13 replies to this topic

[gashinshotan]

I used to play around with linux and learning C a few years ago but then decided that I didn't have time as a bio major. Are there any educational or psychological advantages gained through learning programming? I am working on a career as a medical physician but if this provides some sort of advantage I may pursue it more adamantly.

[caston]

In these days you'll find that web based programming has really left languages like C behind. It depends what you want to achieve though.
Do you want collaborative software that people all over the world can use to work together with or do you want robust inhouse applications? You might be best off to learn something like python, php or perl/ruby on rails.

Of course a lot of open source language have been adapted for use in biology such as bioperl for bioinformatics and biopython for molecular dynamics.

There is even a bioPHP project :

http://biophp.org/

At the moment Perl appears to be the offical bioinformatics language but that could change in the future as Ruby on rails has a lot of advantages with cleaner code and ease of interopation with large and complex databases.

http://www.bioruby.org/

http://bioinforuby.blogspot.com/

Edited by caston, 03 December 2007 - 08:09 AM.

[gashinshotan]

In these days you'll find that web based programming has really left languages like C behind. It depends what you want to achieve though.
Do you want collaborative software that people all over the world can use to work together with or do you want robust inhouse applications? You might be best off to learn something like python, php or perl/ruby on rails.

Of course a lot of open source language have been adapted for use in biology such as bioperl for bioinformatics and biopython for molecular dynamics.

There is even a bioPHP project :

http://biophp.org/

At the moment Perl appears to be the offical bioinformatics language but that could change in the future as Ruby on rails has a lot of advantages with cleaner code and ease of interopation with large and complex databases.

http://www.bioruby.org/

http://bioinforuby.blogspot.com/

There are no more applications for C/C++? I thought this was the defacto language learned by all programmers. I really don't have any programming goals, which was one of the reasons I quit last time. I just want to know it if it provides any psychological and mental advantages.

[eldar]

In these days you'll find that web based programming has really left languages like C behind. It depends what you want to achieve though.
Do you want collaborative software that people all over the world can use to work together with or do you want robust inhouse applications? You might be best off to learn something like python, php or perl/ruby on rails.

Of course a lot of open source language have been adapted for use in biology such as bioperl for bioinformatics and biopython for molecular dynamics.

There is even a bioPHP project :

http://biophp.org/

At the moment Perl appears to be the offical bioinformatics language but that could change in the future as Ruby on rails has a lot of advantages with cleaner code and ease of interopation with large and complex databases.

http://www.bioruby.org/

http://bioinforuby.blogspot.com/

There are no more applications for C/C++? I thought this was the defacto language learned by all programmers. I really don't have any programming goals, which was one of the reasons I quit last time. I just want to know it if it provides any psychological and mental advantages.

Sure there is. If you plan on developing something other than web applications, C++, Java or C# are all great languages to learn. Actually Java or C# might be best languages to start with, as they are much easier to learn than C++, but have pretty much the same capabilities. And you can develop web applications with them.
Later if for some reason you would like to learn C++, it can be done in less than a month as it is very much like the above mentioned languages. Quite likely though you would never even need C++.

Of course if you plan on focusing only on some limited area in which to apply your programming skills, it might pay to find out which language is most used in that particular setting. Other than that, I would recommend learning one of the three languages I mentioned.

[caston]

I just want to know it if it provides any psychological and mental advantages.

I haven't done any real programming for about 5 years so it would be hard to say but I imagine that it could help with your logic and procedure skills.

[Kalepha]

I am working on a career as a medical physician but if this provides some sort of advantage I may pursue it more adamantly.

Yet perhaps be careful that you don't get too far into programming and fall by accident over some computer science and then fall by accident over some cognitive science, lest there's no looking back.

I just want to know it if it provides any psychological and mental advantages.

In light, perhaps more than you'd care.

[eldar]

I am working on a career as a medical physician but if this provides some sort of advantage I may pursue it more adamantly.

Yet perhaps be careful that you don't get too far into programming and fall by accident over some computer science and then fall by accident over some cognitive science, lest there's no looking back.

Hmm, this sounds very familiar...although I see nothing bad in that, were it to happen :thumb:

[gashinshotan]

What about learning UNIX/Linux? Any benefits over learning in Windows?

[Ghostrider]

I just want to know it if it provides any psychological and mental advantages.

I haven't done any real programming for about 5 years so it would be hard to say but I imagine that it could help with your logic and procedure skills.

Yeah, I think programming does help in other areas. And I say this after spending literally all day programming. I need to get more exercise, but the weather is not cooperating.

I agree with the comments above, C++ is probably the most efficient programming language out there. There is no virtual machine that your programs run on top of and you have direct access to the hardware. C is about as close as you can get to the hardware without writing assembly code. So if you really care about performance, use C or assembly language. But this is not 1982 and you probably do not care about performance that much. You want something easy to use that you can quickly bang out 30 lines of code and get what you want quickly. I have programmed in Java, C++/C, Perl, and Python (a little in Lisp). My advice, start with Python. It's probably the easiest starting point and you will be able to see its usefulness the fastest. After you learn Python, maybe move onto Java. Perl is popular in bioinformatics, but the syntax is so ugly, you might want to start with Python first. Although I use Perl more than Python, I keep my code real short so that I don't get into trouble. There is also no good perl debugger so it is easy to get stuck.

RE: Unix vs. Windows. If Linux / Unix can do everything that you need, why pay for Windows? I like Open Source.

[niner]

What about learning UNIX/Linux? Any benefits over learning in Windows?

Unix seems to be favored by programmers, scientists, and the like. If you want to write windows apps, then maybe that would have some advantages. Personally, I much prefer Unix for actual work, although I use a windows box for web surfing and the simplistic mind-numbing video games that I crave.

Purely for reasons of personal/psychological development, you might also want to consider a human language, like Spanish or Farsi.

[Ghostrider]

http://wiki.python.o...e...nersGuide/)

Python.org has some good free python tutorials for beginners.

Python for Science

Course material written by Konrad Hinsen for an introduction to Python aimed at biologists.
(http://starship.pyth...et/crew/hinsen/)

Link is currently down.

[platypus]

I used to play around with linux and learning C a few years ago but then decided that I didn't have time as a bio major. Are there any educational or psychological advantages gained through learning programming? I am working on a career as a medical physician but if this provides some sort of advantage I may pursue it more adamantly.

If you plan to do any kind of research and work with data you'd better learn something like Matlab or IDL.

[Ghostrider]

I used to play around with linux and learning C a few years ago but then decided that I didn't have time as a bio major. Are there any educational or psychological advantages gained through learning programming? I am working on a career as a medical physician but if this provides some sort of advantage I may pursue it more adamantly.

If you plan to do any kind of research and work with data you'd better learn something like Matlab or IDL.

Umm..maybe, software like JMP can go a long ways and requires no programming knowledge.