@flowuenne.bsky.social
Bioinformatics engineer at Seqera (seqera.io) & Nextflow ambassador Genomics 🧬 | Spatial omics🔬 | technology 💻 | soccer ⚽ Working towards scalable and reproducible science with #Nextflow Living in Montreal 🇨🇦
Check out the blog post by Nextflow Ambassador Zohaib Anwar on VIRUS-MVP: a flexible and scalable workflow for genomic surveillance of priority viruses including SARS-CoV-2, Mpox, RSV, and influenza! 🦠
👉 Read now: hubs.la/Q03lM5KG0
#NextflowAmbassador @nf-co.re
Check out this fantastic work on neighbourhood preference in spatial omics data from the Schapiro lab 🚀! Congratulations @chiaraschiller.bsky.social and team on a wonderful project! 👏🤩
16.04.2025 11:27 — 👍 4 🔁 1 💬 0 📌 0You should definitely check out this amazing Nextflow podcast episode with my friend and collaborator @kbestak.bsky.social discussing microscopy and spatial omics workflows in nf-core and Nextflow! 🤩🔬🧪
04.04.2025 14:07 — 👍 2 🔁 0 💬 0 📌 0Glad you enjoyed the training, thanks for attending and the shoutout here @mragsac.com! Always happy to show how #Nextflow works to people and how they can benefit from using it.
For anyone that wants to use the training materials, they are available at training.nextflow.io!
My latest #Nextflow pipeline has just been published in JOSS 🎉
15.03.2025 19:45 — 👍 2 🔁 2 💬 0 📌 0Running Nextflow pipelines on AWS ☁️? Check out the blogpost I wrote about using resource Labels with Nextflow and Seqera to get detailed pipeline run costs 💵.
11.03.2025 13:23 — 👍 2 🔁 0 💬 0 📌 0Major heartbreak when it happened. Reminded everytime I watch the movies 😭. Guess no one ran around with "Hedwig dies on page xxx" shirts at the time to spoil you 😉
10.03.2025 18:43 — 👍 1 🔁 0 💬 1 📌 0If you want to start learning #Nextflow or brush up on your basics of #Nextflow, now is the perfect time 🕑!
New training materials and support from ambassadors and experienced community members during training week help guide you through it, at your own pace!
community.seqera.io/t/nextflow-t...
Come and talk about your amazing projects at the #Nextflow summit in Boston 🎤!
I am very sad to miss this summit this year, but it will be a fantastic event, so make sure you to submit your abstract before the deadline 🤩!
Great opportunity to get together with your colleagues and friends and watch the training videos to learn Nextflow together 👥.
💬 Discussing things not clear to you and sending questions to the community forum are all great ways to accelerate your learning experience and increase the fun 🚀 🤩!
Interesting to see doom and gloom as separate ends of a governance axis!
24.02.2025 18:24 — 👍 8 🔁 2 💬 1 📌 0
New blog post: Exploring the bioRxiv API with R, httr2, rvest, tidytext, and Datawrapper doi.org/10.59350/wzt... #Rstats
10.02.2025 10:59 — 👍 30 🔁 7 💬 1 📌 0
Introducing @gestaltsp.bsky.social
We’re growing with already >1000 members.
Come be part of spatial omics revolution!!! @ioavlachos.bsky.social @lgmartelotto.bsky.social @naturegenet.bsky.social rdcu.be/d8qHT
#spatial #omics #technology #computation #tissue #singlecell
Don't miss this chance to listen to my amazing colleagues Esha and Rob talk about how you can utilize Seqera Platform to help streamline your scientific data analysis! 🤩
27.01.2025 11:52 — 👍 2 🔁 0 💬 0 📌 0📣 We are hiring!
Join Yoshiji Lab at McGill University Dept of Human Genetics in Montreal, Canada!
yoshiji-lab.org/joinus
✅Fully Funded Positions
• 2 MSc Students
• 1 PhD Student
• 1 Postdoc
✅Goal: Using human genetics and multi-omics for drug target discovery and precision medicine
I think I found the talk. Thanks for the recommendation and for sharing your experience! 🙏
youtu.be/2DbuqYKOsrY?...
