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Benchling Engineering
benchling.engineering · Company blog · on HN since 2015
Benchling's engineering team writes about Postgres migrations, React performance, and CRISPR and DNA search for its biotech software.
What HN saysHN commenters call its Lambda-based CRISPR search a compelling use case, and discuss its migration and React performance posts, with one saying the migration post is too high-level.
21HN people shared it
5linked it in comments
37stories submitted
1.1Kstory points
2 years agolast shared
2015people per year2026
Most-shared posts
- 1Move Fast and Migrate Things: How We Automated Migrations in Postgres3 people · 194 points · first shared 2019 · 54 comments on HN
- 2Building a Regex Search Engine for DNA3 people · 118 points · first shared 2016 · 35 comments on HN
- 3Powering CRISPR with AWS Lambda3 people · 110 points · first shared 2015 · 45 comments on HN
- 4Enforcing Transitive Constraints in SQL3 people · 20 points · first shared 2018 · discussion on HN
- 5Performance Engineering with React, Part 12 people · 158 points · first shared 2016 · 38 comments on HN
- 6Optimizing CRISPR: Sub-second searches on a 3 billion base genome2 people · 70 points · first shared 2015 · 33 comments on HN
- 7Building computed fields in a biological database2 people · 16 points · first shared 2017 · 2 comments on HN
- 8Analyzing performance analysis performance (or, why is EXPLAIN ANALYZE slow)2 people · 11 points · first shared 2019 · discussion on HN
- 9Sqlalchemy_batch_inserts: For When It's Slow to Insert Thousands of Rows2 people · 5 points · first shared 2020 · discussion on HN
- 10Jade to React: using prod validation to make modernization safe, fast, and fun2 people · 3 points · first shared 2019 · discussion on HN
- 11From 200K lines of CoffeeScript to zero: making decaffeinate super-stable1 people · 95 points · first shared 2018 · 29 comments on HN
- 12A Deep Dive into React Perf Debugging1 people · 83 points · first shared 2016 · 4 comments on HN
- 13Modeling Science as a Directed Graph1 people · 79 points · first shared 2017 · 17 comments on HN
- 14Parallel C++ on AWS Lambda for CRISPR1 people · 72 points · first shared 2018 · 17 comments on HN
- 15Evolving to Enterprise-Grade Permissions1 people · 26 points · first shared 2019 · 8 comments on HN
What HN people wrote when they linked it
awinter-py · 2022-05-16
programming in time is hard
(especially with migrations, because migrations take time)
this feels too high-level -- different migration operations can afford different guarantees (esp in the multi-node case). In particular this doesn't talk about data migrations, where you might need to lock 2 tables + join them to generate a third. not all migrations are pure-sql either, they may include app code
my favorite article about this is benchling's https://benchling.engineering/move-fast-and-migrate-things-how-we-auto… because it talks about pre + post deploy migrations
wcjordan · 2017-05-25
It is, so a DOM change wouldn't occur, but in these cases you still go through a React rendering to virtual DOM phase (templating) and the DOM tree reconciliation.
Since these can be slow (although much faster than a DOM change), it makes sense to check and skip those steps when you can.
The focus of most of this article is how you can skip those steps when you're components input data is unchanged and common gotchas related to that.
Some other great posts in this vein are:
https://facebook.github.io/react/docs/optimizing-performance.html
and
http://benchling.engineering/performance-engineering-with-react/
leeoniya · 2016-06-23
maybe WRT to https://www.google.com/search?q=genome+sequencing+algorithms which would be needed to find unique patterns among billions of base pairs for CRISPR to target. it's microscopic big data :D
[1] http://benchling.engineering/dna-regex-search/?hn
[2] http://benchling.engineering/optimizing-crispr/
dankohn1 · 2016-01-18
I would be thrilled if they provided an update, but Benchling's CRISPR search is what originally got me excited about Lambda. It's an incredibly compelling use case, as it enabled one second searches at any level of demand. And, their hosting costs dropped from thousands of dollars on EC2 to $60 on Lambda.
http://benchling.engineering/crispr-aws-lambda/
dikaiosune · 2015-12-24
I don't know the answer to how Neon would affect that, but AFAIK, you can already do this:
http://julienblanchard.com/2015/rust-on-aws-lambda/
But that uses a shell command. There's also this way to do so using FFI (article is about C++, but I'm pretty sure you could do the same with Rust):
http://benchling.engineering/crispr-aws-lambda/