[Biodevelopers] Re: Biodevelopers digest, Vol 1 #105 - 2 msgs

[Allen Henry]

I might be reiterating the email below, but the data
model seems very straight forward using a 2-dim array.
The structure would look something like this:

Table spotted array
  size 2-dimArray(columns, rows)
    columns real
    rows real

This will support the 2 different sizes of arrays.
Every spot is referenced using the 2-dim array. 

This is the most effecient way of storing you 1400
reals in one table. I've seen Oracle support 1,000,000
reals in this way, no problem. Graphical data is
stored this way all the time, which is 2k x 2k x
65,536 in size. This is image data, right? I would
also recommend looking at hte developing standards.

Remember, in building the data model, you should
always just use the structures you actually see in the
lab. This is a -static- model, so keep it simple.

Hope this helps


--- biodevelopers-request at bioinformatics.org wrote:
> Send Biodevelopers mailing list submissions to
> 	biodevelopers at bioinformatics.org
> 
> To subscribe or unsubscribe via the World Wide Web,
> visit
> 
>
https://bioinformatics.org/mailman/listinfo/biodevelopers
> or, via email, send a message with subject or body
> 'help' to
> 	biodevelopers-request at bioinformatics.org
> 
> You can reach the person managing the list at
> 	biodevelopers-admin at bioinformatics.org
> 
> When replying, please edit your Subject line so it
> is more specific
> than "Re: Contents of Biodevelopers digest..."
> 
> 
> Today's Topics:
> 
>    1. RE: Biodevelopers digest, Vol 1 #104 - 1 msg
> (Margolin, Adam)
>    2. Re: RE: Biodevelopers digest, Vol 1 #104 - 1
> msg (Mike Benway)
> 
> --__--__--
> 
> Message: 1
> Date: Thu, 1 May 2003 12:54:01 -0400
> From: "Margolin, Adam" <margolia at wharton.upenn.edu>
> To: <biodevelopers at bioinformatics.org>
> Subject: [Biodevelopers] RE: Biodevelopers digest,
> Vol 1 #104 - 1 msg
> Reply-To: biodevelopers at bioinformatics.org
> 
> Mike,
> If you are using a relational database I certainly
> would not make tables
> with variable numbers of columns depending on the
> array configuration.
> What you want to do is make a table called
> Spotting_plates with every
> row uniquely identified by the Plate_ID and the
> well.  When you spot an
> array you want to map each spot back to an entry in
> this table.  To do
> this, define a table called Print_map with each row
> uniquely defined by
> an array configuration, and row, column, block on
> the spotted array that
> maps these values to a well on a spotting plate.
> 
> This is the general idea, but of course, there are
> some other
> intermediate steps.  I can send you the scheme that
> we have developed
> for our arrays if you like, or for a more involved
> description you can
> surf around on this site:  www.gusbd.org.
> 
> -Adam
> 
> 
> -----Original Message-----
> From: biodevelopers-request at bioinformatics.org
> [mailto:biodevelopers-request at bioinformatics.org]=20
> Sent: Thursday, May 01, 2003 12:01 PM
> To: biodevelopers at bioinformatics.org
> Subject: Biodevelopers digest, Vol 1 #104 - 1 msg
> 
> Send Biodevelopers mailing list submissions to
> 	biodevelopers at bioinformatics.org
> 
> To subscribe or unsubscribe via the World Wide Web,
> visit
> 
>
https://bioinformatics.org/mailman/listinfo/biodevelopers
> or, via email, send a message with subject or body
> 'help' to
> 	biodevelopers-request at bioinformatics.org
> 
> You can reach the person managing the list at
> 	biodevelopers-admin at bioinformatics.org
> 
> When replying, please edit your Subject line so it
> is more specific
> than "Re: Contents of Biodevelopers digest..."
> 
> 
> Today's Topics:
> 
>    1. 98/384/1536 well microplate database schema?
> (Mike Benway)
> 
> -- __--__-- 
> 
> Message: 1
> Date: Thu, 1 May 2003 08:03:34 -0700 (PDT)
