Research Computing Engineer at @WEHI_research. #Rstats, #Python, #Rustlang, #javascript, #Bioinformatics. More active on Mastodon: https://xitter.gq/t.co/UNeZnznJmY
Melbourne, Australia
Joined March 2014
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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 github.com/multimeric/Unipre….
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. uniprot.org/help/query-field…
Michael Milton retweeted
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: wehi.wd3.myworkdayjobs.com/W…
Michael Milton retweeted
🧬💻🔥 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!
-> stemangiola.github.io/Curate…
ALT Cartoon of the structure, content and use of the CuratedAtlasQueryR API. It uses #CELLxGENE data, #DuckDB infrastructure, #tidyverse API
Michael Milton retweeted
Pipeline release! nf-core/proteinfold v1.0.0 (Protein 3D structure prediction pipeline)
See the changelog: github.com/nf-core/proteinfo…
Michael Milton retweeted
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.
wehi.wd3.myworkdayjobs.com/e…
I wonder if the new #aws Omics service is using the open source AGC (aws.amazon.com/genomics-cli/) 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
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.
Michael Milton retweeted
"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 jkanche.com/kana/ #biocasia2022
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 😅)
It's delightfully easy to make fake but plausible protein sequences by browsing NCBI protfam, downloading some interesting families as HMMs and using HMMER's hmmemit.
The sequences will make great sample data for an upcoming workshop I'll be running!
#bioinformatics
Just another day using the programming language with the world's shortest name.
#RStats
It's endlessly annoying that #RStats's native pipe doesn't support piping into operators.
You can almost hear the record scratch sound effect when you realise you need to use [ or [[ and have to rewrite your 20-line pipeline into two separate statements.
Today's infinite loop: sourcing an R script which sources itself.
R doesn't seem particularly concerned by this, it just appears to be running very slowly, when in fact it will basically never finish.
Very easy to replicate:
Sys.sleep(1)
source("this_file.R")
#bioinformatics
Love to see @CSIRO using two of my favourite technologies, Dask (@dask_dev) and Apptainer (@SingularityApp) at the #eResAU2022 Conference!
Link: conference.eresearch.edu.au/…
Michael Milton retweeted
The Monash Bioinformatics Platform is hiring, 2 exciting roles available: Senior Technical Officer:careers.pageuppeople.com/513… and Senior Research Fellow:careers.pageuppeople.com/513… @MonashCCS @ACBDresearch @Monash_MTRP #bioinformatics
Apparently the Environment Modules system used in #HPC (ie module load) supports loading modules from within scripting languages like Python 3, R, Ruby and Perl, as well as some new shells like fish, at least since version 4.0.0 (2017): modules.readthedocs.io/en/la…
