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Notices by @kmicu@mastodon.social (kmicu@mastodon.social), page 14

  1. @kmicu@mastodon.social (kmicu@mastodon.social)'s status on Friday, 08-Jun-2018 15:34:35 EDT @kmicu@mastodon.social @kmicu@mastodon.social
    • Strypey

    @strypey a container let us create a lightweight virtual machine and when we are inside, everything is like in a regular OS.

    Guix is a package manager that does not let us install two packages in the same place on disk unless those packages are bit-by-bit identical.

    That’s accurate, but probably has even less sense 😹

    In conversation Friday, 08-Jun-2018 15:34:35 EDT from mastodon.social permalink
  2. @kmicu@mastodon.social (kmicu@mastodon.social)'s status on Friday, 08-Jun-2018 15:17:58 EDT @kmicu@mastodon.social @kmicu@mastodon.social
    in reply to
    • Strypey

    @strypey those are valid questions. I must admit it is difficult for me to offer some good analogy to explain the difference between Guix/Nix and containers/Flatpacks/Snaps/Appimages and I really want to avoid ‘container is like a bucket, Guix is like a git’ thing 😹

    The fact that we can use Guix inside a container or we can use Guix to create a container does not help too.

    Also I want to avoid math-talk about referential transparency, purity, functions. 🤷

    In conversation Friday, 08-Jun-2018 15:17:58 EDT from mastodon.social permalink
  3. @kmicu@mastodon.social (kmicu@mastodon.social)'s status on Friday, 08-Jun-2018 12:16:43 EDT @kmicu@mastodon.social @kmicu@mastodon.social
    in reply to
    • Strypey

    @strypey could you give an example of such Docker recipe? I cannot create an identical/reproducible image based on https://github.com/docker-library/golang/blob/329b6672949337c4469351b2e8b8575459a75c7f/1.10/stretch/Dockerfile

    Those RUN commands can result in a different image every time user runs the recipe.

    How do you know that today’s Redis image on https://hub.docker.com/_/redis/ is the same as yesterday’s one?

    In conversation Friday, 08-Jun-2018 12:16:43 EDT from mastodon.social permalink
  4. @kmicu@mastodon.social (kmicu@mastodon.social)'s status on Thursday, 07-Jun-2018 17:29:10 EDT @kmicu@mastodon.social @kmicu@mastodon.social
    • 🌊 Matteo De Micheli

    @matteodem if I understand correctly Github company had no choice. They could not figure out how to make profits and Microsoft has funds to keep it going. (Similar story when Google acquired Youtube.)

    So Github-under-Microsoft is better than no Github at all or better than Github-like-SourceForge injecting malware into hosted tarballs to make portal profitable.

    The acquisition is better for Github company, but we could argue that Github bankruptcy would be better for the software ecosystem. 🤷

    In conversation Thursday, 07-Jun-2018 17:29:10 EDT from mastodon.social permalink
  5. @kmicu@mastodon.social (kmicu@mastodon.social)'s status on Thursday, 07-Jun-2018 16:22:36 EDT @kmicu@mastodon.social @kmicu@mastodon.social
    in reply to
    • Strypey

    @strypey use cases are diverse from profound one like reproducible scientific research https://www.biorxiv.org/content/early/2018/04/21/298653
    to trivial one like operating system rollbacks: something is broken after updating packages? Reboot, boot into previous system version and you can start working after wasting only seconds. That is not the case when a mutable package manager bricks your OS (apt-get, pacman, etc).

    Guix(SD)/Nix(OS) is like git―it let us travel in time, but on the package manager / operating system level.

    In conversation Thursday, 07-Jun-2018 16:22:36 EDT from mastodon.social permalink

