Forum:Ten Recommendations For Creating Usable Bioinformatics Command Line Software

Question

[Medhat]

Hi,

I found interesting paper that I want to share, It talks about the roles that any one should follow if he want to develop command line tool

Bioinformatics software varies greatly in quality. In terms of usability, the command line interface is the first experience a user will have of a tool. Unfortunately, this is often also the last time a tool will be used. Here I present ten recommendations for command line software author’s tools to follow, which I believe would greatly improve the uptake and usability of their products, waste less user’s time, and improve the quality of scientific analyses.

Ten recommendations for creating usable bioinformatics command line software

Answer 1

[Alex Paciorkowski]

I felt like this was old information, and then was surprised to see the paper's publication date in 2013. Puzzled, I searched and found that's because the author also blogged this back in August '13, so I must have read it then.

Neil Saunders also blogged some similar things earlier in 2013. And Mick Watson had some related thoughts too. And so did Titus Brown back in 2012. FWIW, there's this too, although more general suggestions. All of these contain good ideas.

[Medhat]

I think i found it even me shared it before "four months ago" Minimum standards for bioinformatics command line tools

[Medhat]

Now you confirmed what I thought because I am sure that I did see the same topic before even here in biostars but as you said it is in 2013 so I shared it :) "But the most important is that we need to follow this guiding"

[Sudeep]

Not sure if it is a repost, but I found this related paper: How not to be a bioinformatician a while ago