Covering the bioinformatics niche and much more

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Mr Daniel Swan accused me of not publishing his comment or reply to his comments. I have never seen his reply, either in the comments or as an email to me, so to fulfill his desires it is published here.

I admit that some of the things you have addressed in the past, whilst ‘reinventing’ the wheel, offer important insights into the general problems of programming in general – this particular example was not one of them. From following the course which I assume was outlined by ‘Beginning Perl for Bioinformatics’ (which I do not think is a good reference for beginning Perl at all) a user should already be able to perform the following operations – open a file, iterate over and parse the contents, open a file for writing, and apply some rules for formatting the output. Thus you have already given them the tools to complete the operation should they wish to do so in a Python context. The problem is that you are trying to educate potentially early career/transitional bioinformaticians here – and showing them how to complete tasks in X lines of Python when there is a single command line application to do the trick I think is disingenuous. We wouldn’t dream, for instance, of educating our MRes students in this way. I also would take issue that diversity is a key. You can be as diverse as you like but no-one is seriously going to suggest that you write your next script to parse something out of a GenBank file in assembler. One of the hallmarks of any computer professional in any field is the ability to use the right tool for the job. You should be technology agnostic and be prepared to string together applications or scripts from anywhere to reach your goal – take a look at something like Taverna for instance. I notice in the other post that you mention there is a high proportion of Windows users to this site and therefore command line *nix comments are of no interest. Although I know a number of bioinformaticians who use Windows (generally to integrate with an institutions existing Microsoft heavy infrastructure) they all have logins to dozens of *nix machines, run *nix in a VM or at the very least have a Cygwin installation with which to work with. Basing the availability of technology on the OS of your page imprints is not necessarily indicative. I hope you don’t mind me addressing these points here rather in my blog, as my blog is personal (hence the lack of bioinformatics content on there). I have actually been following these tutorials for a while (as someone who came into Bioinformatics some time ago – my first forays in programming were in Perl) it is nice for me to see tasks that I find intuitive in one language written in another. Consequently the fact that I felt need to comment, merely suggests that I felt strongly on this issue, rather than having any negative feelings towards what you are trying to achieve.

I am sorry for the usual readers of this tutorial, for posting his comments as an article here. We will be back to our uneducated, simple and basic “tutorial for bioinformatics in X lines for the noobie in Windows” soon. Thanks Daniel.