Mahesh Binzer-Panchal

Fundamentals of FAIR biomedical data analyses in the cloud using custom pipelines As the biomedical data ecosystem increasingly embraces the findable, accessible, interoperable, and reusable (FAIR) data principles to publish multimodal datasets to the cloud, opportunities for cloud...

From @plos.org #Computational #Biology | Fundamentals of FAIR biomedical data analyses in the cloud using custom pipelines | #Bioinformatics #FAIR #Cloud #Education #OpenScience #Nextflow #WDL #CWL 🧬 🖥️ 🧪 🔓
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journals.plos.org/ploscompbiol...

Quantification of transcript isoforms at the single-cell level using SCALPEL - Nature Communications Single-cell RNA-seq facilitates the study of transcriptome diversity in individual cells. Here, authors introduce a tool for isoform quantification at the single-cell level using 3’ scRNA-seq data, co...

I’m really happy to present #SCALPEL, a new #Nextflow tool to quantify transcript isoforms at the single-cell level using conventional 3’ scRNA-seq data #scRNA-seq #single-cell #tools #isoforms
www.nature.com/articles/s41...

Ten simple rules for faculty members building just and equitable environments in academic science

From @drvgmartinacosta.bsky.social & colleagues in @plos.org #Computational #Biology | Ten simple rules for faculty members building just and equitable environments in academic science | #Education #PLOSCBTSR 🧬 🖥️ 🧪 🔓
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journals.plos.org/ploscompbiol...

Release v3.0.0 · EBI-Metagenomics/miassembler Massive work from @ochkalova and @jmattock5 What's Changed Add --iontorrent by @KateSakharova in #40 Increase memory for CANU LR by @KateSakharova in #41 Add more time to CANU LR by @KateSakharova...

We have just released a new version of the Microbiome Informatics metagenomes assembler pipeline - github.com/EBI-Metageno.... Jenny Mattock benchmarked a new contigs cleaning process that Sonya Ochkalova implemented. Great team effort with > 100 comments in the PR. #nextflow @mgnifydb.bsky.social

Used EMBL-EBI data resources to find, analyse, or archive your data? 🧬

Now’s your turn: tell us how you’ve used them + why they matter.

It takes 15 mins and helps keep these services open and free for all.

👉 tinyurl.com/bdf73zpp
Closes 16 July

#opendata #FAIRdata

My time as a Bioinformatics Staff scientist at CalTech is coming to a close and I am looking for the next thing. If you need someone with plenty of experience in sequencing analysis, and pipeline building (Nextflow), please connect. I'm hoping to go back to industry but open to anything interesting.

Colora: A Snakemake Workflow for Complete Chromosome-scale De Novo Genome Assembly www.biorxiv.org/content/10.1... 🧬🖥️ github.com/LiaOb21/colora

Best-practice guidance for Earth BioGenome Project sample collection and processing: progress and challenges in biodiverse reference genome creation Abstract. The Earth BioGenome Project has the extremely ambitious goal of generating, at scale, high-quality reference genomes across the entire Tree of Li

Some useful advice for sample collection to generate a reference genome.

academic.oup.com/gigascience/...

You might know that @nf-co.re is crazy about @nextflow.io pipelines, but did you know that we're also mad about laptop stickers? 😆

We have a whole web page dedicated to them where you can see the whole collection so far: nf-co.re/stickers

Setting up the Nextflow Language Server (LSP) with NeoVim | Living Systems_

New short blog: Setting up the @nextflow.io Language Server (LSP) with NeoVim livesys.se/posts/nextfl...

A slide listing our three contributions to the 25th IEEE International Symposium on Cluster, Cloud and Internet Computing (CCGrid 2025): - Wednesday, 21 May, 11 am (SSP2 session on Software Systems and Platforms – Cloud Continuum): Flora: Efficient Cloud Resource Selection for Big Data Processing via Job Classification (full paper) - Thursday, 22 May, 2 pm (SSP5 session on Software Systems and Platforms – Workflows and Workloads): WOW: Workflow-Aware Data Movement and Task Scheduling for Dynamic Scientific Workflows (full paper) - Wednesday, 21 May, 11 am (SIT2 session on Sustainable IT Systems): Exploring the Potential of Carbon-Aware Execution for Scientific Workflows (short paper)

