In bioinformatics, people prefer to use the command line interface in the terminal.
But, my skills are not very good enough, I often find myself looking at the file manager on the GUI desktop screen. I'm using Ubuntu, and in my file manager like nautilus, fasta, fastq, sam, bam, vcf, bcf, and other nice formats show up as just plain text or binary file icons.
screenshot of the htslib/test directory https://github.com/samtools/htslib/tree/develop/test
Beautiful icons. This is important to me.
There are a lot of creative people in bioinformatics. I thought that maybe, somewhere in the world, people are creating wonderful icons that I don't know about.
Do you have any favorite Icons?
Thank you.
3 answers
This is an interesting point,
I will say that since we have to deal with so many files and since selecting files via a GUI is not part of the typical tasks that bioinformaticians do the choice of icons is less important for many.
That being said, this made me think about color and presentation in terminal. Perhaps there should be a color scheme to files when listed in the terminal, so that we can easily see which file contains alignment, intervals, sequences etc.
Now there is a bash variable called LS_COLORS that can be set, I have been playing with it a bit, maybe I'll add this to my bash profile :-)
LS_COLORS="*.bam=1;4;31:*.bed=2;32:*.fq=2;33:*.gff=1;4;34"
that looks like this:
Following up on the suggestion by Joe I did a few searches, and it turns out there is even a paper on this:
- bioSyntax: syntax highlighting for computational biology at https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2315-y
and a cool demo site,
I am surprised that I have not seen this project before.
It was announced here on Biostar as well:
likely not exactly what you are looking for but might still be of interest : https://biorender.com/
they also offer to create "icons", but that will come with a cost I guess (as the normal use of the library already has a cost)
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This LINK should help with changing the icons once you find some that you like.