[BiO BB] Plone and bioinformatics?

lijo skb lijo.skb at gmail.com
Thu Jun 14 00:26:23 EDT 2007

Dear Rick Casey,

I suggest another team, exuberant young researchers group namely soorkiran
bioiformatics <http://www.sooryakiran.com>. Perhaps we could help you to
successful execution of you project.

Warm regards

On 6/14/07, Mike Marchywka <marchywka at hotmail.com> wrote:
> 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:
> http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html
> 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
> end-product
> 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
> stuff-
> that's for researchers not web page designers. Having an "output as text"
> option
> for everything, including spatial data that can be reduced to vectors or
> something,
> 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
> >analysis.
> >
> >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
> >
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