The name of your bioinformatics software is important. A good name should be clear, unambiguous, pronouncable, memorable, and meaningful. Sadly many (most?) names of existing tools do not satisfy all of these criteria. Here is a simple thought experiment that you can use when trying to decide on a new name for your software; this is something which might help you avoid many common naming problems that can arise.
Imagine that you are in an elevator going from the 6th floor of a building to the ground floor. The elevator stops at the 5th floor and a visiting bioinformatics/genomics scholar steps in. He/she is someone that you admire and someone who you would really like to know about the latest software tool that you've been working on.
They press the button for the 2nd floor. You have maybe 30 seconds to introduce the tool and hopefully make them curious enough to check it out when they next get back to their computer. You say something like:
Hi. I'm a big fan of your work. I wanted to let you know that I've been working on a tool that you might be interested in…it's called 'X'
In this example, we will assume that you may never see this person again and that you don't know when they will have time to look up your software tool. It might be days, so the name has to be something that they will remember. The more meaningful and pronouncable the name, the more chance that it will be memorable.
Now, let's consider the names of some recently published bioinformatics tools…do these pass the elevator test? You should always consider how you might have to spell out the name of your software:
- tmle.npvi — tee-em-el-ee-dot-en-pee-vee-aye
- EW_dmGWAS — Ee-double-you-underscore-dee-em-gee-was
- do_x3dna — dee-oh- (or do?) -underscore-ex-three-DNA
- R3D-2-MSA — ar-three-dee-dash-two-dash-em-ess-ay
- Pse-in-One — pee-ess-ee- (or see?) -dash-in-dash-one
- (PS)2 — open-parentheses-pee-ess-close-parentheses-superscript-two
In these examples you would probably choose to omit details of the dots, dashes, underscores, parentheses, and superscript characters that are part of the name. So you should ask yourself whether you really need to include them in the first place.
The bottom line is that it is not enough for the name of your sofware to be comprehensible when read from a screen or page…it should also sound good!