Nathan Sheffield

I'm hosting a virtual open house today at 2-3pm Eastern Time -- Drop in if you're interested in hearing about getting a PhD in Computational Biology at UVA. compbio.med.virginia.edu/meet-cobi/

Interested in learning about doing a PhD in computational biology? Join us for open office hours tomorrow at 11am Eastern. compbio.med.virginia.edu/meet-cobi/

Taming the reference genome jungle: the refget sequence collection standard biorxiv.org/content/10.110… #biorxiv_genomic

We launched a new website for our PhD program in computational biology at UVA. Visit: compbio.med.virginia.edu

Need to combine BED files into a consensus set? Our paper with methods to do this just came out in NAR! --Methods for constructing and evaluating consensus genomic interval sets academic.oup.com/nar/article/52…

BEDMS: A metadata standardizer for genomic regionattributes biorxiv.org/cgi/content/sh… #biorxiv_genomic

@Y_Gilad Here's a somewhat similar encounter I had with it:

I broke ChatGPT

From biomedical cloud platforms to microservices: next steps in FAIR data and analysis: doi.org/10.1038/s41597… -- Read our new perspective on biomedical cloud computing at Scientific Data.

Our paper on standardizing sample metadata is out in GigaScience: academic.oup.com/gigascience/ar…

ATAC-seq pipeline PEPATAC paper now published in NARGAB: doi.org/10.1093/nargab…

New bioinformatics paper: Embeddings of genomic region sets capture rich biological associations in lower dimensions doi.org/10.1093/bioinf…

@labofshort @GuertinLab inkscape > illustrator !

@GuertinLab Use Inkscape instead?

Identity and compatibility of reference genome resources paper is out in NARGAB: academic.oup.com/nargab/article…

New paper in Genome Biology! genomebiology.biomedcentral.com/articles/10.11…

Refget: standardised access to reference sequences biorxiv.org/cgi/content/sh… #biorxiv_bioinfo

Identity and compatibility of reference genome resources biorxiv.org/cgi/content/sh… #biorxiv_genomic

@svheeringen did you figure out a way to do this? you got me thinking about this and I feel like it might not be too hard to write something that could do this with websockets + reveal.js

@BenLangmead I think leaf blowers are the bane of humanity

Anyone else interested in switching from HPC environment modules to linux containers to manage shared group software? Here's how I did it: databio.org/posts/modules_…

@svheeringen @tangming2005 @scarsoncallahan The development version of regenie implements a `refgenie compare` function that uses a bitwise flag system (think samtools flags) to describe compatibility between two genome assemblies. refgenie.databio.org/en/dev/compare/

@svheeringen @tangming2005 @scarsoncallahan we've been thinking a lot about the compatibility question and have some ideas under development -- maybe we can collaborate on ideas for ensuring compatibility. github.com/refgenie/refge…

there are so many genome fasta and gtf files available from different resources: UCSC, Ensembl, genecode. which files are recommended for RNAseq and DNAseq alignment? Heng's post answered some of it lh3.github.io/2017/11/13/whi… what about gtf, gtf should be compatible with fasta