Ask HN: What programming languages are used in hard-sciences?

3 points by alecbibat 12 years ago | 6 comments

I'm going to be graduating in May with a Biochemistry and Molecular Biology degree. I'm mostly interested in doing research (cancer or stem cell if I can), and I'm curious if there's a language that will make me a more competitive job applicant. I've already had a good amount of lab experience outside of school (helping a professor in his lab) and have a decent GPA.<p>I know Python is used in the lab I'm in now to build software that analyzes the data we're spitting out of the lab and I know it's used a lot in physics research as well so I've pinned it as the language I should be learning.<p>I already know a little Python and Ruby (mainly I've just gotten through Zed's tutorials and made a few side projects), but are there any other languages people in the field have seen that are used specifically for research or that have pointed biomedical applications?

infinity 12 years ago |

Perl seems to be used in Bioinformatics, because there are several books out there discussing the application of Perl:

- Beginning Perl for Bioinformatics

- Mastering Perl for Bioinformatics

both are published by O'Reilly (I haven't them, so I can't give a recommendation. Also I don't have any contact with the field of Bioinformatics.).

A search on Amazon reveals quite a lot of books on the combination of Perl and Bioinformatics.

There is another book which sounds interesting:

- Developing Bioinformatics Computer Skills (O'Reilly)

http://shop.oreilly.com/product/9781565926646.do

It also appears to discuss the question why Perl is used for some things in Bioinformatics.

The same author (Cynthia Gibas) has written an introductory article:

Computers + Biology = Bioinformatics

http://oreilly.com/news/bioinformatics_0401.html

I can't tell you if learning Perl will give you a competitive advantage in job applications, but I have enjoyed learning Perl very much :)

kjs3 12 years ago |

Python and R are the cool new kids in bioinformatics, seem to be ubiquitous and there are tons of resources to get you up to speed. SAS, Matlab and to a lesser extent SPSS are more old guard, but there are a lot of folks who still use them. If you want to get really old school, Fortran is still in use, though I see it more on the physics side of the house.

If you're really looking to differentiate yourself, I look at combining Python or R with one of the 'big data' infrastructures (e.g. Mapreduce, NoSql, SQL). Then you'll be able to sell yourself as not only being able to analyze the data, but understand the data collection, handling and storage aspect as well.

iends 12 years ago |

Fortran

Perl

Python

Are the languages I see in talking with biology/biochem PhD students.

Nicholas_C 12 years ago |

My mother is in a biochem PhD program at a top state school and uses R for her work.

dbla 12 years ago |

IDL is used in most Astronomy reserach

alecbibat 12 years ago | |

Yeah, I've got a few friends in Astrophys and they talk about doing work in IDL all the time.