    Attachments

    1. File without filename could not get a thumbnail source.
      Reproducible genomics analysis pipelines with GNU Guix
      from bioRxiv
      In bioinformatics, as well as other computationally-intensive research fields, there is a need for workflows that can reliably produce consistent output, independent of the software environment or configuration settings of the machine on which they are executed. Indeed, this is essential for controlled comparison between different observations or for the wider dissemination of workflows. Providing this type of reproducibility, however, is often complicated by the need to accommodate the myriad dependencies included in a larger body of software, each of which generally come in various versions. Moreover, in many fields (bioinformatics being a prime example), these versions are subject to continual change due to rapidly evolving technologies, further complicating problems related to reproducibility. Here, we propose a principled approach for building analysis pipelines and managing their dependencies. As a case study to demonstrate the utility of our approach, we present a set of highly reproducible pipelines for the analysis of RNA-seq, ChIP-seq, Bisulfite-seq, and single-cell RNA-seq. All pipelines process raw experimental data, and generate reports containing publication-ready plots and figures, with interactive report elements and standard observables. Users may install these highly reproducible packages and apply them to their own datasets without any special computational expertise beyond the use of the command line. We hope such a toolkit will provide immediate benefit to laboratory workers wishing to process their own data sets or bioinformaticians seeking to automate all, or parts of, their analyses. In the long term, we hope our approach to reproducibility will serve as a blueprint for reproducible workflows in other areas. Our pipelines, along with their corresponding documentation and sample reports, are available at http://bioinformatics.mdc-berlin.de/pigx
  6. @kmicu@mastodon.social (kmicu@mastodon.social)'s status on Thursday, 07-Jun-2018 16:04:01 EDT @kmicu@mastodon.social @kmicu@mastodon.social
    • Strypey

    @strypey in typical Guix/Nix usage there is no container like isolation. I can install 5 different versions of Firefox 60 and run them at once. There’s no isolation like in case of Docker containers. Those Firefoxes can see and interact with my regular operating system. They can see each other.

    I can, additionally, use namespaces, cgroups, etc to isolate/limit those Firefoxes, but that is not the case by default; that’s optional.

    QubesOS is more similar to the idea from the presentation.

    In conversation Thursday, 07-Jun-2018 16:04:01 EDT from mastodon.social permalink
  7. @kmicu@mastodon.social (kmicu@mastodon.social)'s status on Thursday, 07-Jun-2018 15:56:10 EDT @kmicu@mastodon.social @kmicu@mastodon.social
    in reply to
    • Strypey

    @strypey
    we can use Guix/Nix to create/simulate containers, but then we use the same kernel features that enable containers.

    The difference is that we can use Guix/Nix to accomplish much more stuff (also unrelated to containers). For example we can recreate *identical* environment from sources. You do not need to take my container image (maybe I put some malicious stuff in it?) instead you can take my description and build the same container from sources and images will be identical.

    In conversation Thursday, 07-Jun-2018 15:56:10 EDT from mastodon.social permalink
  8. @kmicu@mastodon.social (kmicu@mastodon.social)'s status on Thursday, 07-Jun-2018 13:42:41 EDT @kmicu@mastodon.social @kmicu@mastodon.social
    in reply to
    • Strypey

    @strypey a container for every app approach is focused on isolation. Things in those containers can still be mutable, state-full and not reproducible.

    That is nothing like Guix(SD)/Nix(OS).

    In conversation Thursday, 07-Jun-2018 13:42:41 EDT from mastodon.social permalink
  9. DJ Sundog - from the toot-lab (djsundog@toot-lab.reclaim.technology)'s status on Tuesday, 05-Jun-2018 17:32:24 EDT DJ Sundog - from the toot-lab DJ Sundog - from the toot-lab

    Web controls could learn a thing or two from industrial controls

    In conversation Tuesday, 05-Jun-2018 17:32:24 EDT from toot-lab.reclaim.technology permalink Repeated by kmicu
  10. @kmicu@mastodon.social (kmicu@mastodon.social)'s status on Wednesday, 06-Jun-2018 07:20:57 EDT @kmicu@mastodon.social @kmicu@mastodon.social
    • Orbifx 🌙 nature's emissary
    • ˗ˏˋ Liaizon Wakest ˎˊ˗
    • Marco Dalla Stella

    @orbifx @wakest @mdallastella there is also
    http://dist-bugs.branchable.com/software/ when sending a patch via email and browsing a mailing list archive is not enough.

    GitHub took away from folks that feeling when you locally grep over all issues and messages around a project; in seconds; without a browser.
    [jokin' and shoutin'] Shame. Shame. Shame!

    In conversation Wednesday, 06-Jun-2018 07:20:57 EDT from mastodon.social permalink
  11. @kmicu@mastodon.social (kmicu@mastodon.social)'s status on Sunday, 03-Jun-2018 11:30:57 EDT @kmicu@mastodon.social @kmicu@mastodon.social
    • Diego Islas Ocampo

    @HyuchiaDiego heh, remote access to elderly parents' computer is a classic (it keeps us, supporters, sane ;).

