Exciting news! #SAGE is now integrated into quantms.org, thanks to the amazing @OpenMSTeam and @michaellazear. Joining COMET (The STABLE) and MSGF (the Deeper), SAGE brings its speed, efficiency, and youthful vibe to #quantms. Let's celebrate at #HUPO2023! 🎉
✨ In 2022, there is a total of 496 services within #ELIXIR. Including: #LSLogin #ELIXIRAAI @FAIRsharing_org #ELIXIRTeSS @BioContainers #BioTools 👀 Find out more in our 2022 annual report: elixir-europe.org/sites/default/…
#quantms is now a #preprint. quantms: A cloud-based pipeline for #proteomics reanalysis enables the quantification of 17521 proteins in 9,502 human samples. researchsquare.com/article/rs-300… Thanks to @OpenMSTeam @DemichevLab, @nf_core, @BioContainers, #BioConda and @nextflowio team’s. 🧵
Very excited to partner with Genomics England on this one.
Had a lot of fun doing this - a nice beginner friendly tutorial 😊 Take your #Python analysis script and build it into a command-line tool, ready for release via @pypi / #bioconda / @BioContainers 🐍🐳🎉 Watch now on YouTube: youtube.com/watch?v=hOuS6m…
youtube.com
YouTube
nf-core/bytesize: Converting Python scripts into packages for PyPI,...
Hej, todays @nf_core #bytesize talk about python script packaging with Phil Ewels will start in 8 minutes, 1pm CEST. Find the zoom link here: nf-co.re/events/2023/by…
nf-co.re
Bytesize: Converting Python scripts into packages for PyPI, Bioconda & Biocontainers
Phil Ewels - Seqera Labs
Our paper "Automated Discovery of Container Executables" is published in the Journal of Open Research Software! 👉 doi.org/10.5334/jors.4…. This was fun work with @MarcoDeLa83 and Audrey Stott from @PawseyCentre , @mathgeorgia, and Matthieu Muffato of @sangerinstitute.
We created automated pipelines that would not only discover new @BioContainers to add to our online registry, but also executables of interest inside! Our journey included new software, databases, and automation to help developers maintain their own registries. Each of these...
Recent version 1.1.0 of quantms is now out. You can now perform DIA using DIA-NN, DDA-TMT, DDA-LFQ, and Phospho localization analysis. Everything is based on standard file formats including mzML, SDRF, mzTab. Great collaboration with @DemichevLab @OpenMSTeam @nf_core teams.
Pipeline release! nf-core/quantms v1.1.0 (Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.) See the changelog: github.com/nf-core/quantm…
Time for release 🚀. Let me introduce you to the PRIDE Archive USI Viewer @pride_ebi ebi.ac.uk/pride/archive/…. A Spectrum Viewer for every MS in PRIDE Archive. 🧵
Hi there. Today we have written a full tutorial about how to download data from @pride_ebi (ebi.ac.uk/pride/markdown…). We have now 4 options: https, FTP, Aspera, and the new streaming service. 🧵
Would you be interest in a introduction paper about how to use AI tools like Github Copilot in Bioinformatics software development?
I'm so happy today. An open-source, community project I have been contributing for so long from the begining continues flying high. aws.amazon.com/blogs/hpc/bioc…
Announcement at #NextflowSummit - @BioContainers available in ECR @awscloud #container registry aws.amazon.com/blogs/hpc/bioc…
Really excited to announce this one - we've been working with the @BioContainers group to make all of their images available on ECR Public Gallery. This means that bioinformatics containers will not be subject to throttling on AWS. Nice. aws.amazon.com/blogs/hpc/bioc…
Shoutout to @BioContainers for making computing on the cloud easy 😀 More biologist should be using containerized software, and more trainees should be taught how to use it. (or learn on their own)
If you want to learn about the three leading cloud solutions for proteomics data analysis, make sure you register for this workshop. @galaxyproject #TPP @nextflowio #quantms abrf.org/workshops-webi… #Proteomics #MSProteomics #Cloud
Friendly reminder every tool submitted to Bioconda also gets a Docker container from @BioContainers and a Singularity image from @galaxyproject
In this post I discuss software containers and why Binfies can't shut up about them - and reveal one of Bioinformatics' darkest secrets. happykhan.com/posts/dark-sec… tdlr; Containers allows us to hid fragile "academic" code we write in a neat singular black box for you to enjoy.
The @MyABRF Cloud Computing Workshop Registration is Now Open: abrf.memberclicks.net/cloudcomputing… #nextflow #TransProteomicPipeline #usegalaxy
Making @BioContainers compatible with M1 Mac ARM architecture is really important for my work going forwards -- anyone else? github.com/BioContainers/…
If you are interested in collaborating using the workflow, please contact us. !!!!
![bioindocker's profile picture. FREE [Bio in Docker] Symposium, 9-10 November 2015, Wellcome Building, London. #bioindocker15](https://pbs.twimg.com/profile_images/663458187987828736/kisfy_JH.jpg)
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