[Biophp-dev] Zend and Parser-to-SQL scripts

[Serge Gregorio]

Hello all!

>> Serge:Oh, but first I'd have to raise the $ 2,000
>> to afford a copy of Zend. *chuckle*  Or are they 
>> giving it away now? *fingers crossed*

> Nico: It is the Zend 'accelerator' that costs
> money, but the free(albeit not Open Source) 
> appears to be equally fast.

Hey, I just came from the Zend site and they're offering the Zend Studio Personal Edition free for personal, non-commercial use. Has anyone here used it?

Btw, is "Zend Accelerator" = "Zend Compiler"?

>Nico: B.t.w.  there is a nice (and free) accelerator >for php available (www.php-accelerator.co.uk/).  

Darn, there's no version that runs on cgi/Windows.
* Sniff *

>Nico: I will. I will be using Adodb though.  
>Two reasons: 
>1. I have used that code extensively and I am not >going to use time to figure out PEAR DB.
>2. Adodb is (claims to be) two times as fast as PEAR >DB.

Gee thanks.  Will wait for the (converted) scripts.

>Good plan.  We should be able to use these tables to >write seq objects to an SQL database and get them >back out again.  I'll have a look.

Yes.  Initially, the code would write to some pre-designed set of tables.  Later, we can let the user design his own database for, say, holding GenBank DNAs or PDB/mmCIF protein records.  Something like:

=============================================
  GENBANK DATA    SQL TABLE  COLUMN

  1) Entry Name   DNA        Entry_Name
  2) Length       DNA        Seq_Length
  3) Sequence     DNA        Sequence
  4) References
    
     Title        Reference  Title 
     Journal      Reference  Journal
     Author       Authors    Lastname
                             Firstname
=============================================
        
Hmm... is there any open-source tool out there that does this?  Oh well, if there isn't, we can always write one.

Cheers!

Serge


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