Intro to bioinformatics - Department of Computer Science and ...

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2 Οκτ 2013 (πριν από 4 χρόνια και 1 μήνα)

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BIOINFORMATICS IN THE CS CURRICULUM

David Rilett, Mark LeBlanc,
Hongsheng

Wu, John Russo, Mike Werner

p53 bound to DNA from the protein databank file 1tsr (Cho et al., Science
265(1994)346). The p53 molecule is
color
according to frequency of observed
mutations in
tumors
(blue, very few; red, many). Two of the most mutated
residues are indicated with arrows.
http://www.bioinf.org.uk/p53/

WHAT HAVE YOU DONE FOR ME LATELY??

“Due to widespread international cooperation and advances in the field
of genomics (especially in sequence analysis), as well as major advances
in computing technology, a 'rough draft' of the genome was finished in
2000 (announced jointly by then US president Bill Clinton and the British
Prime Minister Tony Blair on June 26, 2000. “ (Wikipedia)

Craig Venter, Bill Clinton, Francis Collins

WHAT HAVE YOU DONE FOR ME LATELY??

Apollo 11 was a once in a lifetime event, so was decoding the genome.

Is was only the first step in a long journey towards understanding who we
are and where we fit in the universe.

Craig Venter, Bill Clinton, Francis Collins

TOOLS TO UNDERSTAND CANCER

Here is one example (Sanger/Cosmic) of a curated site that
tracks human DNA mutations associated with tumors.

(Search CDKN2A)







P
owered by
BioMart
:

INTRO TO BIOINFORMATICS COSMIC LAB: 1

THIS IS THE BIOMART QUERY:

<?
xml version="1.0" encoding="UTF
-
8"?>

<!DOCTYPE Query>

<Query
virtualSchemaName

= "default" formatter = "HTML" header = "0"
uniqueRows

= "0" count = ""
datasetConfigVersion

= "0.6" >






<Dataset name = "COSMIC52B" interface = "default" >



<Filter name = "
hist_primary
" value = "carcinoma"/>



<Filter name = "
samp_gene_mutated
" value = "y"/>



<Filter name = "
site_primary
" value = "lung"/>



<Filter name = "
gene_name
" value = "CDKN2A"/>



<Attribute name = "
id_sample
" />



<Attribute name = "
sample_name
" />



<Attribute name = "
sample_source
" />



<Attribute name = "
tumour_source
" />



<Attribute name = "
gene_name
" />



<Attribute name = "
accession_number
" />



<Attribute name = "
id_mutation
" />



<Attribute name = "
cds_mut_syntax
" />



<Attribute name = "
aa_mut_syntax
" />



<Attribute name = "
zygosity
" />



<Attribute name = "
site_primary
" />



<Attribute name = "
hist_primary
" />



<Attribute name = "
pubmed_pmid
" />


</Dataset>

</Query>

INTRO TO BIOINFORMATICS COSMIC LAB
: 2

____________________________BIOMART___CODE___STARTS___HERE_________________________________

open
(
FH,"cosmic.xml
") || die ("
\
nUsage
:
perl

webExample.pl Query.xml
\
n
\
n");

my $xml;

while (<FH>){


$xml .= $_;

}

close(FH
);

my $path="http://www.biomart.org/biomart/martservice?";

my $request = HTTP::Request
-
>new("POST",$
path,HTTP
::Headers
-
>new(),'query='.$xml
."
\
n");

my $
ua

= LWP::
UserAgent
-
>new;

my @all;

# Request
object

# Make the request

my $res = $
ua
-
>request($request
);

# Check the response

if ($res
-
>
is_success
) {

@all= split('
\
n',$res
-
>content
); # Using array to build the HTML table #
drilett

}

else {


print $res
-
>
status_line

. "
\
n";

}

__________________________
BIOMART___CODE
___ENDS___
HERE_____________________________________



INTRO TO BIOINFORMATICS COSMIC LAB
: 3

INTRO TO BIOINFORMATICS COSMIC LAB
: 3

Image source:
http://geekandpoke.typepad.com/geekandpoke/perl/

STUDENT PROJECTS

There is fun to be had for the student software engineer
adapting to new technologies like smart phones. (You will
need to install Opera Mobile to view as smart phone)

IF THINK OF A QUESTION LATER, GO HERE:


http
://biowit.cs.wit.edu
/


Keep in touch

THANK YOU!

(and have a good
-
protein day)

Created April 15, 2011 by David G. Rilett