Michael Milton

Research Computing Engineer at @WEHI_research. #Rstats, #Python, #Rustlang, #javascript, #Bioinformatics. More active on
Mastodon:

[Michael Milton @multimeric]

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

[UniProt @uniprot]

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

[Peter Hickey @PeteHaitch]

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

[Michael Milton @multimeric]

@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.

[Stefano Mangiola @steman_research]

🧬💻🔥 We are excited to launch #CuratedAtlasQueryR! millions of cells at your fingertips. A thread 🧵.

The harmonized and reannotated #CELLxGENE #singlecell human #atlas can be
explored and retrieved as #SingleCellExperiment. Please RT!

-> https://t.co/8rwqBqPHMQ

[nf-core @nf_core]

Pipeline release! nf-core/proteinfold v1.0.0 (Protein 3D structure prediction pipeline)

See the changelog: https://t.co/E4lQBsM3cO

[Michael Milton @multimeric]

@braincode Does it work for Linux ⇔ Linux situations? The readme makes it sound like it only runs on Windows.

[Michael Milton @multimeric]

@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.

[Michael Milton @multimeric]

@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?

[Melanie Bahlo @MelanieBahlo]

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

[Michael Milton @multimeric]

@jermdemo It has implications for inheritance law

[Michael Milton @multimeric]

@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?

[Michael Milton @multimeric]

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

[Michael Milton @multimeric]

@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.

[Michael Milton @multimeric]

@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.

[Michael Milton @multimeric]

@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.

[Michael Milton @multimeric]

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.

[Peter Hickey @PeteHaitch]

"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

[Michael Milton @multimeric]

@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.

[Michael Milton @multimeric]

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)

[Michael Milton @multimeric]

use of snakemake for viral assembly!

#bioinformatics (2/2)

[Michael Milton @multimeric]

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 😅)