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

[biophp-dev@bioinformatics.org]

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


One last try:

We are talking about two different things.  

One is the ability to extend the functionality of php.  You could for
instance want to have a clustalw function that performs sequence
allignment.  You could simply take the clustalw source code, add some
stuff to the source code such that variables will be passed right between 
php and your code,compile php together with your code, and voila, you now 
have your function clustalw_allign($sequences, $parameters), which
behaves exactly like any other php function. Instructions how to do this
are at:  http://www.php.net/manual/en/zend.php.  The same trick can also
be used when you have code that executes slowly in php.  If you can
compile php, you already have everything you need to do this.

The other subject is acceleration of php.  The Zend accelerator (or
whatever they call it) stores a compiled version of your php script in
memory or on disk.  This is worthwhile mainly for heavy duty servers
(quite a few cpu cycles will be avoided).  

I have the feeling you are mainly interested in option One.  Go ahead,
check it out, you probably have all the tools you need already...


> >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.

Ehmm., shouldn't we write the php scripts that write a seqobject to an
SQL database (with the structure I am getting into the adodb script right now)?

Best,

Nico