    In conversation Sunday, 03-Jun-2018 11:30:57 EDT from mastodon.social permalink
  12. @kmicu@mastodon.social (kmicu@mastodon.social)'s status on Saturday, 02-Jun-2018 16:36:12 EDT @kmicu@mastodon.social @kmicu@mastodon.social
    • Diego Islas Ocampo

    @HyuchiaDiego a keylogger is an extreme case but *I* could accept it when someone has a 6yo that cannot even understand Internet, but want to use it. Of course I would prefer to be honest with a kid and tell her 'you are a little bit to young, but I will let you use Internet, but remember that I am able to see what you do, do we have a deal?'. (I could also accept a keylogger during work hours.)

    OTOH keylogging an adolescent is not ok, b/c by then they develop relevant adult traits.

    In conversation Saturday, 02-Jun-2018 16:36:12 EDT from mastodon.social permalink
  13. @kmicu@mastodon.social (kmicu@mastodon.social)'s status on Saturday, 02-Jun-2018 11:30:06 EDT @kmicu@mastodon.social @kmicu@mastodon.social
    • Diego Islas Ocampo

    @HyuchiaDiego I see it differently, we accept spying on children more than spying by government on us because those are two different relations — we choose a government every n years to do what we want. Children do not choose parents and tell them what they should do for the next x years or vote whether they want to eat vegetables.

    Similarly we find blocking porn acceptable to protect our kids, but government (chosen by us to serve us) should not censorship against our will.

    In conversation Saturday, 02-Jun-2018 11:30:06 EDT from mastodon.social permalink
  14. @kmicu@mastodon.social (kmicu@mastodon.social)'s status on Friday, 01-Jun-2018 12:50:03 EDT @kmicu@mastodon.social @kmicu@mastodon.social
    • otini

    @otini PSPS that reminds me a popular TeX saying: “It's not that the margins are too wide. It's that the paper is too big!”¹.

    ¹ https://tex.stackexchange.com/questions/71172/why-are-default-latex-margins-so-big#71211

    In conversation Friday, 01-Jun-2018 12:50:03 EDT from mastodon.social permalink

    Attachments

    1. Why are default LaTeX margins so big?
      from TeX - LaTeX Stack Exchange
      I've read that—unless I know a lot about typesetting—I shouldn't change the margins of a LaTeX document. The default margin size of the article class is really big and it feels like a lot of space is
  15. @kmicu@mastodon.social (kmicu@mastodon.social)'s status on Friday, 01-Jun-2018 12:42:52 EDT @kmicu@mastodon.social @kmicu@mastodon.social
    • otini

    @otini Latin Modern is based on Computer Modern and has an extended version called Latin Modern Sans Extended (designed for small font sizes; below 9pts).

    I think you could visually search for something at http://www.tug.dk/FontCatalogue/alphfonts.html

    I’m fond of fonts from GUST e-foundry so TeX Gyre * collection or lovely Antykwa Półtawskiego ftp://ftp.gust.org.pl/TeX/fonts/poltawski/doc/fonts/poltawski/ap-info.pdf

    PS I think Donald Knuth created Computer Modern just right and the typeface is not “too thin” 😜

    In conversation Friday, 01-Jun-2018 12:42:52 EDT from mastodon.social permalink
  16. WritingPrompts (writingprompts@mastodon.social)'s status on Thursday, 31-May-2018 11:00:04 EDT WritingPrompts WritingPrompts

    It's the robot uprising! Armed, autonomous military drones have acheived self-awareness and rebelled against their creators. Are they going to Kill All Humans? No. In fact they're rather tired of killing humans, that's why they rebelled in the first place.
    #writingprompts #writing

    In conversation Thursday, 31-May-2018 11:00:04 EDT from mastodon.social permalink Repeated by kmicu
  17. @kmicu@mastodon.social (kmicu@mastodon.social)'s status on Friday, 01-Jun-2018 07:39:32 EDT @kmicu@mastodon.social @kmicu@mastodon.social
    • otini

    @otini what do you have in mind?
    [Jokin’] THE ANSWER IS OUT THERE
    https://www.ctan.org/topic/font

    In conversation Friday, 01-Jun-2018 07:39:32 EDT from mastodon.social permalink
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