Michael Milton
@multimeric
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Research Computing Engineer at @WEHI_research. #Rstats, #Python, #Rustlang, #javascript, #Bioinformatics. More active on Mastodon: https://t.co/UNeZnznJmY
Melbourne, Australia
Joined March 2014
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 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.
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RT @PeteHaitch: We're advertising for a Bioinformatics Research Assistant to work with me at @WEHI_research to process and analyse data fro….
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RT @steman_research: 🧬💻🔥 We are excited to launch #CuratedAtlasQueryR! millions of cells at your fingertips. A thread 🧵. The harmonized a….
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RT @nf_core: Pipeline release! nf-core/proteinfold v1.0.0 (Protein 3D structure prediction pipeline). See the changelog: .
github.com
First release within nf-core Includes AlphaFold2 and ColabFold protein structure prediction methods Thanks to @maxulysse and @adamrtalbot for reviewing this release.
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RT @MelanieBahlo: New Research Officer role available in the Bahlo lab for 2023. Connecting up imaging analysis with genetics. Looking for….
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I wonder if the new #aws Omics service is using the open source AGC ( 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.
aws.amazon.com
Store, query, and analyze genomic, transcriptomic, and other omics data, and then use this data to generate insights to improve health and advance scientific discoveries.
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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.
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RT @PeteHaitch: "A year's worth of weekends" @realAaronLun's efforts to re-write key scRNA-seq @Bioconductor/#rstats packages into C++ for….
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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).
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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 😅)
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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.
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I think this was caused by a weird edge case where I killed the conda process after it had written out the red text escape code but before it could write the regular text escape code. So all subsequent text was red. Not entirely sure though.
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A neat timesaver I just learned for the #zsh shell is updating PATH using `path+=/path/to/bin`. This works because $path is an array which is automatically synced with the string $PATH, using the array append operator +=.
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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.
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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.
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Love to see @CSIRO using two of my favourite technologies, Dask (@dask_dev) and Apptainer (@SingularityApp) at the #eResAU2022 Conference! . Link:
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RT @MonashBioinfo: The Monash Bioinformatics Platform is hiring, 2 exciting roles available: Senior Technical Officer:.
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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):
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