> From: Mike Benway <mbenway at yahoo.com>
> To: biodevelopers at bioinformatics.org
> Subject: [Biodevelopers] 98/384/1536 well microplate
> database schema?
> Reply-To: biodevelopers at bioinformatics.org
> 
> --0-1501308490-1051801414=3D:18737
> Content-Type: text/plain; charset=3Dus-ascii
> 
> Hi.I have a process that generates lot's of data
> from 384 well plates.
> That is, three hundred -eighty four real numbers.The
> entity is the
> plate. Some plates can even be 1536 well formats.
> That's a lot of real
> numbers for a database table.384 columns might even
> be too many for any
> available database?It strikes me that this must be a
> very common
> application, and there has got to be a better schema
> for representing
> plate data. (as columns of arrays, or as blobs or
> what?)Does anyone have
> any knowledge of an open-source implementation that
> stores plate data in
> a database that I could look at?I can't believe that
> databases would be
> used just to store links to spreadsheets.Thanks
> 
> ---------------------------------
> Do you Yahoo!?
> The New Yahoo! Search - Faster. Easier. Bingo.
> --0-1501308490-1051801414=3D:18737
> Content-Type: text/html; charset=3Dus-ascii
> 
> <DIV>Hi.</DIV>
> <DIV>I have a process that generates lot's of data
> from 384 well plates.
> That is, three hundred -eighty four real
> numbers.</DIV>
> <DIV>The entity is the plate. Some plates can even
> be 1536 well formats.
> That's a lot of real numbers for a database
> table.</DIV>
> <DIV>384 columns might even be too many for any
> available
> database?</DIV>
> <DIV>It strikes me that this must be a very common
> application, and
> there has got to be a better schema for representing
> plate data. (as
> columns of arrays, or as blobs or what?)</DIV>
> <DIV>Does anyone have any knowledge of an
> open-source implementation
> that stores plate data in a database that I could
> look at?</DIV>
> <DIV>I can't believe that databases would be used
> just to store links to
> spreadsheets.</DIV>
> <DIV>Thanks</DIV><p><hr SIZE=3D1>
> Do you Yahoo!?<br>
> <a
>
href=3D"http://us.rd.yahoo.com/search/mailsig/*http://search.yahoo.com">T=
> h
> e New Yahoo! Search</a> - Faster. Easier. Bingo.
> --0-1501308490-1051801414=3D:18737--
> 
> 
> -- __--__-- 
> 
> _______________________________________________
> Biodevelopers mailing list
> Biodevelopers at bioinformatics.org
>
https://bioinformatics.org/mailman/listinfo/biodevelopers
> 
> 
> End of Biodevelopers Digest
> 
> --__--__--
> 
> Message: 2
> Date: Thu, 1 May 2003 11:49:08 -0700 (PDT)
> From: Mike Benway <mbenway at yahoo.com>
> Subject: Re: [Biodevelopers] RE: Biodevelopers
> digest, Vol 1 #104 - 1 msg
> To: biodevelopers at bioinformatics.org
> Reply-To: biodevelopers at bioinformatics.org
> 
> --0-1858704015-1051814948=:75422
> Content-Type: text/plain; charset=us-ascii
> 
> Thanks Adam!  When I mentioned "array" I meant it as
> a data type for a column, but you might be talking
> about a microarray. Anyway it doesn't matter because
> the question I meant to ask is also answered. My
> logical error was in thinking of a plate as the base
> entity here, and a plate has 384 or 1536 wells. What
> is the best and correct thing to do is to model the
> WELL as the entity. So there, a plate has wells, and
> wells have well_row, well_column, well_data,
> plate_id, and so fourth. Then a plate entity can
> have  assay_id, detection_technology, reader_type,
> device_protocol_id, 
=== message truncated ===


=====

=================================================================

E-mail is a neccessary evil. If we have never talked on the phone, please call me. If we have talked but never met face-to-face, then I would like to.

Al Henry
408 799-9404 cell


__________________________________
Do you Yahoo!?
The New Yahoo! Search - Faster. Easier. Bingo.
http://search.yahoo.com