[Tutor] Creating a graphical interface to database of gene coordinates

[Liam Clarke]

For graphing you can't really beat Scipy.

On 4/22/06, Srinivas Iyyer <srini_iyyer_bio at yahoo.com> wrote:
> Dear group,
>  I am happy that I am slowly finding pyhonian projects
> related to my research area.
>
> Problem:
> 1. I have a database of human gene coordinates on
> chromosomes.
> 2. I have gene expression data from my lab concerning
> the genes I mentioned above.
>
> 3. I want to visualize expression data laid on
> chromosomes.
>
> Eg.
> Coordinates:
> Chr      Gene       From      To     Exon
> 1         x         100       120    exon:1
> 1         x         200       250    exon:2
> 1         x         350       450    exon:3
>
>
> Expression data:
>
> IDent   sample  Chr    From     To     Expression
> value
> xxx_at  lung     1     110      120     100.35
> x_s_at  heart    1     225      250     124.35
> x_a_at  eye      1     375      400     146.35
>
> What I want:
>
> I want to have a simpler window, that would connect to
> my database.  I want to give a gene, this python/tk
> interfacce or what ever would query the database
> draw a graph of gene according the exons and plot the
> values.
>
> -------_______----------_______-------
>
> -- : exon
> __: regions that are not exons, introns.
>
>
>
> My questions to Tutor/BioPython forums:
>
> 1. What should I decide to work on a. Py/Tk framework
> b. python imaging libraries etc.
>
> 2. I do not want to impress any one with this work,
> except that it should help me understand the
> relationships as the number game in the tables above
> is highly confusing. So, a working version that
> accurately plots the expression values for as many
> samples I have
>
> 3. Are there any available modules to jump-start? or
> do I have to create some from scratch. which would be
> a problem because I am between novice to mediocral
> level of python programing.
>
> 4. Any ideas/suggestions/pointers are highly
> appreciated.
>
> thanks
> Sri
>
> __________________________________________________
> Do You Yahoo!?
> Tired of spam?  Yahoo! Mail has the best spam protection around
> http://mail.yahoo.com
> _______________________________________________
> Tutor maillist  -  Tutor at python.org
> http://mail.python.org/mailman/listinfo/tutor
>