Forum:Do you have favorite icons for bioinformatics?

Question

[kojix2]

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.

[GenoMax]

This LINK should help with changing the icons once you find some that you like.

Answer 1

[Istvan Albert]

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:

[Joe]

I believe there are a few repos scattered around GitHub that implement this and bio specific in-file syntax highlighting.

Answer 2

[Istvan Albert]

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,

• https://biosyntax.org/

I am surprised that I have not seen this project before.

[Istvan Albert]

It was announced here on Biostar as well:

• Announcing bioSyntax: Syntax highlighting for biological files

[Ram]

I recall seeing this post and trying this way back when. It has a dependency that is mostly hit-or-miss even with simple files that have a shebang line on top.

Answer 3

[lieven.sterck]

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)