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

Amir Karger akarger at CGR.Harvard.edu
Tue Mar 8 14:05:26 EST 2005

> From: Stefan Kirov [mailto:skirov at utk.edu] 
> 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). 

You make an excellent point. There are a number of avenues we've thought of
for making this tool more accessible to non-UNIX folks.  However, each one
of them requires some extra work in planning issues like security, command
paths, accessing input files, shell variables, etc. Because we've already
got a bunch of users here who need to use UNIX to use our computing cluster,
I figured I could have a prototype that only works from the UNIX command
line. If it works well on those folks, we can think about extending things
later (with the caveat that I want to be careful to keep the interface VERY
lightweight, because I don't trust myself to build a portable, "intuitive"

> 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:
> > >
> >I was thinking it would be useful to have a toolkit of 
> outrageously simple
> >Perl one-liners.  > >

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