Meetups/Infra/2023-12-04

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(= Meetup - Infra =) 2023-12-04 m

Lesson & lecture in software for biology, from Tim. Discussion of go's "example test" pattern, that provides 1) unit tests, 2) public usage examples, for libraries, and makes

Meetup/Infra

Introductions[edit]

  • loren - running meetup - self-hosting
  • tim, longtime noisebridger - genetic engeering software (synthenthic DNA modelling). Devops CI/CD. Kubernetes playing around with, get into self-hosting 3 old computers that could have a shit-ton of power. Open stack? vs Kubernetes Cluster. For work maki
  • David, Math, Software Engineer. At home setting up home-server. Wrote an SSL Generator (using NGINX, dockerized services) github user: lidj22. Also interested in Kubernetes. Time to bite the bullet, somehow running lots of jobs.
  • Abdul. Background in engineering. Software engineer. Checking out space (working on electronics). Couple of GPU Clusters working LLM models.
  • Brandon: new to software development in and out of tech for past decade recent. Goal: learn docker. More linux (debian)
  • Doug: background in software, physical engineering, light math. Met someone today, in 70s, phone from GA, bought 80 solar panels, said "if it's interesting, I'm interested in it." Here to learn, listen, share (crazy stories)
  • Tess: all software of software development, desktop linux, recently web stuff, building a web server in C. Here to check this out, first time
  • Greg . Rust backend engineer at a fintech start up. 4U Server in kitchen running servers. Nix + Random Programming Projects.
  • Flying Eagle - working on Jet Engines. Meet all of us - how best to support us.


Goals[edit]

docker, self-hosting,

storage, gpu img, SQS

Topics[edit]

  • Old(?) Moore's law (end of?), Dennard scaling. ...
      • Gordon Moore
      • Current sharp end (for further reading): TSMC, and their least price-sensitive customers: Apple, Nvidia, maybe others.
      • Feature size, node numbers
    • Tim - comments? example tests - Go & Rust run them automatically
      • Bio


https://github.com/TimothyStiles/poly can print DNA with inkjet printers, see HP spinoff Agilent. error rate about 1/200, is current standard (current common / acceptable)

friend: 20-30% of the oligo's were correct, proudly published.

certain sites (DNS receptive sites, targets for enzymes) have to be banned from printing, because


Deciding to go Rust (vs go) in the future. Unit tests.

Problem: different pieces of DNA express differently in a different organism. Certain cells favor certain codons (triplets in DNA that encode for amino acids)


Enamoured with example tests in documentation: https://pkg.go.dev/https://github.com/TimothyStiles/poly

Auto-testing: go, rust Harder for, or less common: storybook, playbook.


War stories Excel issues - non-reporducible studies Excel issues - auto conversion of

George Church paper, only perl unspecified version.

ASN.1. GenBank. EU, US, Japan - slightly differing formats. Whitespace constants.

Spec for bio data, only found on European site with sketchy certificates,

Ontology. Projects wanting to build new ontologies, for biology.


Bioinformations commuity. Vectorization? Yes. Microscopy, and DNA reading (many sequencing mechanisms),


  • History of Go?


  • Tim, self-hosting questions - 3 computers, and separate goal of 8TB db.


  • Docker
  • Kubernetes, k8s. k3s, kind / kube in docker, minikube, rancher.


Questions, Discussion, or Coworking[edit]

  • [Issue]

For next time[edit]

  • War stories. Drinking (or alt drinks) Network engineer.


Questions[edit]

Readings & Exercises[edit]

  • Readings
  • Exercises

Join online[edit]

  • Try it yourself!
    • Join libera.chat #nb-meetup-infra

https://www.noisebridge.net/wiki/Meetups/Infra https://www.noisebridge.net/wiki/Meetups/Infra/2023-..-..