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

[Stefan Kirov]

Allow me disagree. My understanding is this project is more about making 
biologist "computational hungry" rather than creating effective 
applications from a computation point of view. So I think it is more of 
an outreach project (did I get this right Amir).  Bioperl. The next 
logical thing for any biologist who is starting to use the computer as 
something more than a typewriter is to use something like Bioperl, 
because it is quite easy to understand and use (in many cases anyway).
Stefan

Andreas Kahari wrote:

>I'm not quite sure what this has to do with bioperl...
>
>On Wed, Mar 09, 2005 at 01:46:17PM -0500, Amir Karger wrote:
>  
>
>>In a private mail, Richard Copley wrote:
>>    
>>
>
>Forwarding private emails to mailing lists are we?
>
>  
>
>>>Amir Karger wrote:
>>>      
>>>
>>>>I was thinking it would be useful to have a toolkit of outrageously
>>>>        
>>>>
>>simple
>>    
>>
>>>>Perl one-liners.  Here's one:
>>>>        
>>>>
>
>http://www.oreilly.com/catalog/cookbook/
>
>  
>
>>>>    # Merge two lists, removing duplicates (logical OR)
>>>>    perl -ne '$seen{$_}++; END {print keys %seen}' file1 file2 > outfile
>>>>        
>>>>
>>>sort -u file1 file2
>>>      
>>>
>>I know that many of the tasks proposed for the Scriptome can be done with
>>grep, sed, cut, Word, or Excel. I'm planning on implementing head, sort,
>>join, and lots of others. But how many experimental biologists are familiar
>>with Unix cut? How many bother to learn even the least fancy Excel
>>functions?  I think not many, because they have other things to worry about.
>>    
>>
>
>Hmmm, comparing 'cut' and 'sed' with Word and Excel?  Oh well.
>
>The philosophy of Unix utilities is to do only one thing,
>but to do it very well.  In the case with the 'sort' utility
>for example, it will most likely use an out-of-core sorting
>algorithm to cope with files larger than the available memory
>of the machine, and will probably be a fair bit quicker and
>flexible than your own implementation.
>
>  
>
>>One reason so many people have created integrated toolboxes is so that
>>biologists only need to learn how to use one tool, rather than learning 30
>>or whatever Unix commands.  The goal of Scriptome is that they only need to
>>learn one tool AND that the learning curve for that tool is very small. And
>>we make the learning curve small by using an extremely lightweight interface
>>(most of solving a problem involves searching on a website) rather than by
>>trying to create an intuitive GUI.  After all, how many folks  other than
>>Apple have created GUIs that are intuitive for more than a small subset of
>>people?
>>    
>>
>
>The reason why so many people are creating integrating toolboxes
>(really, are they?) is probably just because so many people
>before them didn't do it right.  Mind you, doing it "right" is
>not possible.
>
>I do understand that there is a need for integrated utilities
>with easy-to-press buttons, and I won't try to put you off
>working on those kind of projects, but...
>
>What would an experimental biologists, who is not familiar with
>'sort', 'cut' or 'join', do with a Perl script that implemented
>those functionalities?  Wouldn't it be better to provide a
>high-level interface to common tasks, like parsing the output
>from various programs and providing simple ways of accessing
>and manipulating sequence features etc.  If you find ways to
>expand the application area of BioPerl, or if you rationalize
>and improve existing BioPerl code, then I'm sure the BioPerl
>maintainers would be happy to consider commiting your code to
>the project.
>
>
>
>Regards,
>Andreas
>
>  
>

-- 
Stefan Kirov, Ph.D.
University of Tennessee/Oak Ridge National Laboratory
5700 bldg, PO BOX 2008 MS6164
Oak Ridge TN 37831-6164
USA
tel +865 576 5120
fax +865-576-5332
e-mail: skirov at utk.edu
sao at ornl.gov

"And the wars go on with brainwashed pride
For the love of God and our human rights
And all these things are swept aside"