Scientific papers and softwares
This week I recieved from a friend researcher a paper from the scientific journal Bioinformatics. The journal is very famous among bioinformaticians and it describes itself as 'The leading journal in its field'. I'm not gonna specify who is the author or what is the name of the paper because I don't think necessary. In a simple way, the paper is about a software written in Perl designed to increase the performance of a database searching using protein mass-spectra.
I became interested so I downloaded the .rar, what I saw was 7 .pl scripts, 2 .xml and a readme file telling me the right order of execution and the correct inputs and outputs. The first impression I had was not good, there was no organization at all, the documentation was limited to comments above functions and the most important, the authors did not made test files. The scripts were a little messy too, no 'warnings' and 'strict' pragmas were used and some scripts weren't even indented.
My point here is that I think scientific journals should have better peer-review systems for papers based on softwares, specially those between biology and informatics, I know that it could be hard for someone who don't code in Perl to see some of those points, but good practices are a common thing among all languages. In scientific projects if bad laboratory work can be refused why can't bad coding be refused as well? This kind of project became a publication in a scientific journal and with this software I can't have sure that it works exactly like the authors described and I can't know if I will have reproductible results.
Good practices in software development are as important as laboratory good practices, everyone should respect it.