman··on My Problem with the Four-Document Model
I like the four-document model. While it isn't a perfect fit for all cases, for many it is a good start.

We wrote a review of bioinformatics software documentation, which includes a taxonomy of research software documentation (Table 1) and examples of which popular bioinformatics software packages use each two (Table 2). It is clear that not every kind is needed for everything, and it's more of a menu than a prescriptive set of documentation types needed for everything:

https://academic.oup.com/bib/article/19/4/693/2907814

michaelhoffman··on Judge rules Wyoming corner crossers did not trespass
How else are they supposed to cross from one corner to the other?
michaelhoffman··on Choosing a Name for Your Computer (1990)
Here, "GB" stands for "United Kingdom of Great Britain and Northern Ireland", not "Great Britain".

> The codes are chosen, according to the ISO 3166/MA, "to reflect the significant, unique component of the country name in order to allow a visual association between country name and country code".[5] For this reason, common components of country names like "Republic", "Kingdom", "United", "Federal" or "Democratic" are normally not used for deriving the code elements. As a consequence, for example, the United Kingdom is officially assigned the alpha-2 code GB rather than UK, based on its official name "United Kingdom of Great Britain and Northern Ireland" (although UK is reserved on the request of the United Kingdom). Some codes are chosen based on the native names of the countries. For example, Germany is assigned the alpha-2 code DE, based on its native name "Deutschland".

https://en.wikipedia.org/wiki/ISO_3166-1

michaelhoffman··on GCC 13 Released
It's based on the errors the proposers actually found in the wild, which seem to mostly be people attempting to use constant powers of 2 or 10.
michaelhoffman··on GCC 13 Released
My understanding is it only triggers when the left side is 2 or 10.
michaelhoffman··on Ban on Tenure for New Faculty Hires Passes Texas Senate
I doubt they will have much problem finding people who are qualified to teach.

But it's going to make it more difficult to continue hiring people who are seen as some of the best in the world in in-demand areas.

michaelhoffman··on There are no fees at America’s smallest bank
The old-school way to document savings accounts is with a passbook:

https://en.wikipedia.org/wiki/Passbook

If this bank offers that, then you have the redundant documentation yourself.

michaelhoffman··on RePalm
I wish that were true, but unfortunately some apps do not seem to be designed well in the case of data being turned off.
michaelhoffman··on RePalm
I don't use non-smartphone PDAs anymore, but I really miss:

1. Their ability to do absolutely everything offline. No need to worry that I won't be able to access something because somewhere without data service

2. The ability to have all the PDA features at my fingertips without being hooked up to the world's biggest attention-killing distraction network.

michaelhoffman··on How HyperCard got its color back
HyperStudio was popular in education.
michaelhoffman··on Ubuntu stops shipping Flatpak by default
I started using a snap to run Emacs 28 on my Ubuntu 22.04.2 LTS system. The snap is maintained by a Canonical employee, and I like it better than any of the other ways I have used to get more bleeding-edge versions of software in the past, such as using a random Personal Package Archive (PPA) or building from source myself.

Would I rather have the deb package be up-to-date? Sure. But when I've used distributions that try to stick closer to the bleeding edge everywhere, I've had bad experiences with stuff breaking. This lets me keep a stable, well-tested distribution for everything except for the one package I want to be newer.

I can't compare to Flatpak or AppImage because I've never used them.

michaelhoffman··on Stanford’s war against its own students
I wouldn't call her "professional"
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