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Bioinformatics in the CS curriculum

David Rilett, Mark LeBlanc, Hongsheng Wu, John Russo, Mike Werner. Bioinformatics in the CS curriculum. What have you done for me Lately??. Craig Venter, Bill Clinton, Francis Collins.

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Bioinformatics in the CS curriculum

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  1. David Rilett, Mark LeBlanc, Hongsheng Wu, John Russo, Mike Werner Bioinformatics in the CS curriculum

  2. What have you done for me Lately?? Craig Venter, Bill Clinton, Francis Collins “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)

  3. What have you done for me Lately?? Craig Venter, Bill Clinton, Francis Collins 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.

  4. Here is one example (Sanger/Cosmic) of a curated site that tracks human DNA mutations associated with tumors. (Search CDKN2A) Tools to understand Cancer Powered by BioMart:

  5. 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: 1

  6. ____________________________BIOMART___CODE___STARTS___HERE_____________________________________________________________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: 2

  7. Intro to bioinformatics cosmic lab: 3

  8. Intro to bioinformatics cosmic lab: 3 <= “click me” Image source: http://geekandpoke.typepad.com/geekandpoke/perl/

  9. 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) Student projects

  10. http://biowit.cs.wit.edu/ Keep in touch THANK YOU! (and have a good-protein day) If think of a question later, go here: Created April 15, 2011 by David G. Rilett

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