Research Interests
I
am interested in how computer science interfaces to biology.
Whether the field is informatics, computational biology or systems
biology, I find it all quite fascinating.
Most of the code I write is in Perl and have given myself the title of
Perl GrandFunkMaster, although I also use Java, SQL, and enough C to
get myself in trouble.
Given the blessing of Dr. