I've developed a #python package for querying UniProt's new REST API! Maybe the first to fully support the new format. Check it out at https://t.co/tUtK0XI7vv.
In particular I've tried hard to integrate with Python tooling, giving you great code completion:
#bioinformatics
We are now providing a new API to access UniProt's data and tools. Here are the supported query fields for searching specific data in UniProtKB. https://t.co/7m8B0RJutI
We're advertising for a Bioinformatics Research Assistant to work with me at @WEHI_research to process and analyse data from a range of single-cell and spatial 'omics technologies.
Full details of the role & how to apply: https://t.co/THXO1Dyybd
@ClausWilke @iferres91 @jessenleon @yutannihilat_en @quaternioso@minigamedev@jessenleon You are welcome to join the extendr discord! My understanding is that the CRAN machines now have Rust + Cargo installed so they can compile Rust packages: https://t.co/sUQxWRFFl6.
@tgamblin@FluxFramework This is a good summary, I didn't realise Flux was a job scheduler? Each of the many times I've gone to https://t.co/UzWejSSltm and read "Flux is a flexible framework for resource management", my eyes glaze over and I go do something else. I wish there was a "Flux vs SLURM" page.
@charliermarsh I suspect that PEP 582 will mostly solve this by removing the need for virtual environments and therefore needing a wrapper script (like poetry run) at all. PDM is the most popular package manager to implement PEP 582, so maybe chuck that in to the benchmark?
New Research Officer role available in the Bahlo lab for 2023. Connecting up imaging analysis with genetics. Looking for an image analysis specialist with interest in learning about genetics in a highly collaborative lab.
https://t.co/jeAixmGbcL
@jdidion@geoffjentry True about containers, but this goes beyond that, down to the level of the nextflow integration. Why write two sets of nextflow-on-AWS infrastructure?
I wonder if the new #aws Omics service is using the open source AGC (https://t.co/iK6JUK5BrH) behind the scenes? It would make sense to develop and road test the workflow system separately in this way, before providing it later as a paid service.
#bioinformatics
@geoffjentry@fiamh It even supports snakemake! (https://t.co/WwxqiXCAx5). It's really quite a nice system, it would be a shame if it gets replaced entirely by Omics.
@fiamh@geoffjentry Another good catch. Although possibly they dropped CWL/Toil because it was their smallest user demographic and don't want to support it commercially. Which wouldn't necessarily rule out AGC internals, although it probably does.
@geoffjentry Interesting! If that's true, I wonder why they developed two separate workflow integration layers. Admittedly there are some visible differences like the lack of `agc-project.yaml` type config file in Omics, but that may just have been abstracted away.
Well, I'm a total convert to the #podman container engine. Full (?) implementation of the #docker API + CLI, fully open source, super easy to install, built-in support for MacOS via virtualisation, and even installs + runs without root. I think it even beats out #apptainer.
"A year's worth of weekends" @realAaronLun's efforts to re-write key scRNA-seq @Bioconductor/#rstats packages into C++ for use with WASM for the magic that powers https://t.co/urLNxFPBBo #biocasia2022
@jermdemo I think the question was just an earnest version of the standard question "how is <TOOL Y which is new to me> better than <TOOL X that I have been using for years>". It was only funny to people who know how hotly debated this particular horse race is.
The eternal battle between #nextflow and #snakemake continues at #ABACBS22 as the invited speaker from nextflow's parent company is challenged by the audience to compare the two workflow managers. Immediately following is a contrasting presentation which demonstrates the (1/2)
A prize to the first person who can successfully allocate a >1 quettabyte (10^30 bytes) vector in #rstats and manage to call object.size() on it!
(I take no responsibility for bankruptcy from cloud charges and/or murder by sysadmin that may result from attempting this 😅)