Some hard truths for open source adoption from @bert_hubert

His #1 is also my #1:

"Whatever you’re building, you have NO margin to get away with being uglier/harder/more difficult than big tech"

and "If you don’t have people who deeply care about user-experience in your team, you’re doomed"

Open source has so many adoption barriers that only people who care a LOT will get over them. But honestly, most people don't have enough care to spare right now.

Worth a read.

https://berthub.eu/articles/posts/what-the-open-world-must-do-better/

Bioinformaticians are impatient👇
Conda is notorious slow... then I found mamba https://github.com/mamba-org/mamba, then I found
pixi https://prefix.dev/blog/pixi_a_fast_conda_alternative : Blazing fast cross-platform package management for teams.
By the creators of the mamba package manager. #bioinformatics

Hostile 1.0.0 released and live on Bioconda
- Adds human genomes masked against bacteria, viruses and phage
- Improved automatic index download
- Improved genome masking
- Bug fixes
https://github.com/bede/hostile

Clear Aeropress confirms long-held hypothesis that even the most gentle swirling after inversion (to remove stuck grounds on plunger) creates a problematic domed coffee bed

After positive reviews, the paper about our host decontamination approach 'Hostile' was accepted in Oxford Bioinformatics:
https://doi.org/10.1093/bioinformatics/btad728

Related blog post:
https://log.bede.im/2023/08/29/precise-host-read-removal.html

Simple utility for making robust sequence checksums from one or many FASTA/Q records
https://github.com/bede/seqsum

Just published in JOSS: 'gesel: a JavaScript package for client-side gene set enrichment' https://doi.org/10.21105/joss.05777

We've made it even easier to discover new viruses! Consensus genomes are now part of the standard output for the Twist Comprehensive and Respiratory Viral Research analyses. Find out more in our blog post: https://www.onecodex.com/blog/2023/08/22/consensus-genomes-using-twist-research-panels/

Blog post: precise removal of host DNA sequences https://log.bede.im/2023/08/29/precise-host-read-removal.html

On that story about scientists leaving X and coming here. Please, please lean into the feature of hashtag following and tag your stuff. A lot of us would love to find you and hashtag discovery is the easiest way here.

#scientists #scientist #mastodon #followers #discovery #news #science

@pvanheus @karinlag IKR, at one point I swear it it read 101% and yet I was still receiving email

@timbray Anticipating dramatic improvement in the quality of their journalistic outputs…

@karinlag I had been at 99-100% for years 🥲

Motivated by the recent discussion around the cancer microbiome, I’ve written a small blog investigating some of the difficulties in normalising microbiome data. https://github.com/gtonkinhill/TCGA_analysis

@karinlag I finally caved in last week 💸

Major data analysis errors invalidate cancer microbiome findings https://www.biorxiv.org/content/10.1101/2023.07.28.550993v1.full #cancer #microbiome

Recording of my talk on host DNA decontamination to CDC's Technical Outreach and Assistance for States Team 🍞
https://centersfordiseasecontrol.sharefile.com/share/view/sd2b41f03c8c846499828a125a348659e

@phylogenomics I've been impressed with the Levoit Core 300. If I wanted smart features I'd spend double and get a Philips.

The One Codex search UI is simply delightful

Who's excited for Threads