Question: (Closed) If ideally learning Python, Ruby or Perl... what could be a collateral language of interest?
gravatar for K
4.7 years ago by
K180 wrote:

If I have zero-knowledge of programming and I had the chance to learn for free either Java or .net (visualstudio), which of these languages would be a better indirect gateway to the more or less "mainstream" bioinformatics languages Perl, Python and Ruby? (I mean, to become familiar with their logic and workflow)

I am interested in protein-oriented bioinformatics, if that is a factor.

Thanks a lot in advance.

.net forum java python • 2.9k views
ADD COMMENTlink modified 4.7 years ago by mikhail.shugay3.3k • written 4.7 years ago by K180

Hello K!

We believe that this post is does not fit the main topic of this site.

Duplicate post of question asked many times, pertinence to bioinformatics?

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.


ADD REPLYlink written 4.7 years ago by Josh Herr5.6k

Hi, Josh.

I feared that the question might be perceived as not bioinformatic enough. Nevertheless, I would like to make my point here: Programming is key, an indispensable tool in bioinformatics. My question is motivated by the believe that the learning of a programming language substantially helps you with the next.

It seemed already clear from what I had read that Ruby, Perl and Python are the most bioinformatics-relevant languages to date, and my question was asked with those three in mind. I was actually asking for kind of a "side-door" into those bioinformatics-relevant languages. I have not seen what I meant addressed elsewhere, which could mean either I simply could not find it, or that it has actually not been addressed (or not as much as the topics pointed at above by Pierre).

I mentioned a couple of specific programming languages due to an irrelevant personal circumstance (maybe I should for instance have mentioned R, C, or C++ too), but my question could be reformulated as: "Prior knowledge of certain programming languages helps the learning of others. Which languages make a better gateway into Python, Perl or Ruby, as those seem to be among the most relevant in bioinformatics?"

Thus I think my question is relevant in the sense that it addresses an essential tool or tools of bioinformatics, and how to learn to use them. I mean, pyppetting is as essential for a bench scientist as programming is for a bioinformatician, right? (just to draw an analogy)

ADD REPLYlink modified 4.7 years ago • written 4.7 years ago by K180

Yes, K, you have a valid question, but it's one which has been asked here and elsewhere many many times over numerous years, even by myself.  We're just attempting to reduce the noise by reducing the number of identical questions.

ADD REPLYlink written 4.7 years ago by Josh Herr5.6k

In the meantime I've been looking elsewhere and it seems that C would be a great entry gate (specially as a foreroom to Perl), according to the chart in the link below which kind of visually addresses my question:

Well, in any case, please accept my apologies for any bother. Please receive my kindest regards from Barcelona, Spain,


ADD REPLYlink written 4.7 years ago by K180

I'm not familiar with .net, but I'll mention that you can easily find bioinformatics tools written in java (e.g., picard tools). I wouldn't recommend learning .net unless you want to chain yourself to Windows.

ADD REPLYlink written 4.7 years ago by Devon Ryan88k

about .NET and bioinformatics: Using Microsoft .Net Framework For Biological Application Development In Europe

ADD REPLYlink written 4.7 years ago by Pierre Lindenbaum118k
gravatar for mikhail.shugay
4.7 years ago by
Czech Republic, Brno, CEITEC
mikhail.shugay3.3k wrote:

I believe that the question "which language is better" has been asked dozens of times here, still I expect many comments here :)

As for "mainstreamness" have a look at this relatively shallow GitHub survey:

ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by mikhail.shugay3.3k

ActionScript is awfully high up on the #sequencing results. That's kind of a surprise...

ADD REPLYlink written 4.7 years ago by Dan D6.7k

Thank you! Very interesting to see. :)

ADD REPLYlink written 4.7 years ago by K180
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