Beefy Boxes and Bandwidth Generously Provided by pair Networks
Think about Loose Coupling
 
PerlMonks  

comment on

( #3333=superdoc: print w/replies, xml ) Need Help??
Some define bioinformatics narrowly as computational genomics and proteomics. Others use bioinformatics more broadly as a term for computational biology in beneral.

I fall into the latter category. I am a computational neurobiologist who studies how neurons in sensory systems code information using action potentials or "spikes". The analysis is purely mathematical and draws from algorithms in signal processing, nonlinear physics, and information theory.

Perl is my first choice of language for programming in this domain. It allows me to try ideas quickly and is often fast enough for what I need. Some algorithms are CPU and/or memory intensive, in which case I'll turn to the Perl Data Language (PDL) to cut the problem down to size. PDL is the tool of choice for signal filtering, FFTs, and correlational analysis.

I occasionally write applications in C++, but it is more to keep up my skill set than desperate need. Others in my department use Perl or Python for a similar tasks. I think Python seems to attract more numerical analysts for some reason, but PDL is nicer than the melange of numerical modules one has to deal with in Python.

I have also worked in bioinformatics in the narrow sense. I used Perl to attack the protein folding problem using a genetic algorithm Monte Carlo technique. I am interested in doing more work in genomics and proteomics. There are a lot of fascinating problems in those domains.

-Mark


In reply to Re: Other Bioinformatics Monks Out There? by kvale
in thread Other Bioinformatics Monks Out There? by BioGeek

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post; it's "PerlMonks-approved HTML":



  • Are you posting in the right place? Check out Where do I post X? to know for sure.
  • Posts may use any of the Perl Monks Approved HTML tags. Currently these include the following:
    <code> <a> <b> <big> <blockquote> <br /> <dd> <dl> <dt> <em> <font> <h1> <h2> <h3> <h4> <h5> <h6> <hr /> <i> <li> <nbsp> <ol> <p> <small> <strike> <strong> <sub> <sup> <table> <td> <th> <tr> <tt> <u> <ul>
  • Snippets of code should be wrapped in <code> tags not <pre> tags. In fact, <pre> tags should generally be avoided. If they must be used, extreme care should be taken to ensure that their contents do not have long lines (<70 chars), in order to prevent horizontal scrolling (and possible janitor intervention).
  • Want more info? How to link or How to display code and escape characters are good places to start.
Log In?
Username:
Password:

What's my password?
Create A New User
Domain Nodelet?
Chatterbox?
and the web crawler heard nothing...

How do I use this? | Other CB clients
Other Users?
Others about the Monastery: (2)
As of 2023-01-30 04:23 GMT
Sections?
Information?
Find Nodes?
Leftovers?
    Voting Booth?

    No recent polls found

    Notices?