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/latest/MIGR…

The Monash Bioinformatics Platform is hiring, 2 exciting roles available: Senior Technical Officer:careers.pageuppeople.com/513/cw/en/job/… and Senior Research Fellow:careers.pageuppeople.com/513/cw/en/job/… @MonashCCS ACBD Monash Research Infrastructure #bioinformatics

Love to see CSIRO using two of my favourite technologies, Dask (Dask) and Apptainer (Apptainer (formerly Singularity)) at the #eResAU2022 Conference! Link: conference.eresearch.edu.au/2022/08/portab…

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

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.

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 +=.

Just another day using the programming language with the world's shortest name. #RStats

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

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 😅)

"A year's worth of weekends" Aaron Lun'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

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.

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

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/en-US/WEHI/det…

Pipeline release! nf-core/proteinfold v1.0.0 (Protein 3D structure prediction pipeline) See the changelog: github.com/nf-core/protei…

🧬💻🔥 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/CuratedAtlasQu…

We're advertising for a Bioinformatics Research Assistant to work with me at WEHI (Walter and Eliza Hall Institute) 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/WEHI/job/Parkv…