Check out the first release of our @nf_core @nextflowio pipeline for processing @ResolveBioSci Molecular Cartography data🤩! Had a lot of fun working on this with @KresBestak 🎉. Reach out to us if you have any questions or need help getting started!

Aggregating Residue-Level Protein Language Model Embeddings with Optimal Transport 1. This study introduces a novel protein representation method using sliced-Wasserstein embedding (SWE) to aggregate residue-level outputs from protein language models (PLMs) into fixed-length, protein-level embeddings. SWE addresses limitations of traditional average pooling by capturing essential sequence information often lost in standard aggregation methods. 2. SWE interprets token-level embeddings as samples from a distribution and maps them onto a reference set using optimal transport, creating embeddings that retain critical information from variable-length protein sequences. This approach significantly outperforms average pooling, especially for longer sequences, by preserving details vital for accurate predictions. 3. Using SWE, small PLMs achieved comparable or superior performance to larger models with average pooling across several tasks, including drug-target interaction (DTI), enzyme commission (EC) prediction, and subcellular localization, making PLM use more accessible for researchers with limited computational resources. 4. This approach enhances interpretability, as the learned reference embeddings represent key features of protein-level tasks, providing insights into protein structure-function relationships and offering a scalable solution for protein-level prediction tasks. @rohitsingh8080 💻Code: github.com/navid-naderi/PLM_… 📜Paper: biorxiv.org/content/10.1101/… #ProteinLanguageModels #MachineLearning #Bioinformatics #OptimalTransport #ProteinRepresentation

Happy to release a concise review of recent progress in sequence-structure co-generation for protein design. with our amazing intern @WChentong @SarahAlamdari Carles Domingo-Enrich and @avapamini

Writing the Response to Reviewers document

Really excited for this talk by @GrapotteM about how to use Nextflow for training deep learning models! Really great to see Nextflow adoption in many new areas & fields!

It’s time for the #NextflowSummit BCN speaker series! 🎉 Let's welcome our first speaker Ziad Al Bkhetan, Product Manager at @AusBiocommons 🎤 He’ll present "The Australian ProteinFold Service: Interactive Prediction & Visualisation of Protein Structure" summit.nextflow.io/2024/barc…

Happy to share Novae, our new foundation model for spatial transcriptomics data 💫 Load a pre-trained model and start using Novae in two lines of code! biorxiv.org/content/10.1101/… github.com/MICS-Lab/novae

Are you looking for job opportunities where your #Nextflow skills are valued? Check the list we've compiled below. #Jobs #Opportunities

#scverse2024 conference is on! We, @scverse_team, couldn’t be more excited to meet everyone here! We all know each other and finally get to hang out together. Amazing moments for the “young” science!

Come join us at 5Prime as we build software and algorithms to bring more medicines to patients. Senior Full Stack Engineer posting: linkedin.com/jobs/view/40215…

I remember using @nextflowio for the first time and experiencing the portability, reproducibility and parallelization it provided. With Seqera you can now take this one step further and optimize your workflow resources, manage teams and scale your workflow executions! 🚀

Still time until 15th September to submit an abstract to join us in Berlin in the @SpatialBio conference 👇

Watch the talk from Joseph Rich, grad student in @lpachter's lab, from BioC2024 timestamp ~12:30 youtu.be/T6cOyKHlxpE?si=2_Wz…

Processing raw data using efficient, scalable @nextflowio pipelines and then performing interactive data analysis is a common use case for scientists! @SeqeraLabs Data studios brings the tools you love next to your data in the cloud 🤩☁️.

I find it really interesting that biotechs & institutes often build their own bioinformatics workflow managers: - Insitro: Redun - GRAIL: Reflow - 10X Genomics: Martian - Invitae: in-house engine - CZI: Swipe - Broad: Cromwell - UCSC: Toil What does the future look like?

Nextflow Jobs🤩. Do you know of a #job opportunity where #Nextflow skills are valued? Let me know 🙏

What an amazing conference! Congrats to the organizers for doing an amazing job of putting this event together. It was awesome to meet so many amazing people, discuss their work and how @nextflowio can help make their research reproducible and scalable!

If you are in Montreal at #ISMB2024 or #BOSC2024 find us at Table #15 to talk all things #Nextflow and @SeqeraLabs ! Excited to see you there 🤩!

🚀 Big news in Nextflow! The latest 24.04 release is packed with genuinely groundbreaking features and enhancements that transform your pipelines. From job arrays to new resource limits and Seqera Containers, new "topic channels" and a workflow output definition (adios publishDir!). This release has it all. Let's jump into the details!