[BioPython] Creating a graphical interface to database of gene coordinates
Srinivas Iyyer
srini_iyyer_bio at yahoo.com
Fri Apr 21 22:49:28 UTC 2006
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
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