You can now use Seqera AI with MultiQC! 🤖
Get insights from your reports and chat about potential QC issues with Seqera AI, directly from inside your MultiQC reports! Fantastic new update by everyone involved at @seqera.io !
Protein structure embeddings reveal undersampled and de novo structure space. (B) First two principal components of mean-pooled ESM3 embeddings colored by helix content determined by DSSP. The indicated dashed guide lines denote visual boundaries of native structure space not sampled (Undersampled) and novel regions of protein structure for this space only observed in samples but not in native structures (De novo). (C) Rasterized visualization of panel B with 16 equally spaced grid squares in each principal component axis. A representative structure from each grid was chosen at random. Empty grid squares indicate the absence of any structure in the enclosed region. De novo alpha helices are shaded along the lower-right diagonal and the structures from CATH which do not have corresponding structures in the samples are shaded along the left and top rims. The structures are displayed in CATH raster plot are given in the Supplementary Information.
Protein backbone diffusion models consistently undersample catalytically important motifs, and oversample idealized helices, raising questions about the appropriateness of these methods in designing starting points for enzyme design & evolution. From www.biorxiv.org/content/10.1...
19.01.2025 16:40 — 👍 86 🔁 16 💬 2 📌 0That looks amazing, congrats @sunjaelee.bsky.social 👏! Is the code to make the sankey diagrams available somewhere? Would love to play around with that 🤩!
17.01.2025 17:05 — 👍 2 🔁 0 💬 1 📌 0Are you looking for job opportunities where your #Nextflow skills are valued? Check the list we've compiled below. #Jobs #Opportunities
14.01.2025 14:44 — 👍 2 🔁 3 💬 1 📌 0Extra! Extra! If you're into cardiovascular development and regeneration, and you want to hobnob with all them awesome scientists, then follow @weinsteinconf.bsky.social and submit an abstract for the 2025 Weinstein Conference in Milwaukee!! #favorite #conference #ever
14.01.2025 20:37 — 👍 1 🔁 1 💬 0 📌 0
Interesting concept. jetty::run() executes R code in a Docker container and passes the results back into the local environment https://cran.r-project.org/web/packages/jetty/index.html (source: https://github.com/dmolitor/jetty)
13.01.2025 21:00 — 👍 17 🔁 3 💬 1 📌 0I am organizing a local site in Montreal for this @nf-co.re hackathon 🇨🇦. Anyone in the area who is interested to help organize or join this hackathon and a potential #Nextflow training before, please DM me 😊!
08.01.2025 16:36 — 👍 5 🔁 1 💬 0 📌 0Do you want some AI guided help to write #Nextflow pipelines or convert your old legacy pipelines to #Nextflow? Go to seqera.io and try out Seqera AI now 🤩!
08.01.2025 15:33 — 👍 1 🔁 0 💬 0 📌 0
Nextflow4MS-DIAL: A Reproducible Nextflow-Based Workflow for Liquid Chromatography–Mass Spectrometry Metabolomics Data Processing #JASMS pubs.acs.org/doi/10.1021/...
05.01.2025 19:20 — 👍 7 🔁 3 💬 0 📌 0
For anyone that loves poker and card games, Balatro is such a great game! Just started playing it again on my tablet via Apple Arcade and having a blast 🎮🃏!
apps.apple.com/ca/app/balat...
I hope you enjoyed this Advent calender experience and discovered some new aspects around Nextflow you might have not been aware of.
If you made it to the end of this thread and simply wanna play Nextflow snake 🐍, this is for you 🎁:
flowuenne.github.io/nextflow_adv...
The entire Calender was developed with cursor.com using the Claude-3.5-sonnet model 🧑💻. The music 🎵 was also generated using AI with suno.com.
I didn't put a lot of emphasis on protecting the different secrets in the source code, mainly as a backup for people to proceed if getting stuck.
To use the final password, click on the reindeer and Santa emojis flying past on the final page for Day 24. This will reveal the final surprise, which I won't spoil for you here 😉
30.12.2024 15:54 — 👍 0 🔁 0 💬 1 📌 0
Santa's pipeline requires a specific parameter to be run, which you can reverse engineer or guess from the tip. It's of course: Rudolph.
Once you run the pipeline with:
nextflow run SantaFlowHoHoho.nf --reindeer Rudolph
You will get the next secret key: MerryNextChristmas
