Shawn M. Simpson

Computer Scientist||Data Scientist||Bioinformatician||Real-Life MacGyver||Jack Of All Trades|| 🇧🇧 || views are my own||

[Shawn M. Simpson @ShawnSimp246]

@martinalexsmith Congrats!!!

[Shawn M. Simpson @ShawnSimp246]

Bioinformatics the poem by #ChatGPT #Bioinformatics

[The Smith Laboratory @TheRealSmithLab]

We tested the @OmixonBio NanoTYPE HLA typing kit on PromethION. A sample with 100k reads took ~7m to analyze with the NanoTyper tool. Results look good, easy to interpret with many details. Could benefit from better confidence score in report than 🟢🌕🔴 & less complex than this:

[Shawn M. Simpson @ShawnSimp246]

@MudabirAbdullah

[Shawn M. Simpson @ShawnSimp246]

@MudabirAbdullah @brittanygreco18 @devinasingh30 Congrats!! @MudabirAbdullah 🎉🎉🎉 Well done!!

[James Ferguson @Psy_Fer_]

Want to basecall faster? Want to scale your basecalling with hardware? Use our new tool: buttery-eel, to basecall SLOW5 files with the latest guppy basecaller and models, including methylation with remora -> uSAM.

https://t.co/atoX9QvWs4

[Shawn M. Simpson @ShawnSimp246]

*Flashbacks*

[Martin Smith @martinalexsmith]

2 new PhD students are arriving to Montreal from tropical or warm countries in the next day or so. I can only immagine how much of a shock this will be!
https://t.co/3gYXLO39Ij

[The Smith Laboratory @TheRealSmithLab]

Great cancer research session at #NanoporeConf 👏
Feel free to ask unanswered questions for @melanie_sagniez here as well :)

[Martin Smith @martinalexsmith]

I'm #hiring 💰 a #fullstack #developer 👨‍💻 to help us bring #realtime #clinical #genomics 🧬 to the clinic and help save lives⚕️

This project involves deploying a #diagnostics reporting workflow using an #AI algorithm applied to #RNA… https://t.co/xnaqdGHrbR

[Oxford Nanopore @nanopore]

How is #nanopore sequencing helping in our understanding of the #transcriptome in #cancer? How has it benefitted your work? What first ignited your interest in #genomics and #bioinformatics? @melanie_sagniez shares her thoughts during this interview: https://t.co/EULq3rP76Q

[Shawn M. Simpson @ShawnSimp246]

@MariekeR4 😅😅

[Shawn M. Simpson @ShawnSimp246]

Coding via an unstable VM must be considered an extreme sport.

[Chris Seymour @iiSeymour]

Happy to share our first release of dorado 🎉

- Multi GPU support
- Latest quantile scaling
- Automatic parameter selection for best performance

Plus a whole lot more!

Make sure to try it with Pod5 to really see it fly 🔥

https://t.co/vkNVVA8rlt

[Shawn M. Simpson @ShawnSimp246]

@martinalexsmith @danrdanny @Hasindu2008 @nanopore Before and after slowtools compression of a 3-4hrs sequencing test run with the PCS111 kit.

[Shawn M. Simpson @ShawnSimp246]

@martinalexsmith Time to progress away from plain old R terminal and immerse yourself into Rstudio and VScode. The time is now.

[Kareem Carr, Ph.D. @kareem_carr]

her: babe what you thinking about

me, a data scientist:

[Shawn M. Simpson @ShawnSimp246]

very niceee

[Martin Smith @martinalexsmith]

Our latest preprint is out: Ultra-fast (like 5 min) molecular #diagnosis of #leukemia using #nanopore #transcriptomics !! 👇🧵

[Shawn M. Simpson @ShawnSimp246]

@BiologistQuirky @TheRealSmithLab Depends on available resources allocation and process run-time.

[Shawn M. Simpson @ShawnSimp246]

Making good use of the interns. @TheRealSmithLab #TeamBonding #ManyHandsMakeLightWork