[BiO BB] Plone and bioinformatics?

Mike Marchywka marchywka at hotmail.com
Wed Jun 13 16:52:20 EDT 2007

Knowing absolutely nothing about your objectives, I will assume they
are similar to mine :)
That is, they want a database to facilitate research and data mining.
First, these guys seem to have gotten just about everything right:


and claim to have tools available ( mostly c++ code for their apps
but they maintain a bunch of gene/protein sequence databases and
even expression array data).

Second, my own personal comment, don't worry about a web interface
as much as an API and put the graphics stuff on top of that. Any "serious"
work almost always requires working around the gui. If they have
any public stuff or even internal use equivalntes-
like an epitope database or gene expression array data or
specialized servers ( upload a sequence, get an analysis back) just
make the data available with an API and let the specialized users write the
code to implement their one-off ideas. Many people think
the graphics ARE the science- obviously I don't work for Microsoft  :)

In short, I am essentially advocating that you write some terse code to
make a GENERAL, user-sensible query into SQL for postgres. Check boxes, 
common queries,
trying to out guess the serious user is essentially impossible but you 
always need
common pages for the casual user, users testing scripts, and demonstrations. 
Obviously, if your
sponsor has a different idea it may take some selling but I think the 
would be more usable and even more maintainable ( don't try to design
an interface or database around a gui). Even if they have just one "thing" 
they want
everyone to do, you can write a simple web page for that and have the
other stuff ready when they change their mind.

So, I guess my response is store the data in the most flexible possible way 
and make
general programmatic access availabe in an API and don't worry about clever 
that's for researchers not web page designers. Having an "output as text" 
for everything, including spatial data that can be reduced to vectors or 
is a big help.

>From: Rick Casey <rick.casey at colorado.edu>
>Reply-To: "General Forum at Bioinformatics.Org" 
><bio_bulletin_board at bioinformatics.org>
>To: bbb at bioinformatics.org
>Subject: [BiO BB] Plone and bioinformatics?
>Date: Tue, 12 Jun 2007 09:51:43 -0600
>I am new to this site, so have not had any experience here yet; but wanted 
>to ask this community a question.
>I work at the Institute for Behavioral Genetics in Boulder 
>(ibgwww.colorado.edu), where I am constructing an inhouse, web-based 
>database to serve as a central repository for their research data and 
>I've been working on this for about two and half years now, using PostGres 
>as the backend database, and PHP for the web interface, with some 
>occasional Perl. Progress has been steady but slow, and I am searching for 
>better software development tools to use on this project.
>I would like to ask if anyone here has experience using Plone? It seems to 
>be a leading candidate for the kind of tool I need. Where this project gets 
>bogged down is developing webpages that communicate with the database, and 
>in using a relational schema.
>It would seem that an object-oriented schema would be better for the 
>complex data structures required in a genetics laboratory environment. 
>Making schema changes to a relational structure, and then modifying PHP 
>code tied to it, is quite labor intensive. I am hoping that an O-O schema 
>plus using a content management system will help with this; but would like 
>to "look before I leap", so to speak.
>So if anyone has experience relevant to this type of development, I would 
>like to hear about it. I would also be willing to share more details about 
>our project, if anyone should be interested.
>Best regards,
>Rick Casey
>rick.casey at colorado.edu
>Professional Research Assistant
>Institute for Behavioral Genetics
>University of Colorado at Boulder
>General Forum at Bioinformatics.Org - BiO_Bulletin_Board at bioinformatics.org

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