1/4: If you are at #IEEE #CCGrid 2025 in #Tromsø next week, catch Jonathan, Fabian, and Kathleen (@westkath.bsky.social) presenting joint work! 📰🧵👇

#CCGrid #distributed #sustainable #cloud #computing #research #Spark #Nextflow

We’ve just dropped some powerful new @nextflow.io features as part of the 25.04 release, all designed to enhance clarity, control, and collaboration in workflow development. 🎉

💡Learn more: hubs.la/Q03mQ2_10

Docs: Docker permission errors How to troubleshoot common mistakes and issues

Try with the runOption described nf-co.re/docs/usage/t..., otherwise try the advice further down.

Are you setting your user in the docker.runOptions in the config?

Are you running with docker or some other container platform? Post the issue on the community forum. There's no harm posting and you might find the solution shortly after. Explaining the issue to others might help make an idea pop in your head.

In this (rebutted) grant proposal I wrote that I thought we could see circular RNAs with Vizitig, despite being hard to detect and with low expression. Guess what? Looks very much like a circular RNA to me 😎 (in TET2 gene, human co-assembled cancer RNA-seq samples).

Anaconda Licensing Changes How to use Conda without running afoul of Anaconda licensing.

Nice blog post by @charlottetolonen.bsky.social from a couple of weeks ago about how to use conda for #bioinformatics without running afoul of anaconda licensing:
blog.fulcrumgenomics.com/p/anaconda-l...
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From a single researcher to global R&D teams, the needs stay the same: reliability, scalability, simplicity.

Junior faculty job alert in Germany - Marine Evolutionary Genomics @geomarkiel.bsky.social / University of Kiel www.geomar.de/en/karriere/... Marine study system of your choice (no microbes, sorry…), excellent infrastructure and ship access, moderate teaching requirements, closing date 6 June

Unique investigation of some errors in long read assemblers.

In particular these remarkably chimeric contigs are 😱, if rare....

Improving long read assemblers is definitely the space to be in when it comes to the future of metagenomics, as short reads won't be part of it 😉

Igor and Lucas on Recomb's stage presenting their work

Continuing with @imartayan.bsky.social and Lucas Robidou presenting Hyper-k-mers a novel efficient streaming k-mers representation. A joint work with @npmalfoy.bsky.social and Yoshihiro shibuya

I learned so much in researching this article. Thanks, as always, to the many sources who were so generous with their time, not all of whom made it into the final article, inc. @titus.idyll.org @robp.bsky.social @gvwilson.bsky.social @noamross.net @yabellini.bsky.social and more.

@camillemrcht.bsky.social is back on stage to present Vizitig, an interactive visualization tool for sequencing datasets developped by @bdegardins.bsky.social

Vizitig: context-rich exploration of sequencing datasets www.biorxiv.org/content/10.1... 🧬🖥️🧪 gitlab.inria.fr/vizisoft/viz...

Learn all the basics of pixi tasks.Pixi uses a task runner that allows you to run commands in a cross-platform way.0:16 Simple commands1:12 Depend on other t... Tasks 101 - Pixi - Explainer

Discover Pixi Tasks! 🪄

Watch here: youtu.be/SW3yH9xZBTE

One day left to apply! Not seeing many American applications so far, which puzzles me a little bit. If you have a four-year degree including advanced courses in Ecology or Evolution, you are likely eligible. Happy to answer detailed questions over DM or email.

Headline that says mushrooms may talk to one another with up to 50 words

so they're mycoblogging

Annotation of 200 Insect Genomes with BRAKER for Consistent Comparisons across Species The annotation of genomes lags behind their sequencing and assembly. For example, of 5,092 insect species in GenBank, as one of the most widely used databases, only 375 currently have annotated genome...

Annotation of 200 insect genomes. Work driven by @stepbystepsolution.bsky.social and Mario Stanke within @gevol.bsky.social : www.biorxiv.org/content/10.1...

Plenty of tortured phrases (arxiv.org/abs/2107.0...) in this #IEEE paper. ieeexplore.ieee.org/...

My pubpeer report: pubpeer.com/publicat...

Really cool that the latest VSCode extension for Nextflow shows nf-test test coverage! 🚀