Bioinformatics programming languages - What are the major languages in Bioinformatics? (Aug/27/2005 )
I am a medical student/part time programmer. I discovered the great Bioinformatics world when I started a molecular project in the field of cancer. I have 6 years experience of web programming. I write most of my applications with Macromedia Coldfusion (Mx 6.01 - 7).
I am interested in Bioinformatics and want to start working on this field. Should I migrate to a new programming language like PHP/perl or there are some people/communities work with Macromedia Coldfusion?
As you know Macromedia Coldfusion backbone is on Java so there are many great options and easy shortcuts for making applications. Did anybody tried to do Bioinformatics projects with Macromedia Coldfusion?
If there is no way to use Macromedia Coldfusion in bioinformatics, please let me know which programming language is the major and more useful one in Bioinformatics.
Coldfusion is just a software for developing webpages and I guess fewer and fewer people are using it. Strictly speaking, it is not a programming language.
I would say Perl and Java are the major programming languages for developing bioinformatics applications.
I agree, I think perl is most popular one. for web-based programe, php, jsp are most popular.
I agree that Perl should be the next step. However, you should think about learning a "real" language, such as Python, in addition to Perl. Java would be another choice, but I would suggest Python instead.
I got that there is no hope for coldfusion in such a field. I should add this description that coldfusion IS a language (tag based, easy and very flexible). But I have some questions. Fisrt of all is PHP good enough or I will need JAVA? What is great about python that puts it ahead of others like JAVA or PHP? Is python a language that helps me make website?
Hi, I don't know anything about macromedia but I can say that
Perl/Bioperl is really powerful also if you interface it with web
html. Try this: http://www.bioperl.org/ and from the moltitude of
bioperl modules you can solve or speed a lot of problems.
Thanks for the reply.
My question is which one is better and more useful in bioinformatics?
Perl? Java? Or Python?
Each language has it's own advantages and disadvantages. I'd pick one and stick with it until you are fairly comfortable. Once you know a language well enough it really negates the need to switch over to another. Personally, I think Perl is well suited for the majority of bioinformatics tasks (it can manipulate strings with ease and, frankly, that's what bioinformatics revolves around). The fact that there is an entire community utilizing Perl for bioinformatics further supports this (www.bioperl.org).
I haven't had much experience with Python, but I'd definitely use Perl over Java anyday. I'm currently writing an oligo analysis program using Perl.
Thanks for the reply.
Please see what I have entered in my blog at http://www.protocol-online.org/forums/blog/benign/ . I described my problems in more details. I will appreciate any comments.