[Bioperl-l] Application using Bioperl

Barry Moore barry.moore at genetics.utah.edu
Wed Jan 28 19:24:44 EST 2004


You could keep everything on Linux by using OpenOffice Calc 
<http://www.openoffice.org/product/calc.html> (or others) as a 
replacement for Excel.  You can probably recreate most of the 
functionality of Excel's formulas etc. with perl if Calc doesn't do what 
you need, and just use Calc as a way to interface with your end user.  
Of course you lose the familiar interface of Excel for your end user if 
that is what they are used to. 

You could keep everything on Windows.  Most of perl, MySQL and much of 
Bioperl will operate quite happily on recent versions of Windows.  VB is 
able to interface with MySQL directly http://www.vbmysql.com/, and of 
course MS has it's own set of database applications that would link 
seamlessly with Excel (at a cost of course).

Regardless of where your database is, if you plan to use perl as an 
interface with Excel search CPAN for Excel 
<http://search.cpan.org/search?query=Excel&mode=all> and you'll come up 
with quite a lot of modules related to Excel.  In particular for the 
things you mentioned you might look at  DBD::Excel 
DBIx::Dump <http://search.cpan.org/author/ISTERIN/DBIx-Dump-0.04/Dump.pm>.

Barry Moore

Law, Annie wrote:

>I would appreciate help on the following.  I would like to create a small
>application that would involve Excel XP on 
>Windows 2000, and 
>Bioperl and mysql on RedHat linux 9.0
>The database will consist of clone IDs, accession numbers, and unigene IDs,
>and allow a user to 
>add his own personal annotation as well.  Later on, I would like to annotate
>with other information as well.
>I am trying to map things out and see if all of the parts in my application
>will fit together prior to doing 
>too much developing.
>Basically my main concern now is to create the flow of information.
>There is the Excel workbook part and then there is the UNIX mysql database
>Writing a shell or perl script in the linux environment that will ftp files
>from unigene, locuslink 
>Etc and then user bioperl to parse the data,
>Then use perl DBI to insert to information
>Also using perl DBI to upload information from the Excel sheet (user's
>personal annotation)
>Into the database.
>The part that I'm not too sure about is how to send the information from the
>Excel sheet to the database
>And how to grab the information from the database and update the Excel
>On top of that I am using two different operating systems.
>Are there some tools in VBA or in perl that I could use to build this bridge
>I am using Excel since there are functions within Excel that are useful.
>Thanks for your help,
>Bioperl-l mailing list
>Bioperl-l at portal.open-bio.org

More information about the Bioperl-l mailing list