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Re: advice for the undergrad (OL)

On Sat, Jul 5, 2008 at 8:17 PM, Graydon <oak@uniserve.com> wrote:
> If you're going to be swoggling lots of character data (data represented
> by text strings, I mean) -- genetic or molecular analysis -- something
> like Perl is probably your best choice.  (There's a lot of it; being
> made of ancient effective Unix evil may or may not warp your mind; other
> people are already using it; for this very specific problem realm,
> nothing else is as good.)

Well, I think the primary utility of Perl in this regard is regular
expressions (a.k.a. regex, regexp, etc.), and many programming
languages have adopted these from Perl (or at least provide toolkits
for them). Regex strings are part of native Java and PHP, and are
actual elements of ActionScript. A great number of text editors allow
search and replace by regular expression patterns, too.

Regular expressions are very useful and really *are* something that
can be learned in a relatively short amount of time. (They're not a
programming language in and of themselves, though, more like a textual
query language.) The syntax is kind of odd, but it's succinct and
powerful. Good place to start:

>> Also very important in science are other types of computer languages,
>> like query languages (SQL and variants thereof, XQuery, etc.), markup
>> languages (XML, HTML, etc.), data languages (XML again, HTML
>> microformats, YAML, weird little specialized languages like DOT and
>> NEXUS, etc.),  etc. It's not all programming.
> Pretty much all of that is data representation of one kind or another.

Didn't mean to imply otherwise.

> That's a good thing to understand, but if the idea is to be able to
> prove you can program, as distinct from a career in programming, I'd
> suggest hauling in specialist help for that category of problem.

I dunno, knowing the basics of XML, for example, can help an awful lot
for many tasks.

A good introduction: http://w3schools.com/xml/xml_whatis.asp
(Although that page lists a basic understanding of HTML and JavaScript
as prerequisites, that's not really true, at least for the "XML Basic"
T. Michael Keesey
Director of Technology
Exopolis, Inc.
2894 Rowena Avenue Ste. B
Los Angeles, California 90039