Currently inactive but keeping the profile so it's not taken over. Read more about me on GitHub.
Joined July 2016
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I would go further and say, that not only did we fail, but we were actively obstructed. Every day, #media has the opportunity to make the #ClimateCrisis the foremost issue on everyone's minds. Every day, they have chosen not to.
Many thanks to @SeqeraLabs for sponsoring the @nf_core mentorships. The gift card was a good excuse to splurge on expanding my library =P
ALT Two stacks of books related to software design, systems, and architecture.
Great overview on the newly released taxprofiler pipeline.
📯 A brand new @nf_core @nextflowio pipeline for #metagenomics is out!
🧬 Looking to taxonomically classify or profile your short- or long- shotgun metagenomic reads, but don’t know which tool and/or database to use?
🤩 Why not use all with nf-co.re/taxprofiler !
[🧵1/8]
ALT Metro-map style pipeline diagram of the nf-core/taxprofiler nextflow pipeline, with different 'metro-line' like lines visting stations of different tools used in sequencing quality control, adapter-trimming and merging, complexity filtering, host-removal, run-merging, taxonomic classification/profiling, visualisation and standardisation.
Check out our work on making metagenomic profiling more accessible, reproducible, and run at production scale using @nextflowio
Pipeline release! nf-core/taxprofiler v1.0.0 (Highly parallelised multi-taxonomic profiling of shotgun metagenomic data)
See the changelog: github.com/nf-core/taxprofil…
![Release v1.0.0 - Dodgy Dachshund [2023-03-13] · nf-core/taxprofiler](https://pbs.twimg.com/card_img/2117466189719060480/G6zGaJ_0?format=jpg&name=800x419)
Typically not what I tweet about but it certainly seems important to consider how we engage.
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Got a delivery from you @InformIT, no padding -> books damaged, one 1/4 missing from the order, and now four business days no reply from customer support. What's going on with you? 😠 I expected better from you, much better.
Calling all folks in #Microbiome #Stats, we know that different taxonomic profilers can give different answers. Is it reasonable to try and build a consensus and do you know of good approaches?
To everyone who would like to talk more without Twitter limits, come join us on our Slack channel:
nfcore.slack.com/archives/C0…
e.g., @BenSiranosian @JWoodelius @ctitusbrown @WashburneAlex @piro_vc @alessio_mila @ZellerGroup @thaasophobia
As dev: Thanks for your bug report. Please tell me your OS, #Python, package, and dependencies versions. So useful, k thx <3
As user: They want me to report what? Ugh, that's ridiculous, so annoying.
Enter pypi.org/project/depinfo/
Try it with `depinfo rich` (add --markdown)
ALT Terminal output showing system and package information with versions in a simple tabular format. Ready to be pasted anywhere.
ALT Terminal output showing system and package information with versions in markdown table format. Ready to be pasted into any issue.
For the #Bioinformatics folks using @nextflowio and @nf_core, I've started to document some of the things that have tripped me up.
github.com/Midnighter/nextfl…
I plan to add more as I come across them. If you have other examples or suggestions, please open an issue. 😌
P.S.: I have reorganized the repo a bit better and the whole thing now renders nicely using @squidfunk 's Material for @MkDocsProject
See the result at midnighter.github.io/nextflo…
Happy to see so many people willing to put in the "boring" work that will improve the reproducibility of all modeling results. And of course thrilled to see MEMOTE used @biomodels 💖
Hurray! We started to curate #constraint_based_models such as genome-scale metabolic models using #FROG, a @combine_coord standard developed over the past 2 years. Help us to reproduce your models and contribute to our community manuscript. More info at ebi.ac.uk/biomodels/curation…
I wasn't aware of the origin of the p-value threshold 🤯Makes the whole debate even more dreadful.
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Completely agree but would like to add, there was a very positive atmosphere early on in 2015, then the media and politics did a complete 180.
If you do anything related to #Bioinformatics and always wanted to try @nextflowio but never got to around to it. This is a great opportunity. I work on #Pipelines almost daily now and I can highly recommend it.
🚨 NEW INITIATIVE 🚨 With funding from @cziscience we are offering a new mentorship program for @nextflowio and @nf_core 🎉
If you're looking to get into the world of workflows, have a look! Applications are now open for both mentors and mentees: nf-co.re/mentorships 🤝 (1/4)
Moritz E. Beber retweeted
This isn't Nature PR being thick.
This is a deliberate misinformation attempt to gaslight advocates of open science for denying low income researchers access to publishing.
Nature is doing what corrupt governments do to silence the opposition and break their momentum. – at Oldenburg (Oldenburg), Deutschland
Study finds open-access papers have fewer lead authors from low-income countries than paywalled articles go.nature.com/3gOFVdR