[Bioperl-l] Request for advice and pointers on a project to help biologists d o simple formatting and analysis

Rex Nelson nelsonrt at iastate.edu
Tue Mar 8 18:36:57 EST 2005

Todd and Amir:

If you are running OS X there is a program 
Platypus which makes applications which would be 
quite suitable for simple perl/shell scripts. 
The output and input options are a little limited 
but to do defined little jobs it would work.  It 
allows you to put scripts inside an OS X 
application with or without drag and drop 
ability.  I don't know about "does (amazingly) 
what the biologist types in" but it would do 
defined jobs by clicking or drag-n-drop.


>Hi Amir -
>I like this idea.  You could also have the scripts process @ARGV so no
>hand-editing would be necessary.   You might even just make the scripts
>executable droplets which would be even easier to use.
>>  On 3/8/05 11:20 AM, Stefan Kirov wrote:
>>  I like a lot this idea.
>>  First my answer to your first 2 questions: no, no.
>>  But I bet may biologists would scream in pain just hearing the word
>>  console (as you mentioned). So I offer 0 step (bait to learn a little UNIX).
>>  Imagine a simple web form that is hooked to the perl interpreter (might
>>  be tricky from a security point, still it could be restricted in several
>>  ways) and does (amazingly) what the biologist types in. This would have
>>  to include file uploads/downloads as well. Of course the capabilities
>>  will be quite restricted, but the appetite comes with eating as some say
>>  and suddenly the console might be not a bad idea (thus Mac shares would
>>  go up :-) ).
>>  Amir Karger wrote:
>>>  Hi.
>>>  I've gotten the impression - in my short time in bioinformatics - that
>>>  biologists get very frustrated with data formatting and analysis tasks.
>>>  Which is too bad, because many of these tasks 
>>>are trivial for someone with a
>>>  bit of Perl knowledge. Then again, we can't force them to learn Perl, even
>>>  if it would be For Their Own Good.
>>>  I was thinking it would be useful to have a toolkit of outrageously simple
>>>  Perl one-liners.  Here's one:
>>>     # Merge two lists, removing duplicates (logical OR)
>>>     perl -ne '$seen{$_}++; END {print keys %seen}' file1 file2 > outfile
>>>  A biologist (call her Sue) would look through a website containing a bunch
>>>  of (searchable, categorized, etc.) scripts, cut & paste the Perl into Unix
>>>  (from a website), then backspace over the filenames and type in their own
>>>  filenames, and end up with something like this on the command line:
>>>  myhost>perl -ne '$seen{$_}++; END {print keys %seen}' genes1 genes2 >
>>>  all_genes
>>>  The biologist hits return & voilà! Instant data munging!
>>>  Of course, I'm not the first one to identify this problem or try to solve
>>>  it.  But I think I'm working on a slightly different problem than previous
>>>  solutions, and my (complete lack of) 
>>>interface is different too.  Here's the
>  >> "prior art" I've seen in this area, compared and contrasted with my idea

Rex Nelson Ph.D.
Postdoctoral Scientist
nelsonrt at iastate.edu
(515) 294-1297
~~~_/) ~~~

More information about the Bioperl-l mailing list