poly
pg-mem
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poly | pg-mem | |
---|---|---|
24 | 14 | |
648 | 1,790 | |
2.5% | - | |
8.2 | 7.0 | |
about 1 month ago | 15 days ago | |
Go | TypeScript | |
MIT License | MIT License |
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
poly
- Looking for an Open Source project to participate in for Google Summer of Code
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GitHub Accelerator: our first cohort and what's next
- https://github.com/TimothyStiles/poly: Poly is a fast, well tested Go package for engineering organisms.
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These 20 startups are in 1st ever batch of GitHub OS Accelerator
Poly: Fast Go package for engineering organisms
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Ask HN: Burnt out from big tech. What's next?
You might want to look at computational biology. Jim Allison won the Nobel Prize back in 2018 for his work on immunotherapy for cancer and there's a lot of basic research work to be done to perfect this approach. Epigenetic clocks are really interesting too (see Steve Horvath's work). Also, there's synthetic biology, where you could, for example, explore this package that's written in Go: https://github.com/TimothyStiles/poly
- Any corner cases for Needleman-Wunsch that should be tested?
- Where can I find well-written go code to learn from?
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High-performance language recommendation
Check out poly. It’s written in go and I’m using it for one of my projects too. The goal is that we should have high performance libraries that we can use knowing what people are working on the forks will give the community a leg up.
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How is GO used in bioinfo?
The most popular bioinformatic package I've seen in go is poly.
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Software engineers: consider working on genomics
I write synthetic biology software for a living and maintain this open source, Go package for engineering DNA that has high test coverage and a nice little dev community around it.
https://github.com/TimothyStiles/poly
A large part of my project's community are devs that want to get into the field but can't tolerate the ridiculously low pay, laughably bad management, disrespect, and what amounts to 40+ years of technical debt that's endemic to biotech software.
I've had companies here in the Bay Area offer me 100K a year with a straight face. I've had companies during interview tell me they're looking for someone to help, "set up GitHub". I've seen job listings for low paid web dev positions require applicants to have PhDs.
The reality is that except for a growing handful of places management straight up won't know the difference between IT and software engineers. It's what I call the naive buyers problem.
The demand for software engineers in biotech is generated by naive buyers that don't know what they need, why they need it, or how to get it.
Benchling and Recursion Pharmaceuticals have reputations in the industry of paying, "standard software salaries". So do the research divisions at places like deepmind/microsoft/google but in my experience there's even new multi-billion dollar institutes where senior management has never even heard the term devops.
Most places advertise for "data scientist", positions or some analog, instead of software engineers. This is mostly because upper management has never met an actual practicing software engineer in a professional setting. Many come from academia where the culture and work requirements heavily disincentivize standard software engineering practices.
It's also not uncommon for a biotech company to either have a very under qualified CTO whose main programming experience is what they learned doing ML research like stuff during their PhD or not even have one at all which has huge downstream consequences.
This week a software engineer trying to make the switch to biotech actually DM'd me to ask why they were seeing a ton of data science / ML job positions but no software engineering / devops positions.
They were worried that these companies were trying to save on costs by forcing their data scientists to create infrastructure but it's actually worse than that. Most of these companies aren't even aware that there's supposed to be infrastructure.
Despite all of this the future is looking better and I'm starting to find new companies and positions that are well... reasonable. I learned about this thread from a friend at a party last night that works at one of these companies. There's a small, strong new wave of companies and developers out there pushing biotech software forward. Hopefully some (including myself) make it big while pushing the idea that better tech equals better biotech.
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Ask HN: What interesting problems are you working on? ( 2022 Edition)
It is more like the X Y Z W. However, the X Y Z W bits I am working on as well (https://github.com/TimothyStiles/poly , https://github.com/TimothyStiles/allbase , trilo.bio, freegenes.org). Going for fully automated "make bacterium X produce molecule Y", but still a while away (but surprisingly not THAT far off)
pg-mem
- Setting up PostgreSQL for running integration tests
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Show HN: I open-sourced the in-memory PostgreSQL I built at work for E2E tests
I've used pgmem https://github.com/oguimbal/pg-mem for the last couple of years for the same thing.
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Ask HN: How do you test SQL?
I was wondering the other day how to classify tests that use a test double like pg-mem, which isn't a mock but isn't the Dockerized test DB either :
https://github.com/oguimbal/pg-mem
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How to test nestjs modules?
In my case, I use TypeORM with PostgreSQL, and there's pg-mem to run an instance in memory, it supports most of the common functionality of PostgreSQL but you will need to do some adjustment to your code to be within the limits.
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Working with offline data
Postgres in the browser is possible through pg-mem: "pg-mem is an experimental in-memory emulation of a postgres database" but it also suffers from no persistence. If you can persist to a file somewhere then read it in on startup (and if your local data isn't huge) this might work.
- Pg-mem: An in-memory re-implementation of PostgreSQL in JavaScript
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Haskell as a first timer - Am I missing something ? Or is something broken ?
Dont get me wrong: I am trying to contribute to opensource as well, so I get that supporting small projects can be demanding. There's nothing wrong in not spending your weekends on OS. But not asking for help, nor specifying that a project is unmaintained, nor even answering issues & pull requests for years feels just wrong.
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Ask HN: What Are You Working On?
A pure Javascript in memory emulation of Posgres, to help writing better node tests https://github.com/oguimbal/pg-mem
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pg-mem, an in memory postgres DB instance for your unit tests, is now bound to multiple libraries (Knex, Typeorm, Slonik, pg, pg-promise) ... suggestions for the next one ?
Okay, I had a bit of spare time,I've implemented that, and it is now available with [email protected]
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Zero delay development & unit testing iterations
To get a glimpse of what I'm talking about, you can clone this repo and follow "Development" instructions (by the way this is a small OS lib I maintain, I wrote about it here)
What are some alternatives?
Raylib-CsLo - autogen bindings to Raylib 4.x and convenience wrappers on top. Requires use of `unsafe`
NeDB - The JavaScript Database, for Node.js, nw.js, electron and the browser
linaria - Zero-runtime CSS in JS library
Prisma - Next-generation ORM for Node.js & TypeScript | PostgreSQL, MySQL, MariaDB, SQL Server, SQLite, MongoDB and CockroachDB
seq - A high-performance, Pythonic language for bioinformatics
Lowdb - Simple and fast JSON database
m4b-tool - m4b-tool is a command line utility to merge, split and chapterize audiobook files such as mp3, ogg, flac, m4a or m4b
typescript-clean-architecture - It is my attempt to create Clean Architecture based application in TypeScript.
full_spectrum_bioinformatics - An open-access bioinformatics text
maplibre-gl-js - MapLibre GL JS - Interactive vector tile maps in WebGL2
procedural-gl-js - Mobile-first 3D mapping engine with emphasis on user experience
database-js - Common Database Interface for Node