Which programming languages are used most in bioinformatics?

i want to escape the bench! i think the computer is a suitable refuge, i think if i knew more about the programming side that could help, so i am going to try to learn some programing, which langauges wold be useful to learn for bioinformatics?Which programming languages are used most in bioinformatics?
Must know languages C++, SQL, HTML, PHP, Javascript


Helpful languages Python, Gambas, XML, Smalltalk, Java





Skip .NET as it'll be unsupported in a few years. M$ doesn't like to keep languages around very long so they can sell you a whole new language with almost no backward compatability.





The other languages are good choices. C/C++ is important to know at least a smattering of if you program at all. SQL is a must learn for any language. Start with ANSI SQL as it will give you a firm foundation of the concepts and will apply to a greater or lessor extent with all the SQL Varients like PLSQL.





When learning SQL this book cannot be beat.





http://www.amazon.com/Practical-SQL-Hand鈥?/a>





Python is a handy language to know even as just a computer user. Gambas if you run Linux is a language you can learn quickly, is quite powerful and easy to use, it only runs on Linux at this time. Java is not a language but an institution. I suspect nobody knows everything about Java programming. Even knowing everything about a specialty in Java programming would be difficult. It is a vast language. If you know C++ Java will be easier to learn. It's excellent for web based apps and has better portability than most languages but is complex in deployment.





PHP is another language you'll want to know. It is the web development language. Writing in any other is mostly a waste of time. .NET will be unsupported as M$ forces everybody into it's propriatory version of cloud computing. Cold Fusion is basically obsolete. Writing whole websites in javascript is begging for headaches.





You will do web development, no way around it in todays world. Somebody finds out you know anything about coding you'll be hit with some web development. As such you should know not only PHP but javascript. It's not Java at all and essential to augment other languages. HTML and XML are two other must knows but both are rather easy to learn the basics of.





Smalltalk is a very different bear but it's ability to create agents with self modifying code is quite useful in data mining. Smalltalk is much better supported and easier to learn than LISP. Smalltalk is well supported on most platforms where LISP is only supported on Windows in commercial form. Linux support for Linux is pretty decent including commercial versions, however graphics libs tend to be it's achilies heal on all platforms. Smalltalk comes without those headaches and nightmares. Smalltalk under Linux has some good IDEs to work from.





Last you'll want to at least dual boot. Linux provides far too many tools and advantages in this endeavor to ignore. Many of your end users will be Linux users, possibly the majority today.Which programming languages are used most in bioinformatics?
This benchmark compares the memory usage and speed of execution for three standard bioinformatics methods, implemented in programs using one of six different programming languages. Programs for the Needleman-Wunsch algorithm, the Neighbor-Joining tree construction algorithm and an algorithm for parsing BLAST file outputs were implemented in C, C++, C#, Java, Perl and Python.


A survey (bioinformatics.org) on which languages would be the most useful to learn ranked the following languages in decreasing order: Python, Perl, Java, C/C++ and the framework .NET which includes C#.


Requirements:6 programming languages: C, C++, C#, Java, Perl, Python


3 programs: Needleman-Wunsch global alignment algorithm, Neighbor-Joining tree algorithm and BLAST parsing program.


2 Operating Systems: Linux (Fedora) and Windows (XP)
To start off, learn C, C++, or Java (or all three). They are the basics for just about any programming language. Other than that, I would assume you are planning on storing a lot of data using bioinformatics, so possibly look into storage based languages such as SQL. But once you know one language, it seems that most of them are usually similar in some way. C, C++, and Java are definitely where you should start though.
OK - in order of what works best or what languages would be the most useful to learn. The general opinion would be the following languages ranked in decreasing order: Python, Perl, Java, C/C++ and the framework .NET which includes C#.
I'd suspect its matlab. But you have to have the math and biology background to use it. Programming shops are highly individual and sometimes contrary to what one might think. If you have a particular shop in mind, ask
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