How Lisp-family languages facilitate building bioinformatics applications
When I started working in bioinformatics I was excited to use Lisp for my work. I wrote a considerable amount of library code and programs at first. But I always found resistance when it came to other people using my programs and even more if the program was to be published and released for general use.<p>There is a large amount of really, really bad Perl code still in use in biology. Trust me when I say to those outside of the field, I&#x27;ve seen things you people wouldn&#x27;t believe. I try to discourage Perl use between it makes it so easy for biologists to write terrible code.<p>I&#x27;ve found a compromise in Python. People will happily use it because it&#x27;s trendy and ubiquitous. And I think it makes it easier to write OK code. But I miss using Lisp. The style of programming when you have a REPL is perfect for this kind of thing. The ability to quickly write prototypes which can later be improved is an advantage which cannot be stressed enough. C is fantastic when you have a good idea of the algorithms and data structures you want to implement and are concerned with implementing them efficiently. But that&#x27;s rarely the case when writing bioinformatics code. I need to know if the damn thing <i>works</i> first before I spend time making it work fast. And why would you not use a language where both things are equally easy?<p>I&#x27;m happy to see this paper because it means that I have a way to justify my usage of Lisp in the future. Big thanks to the authors.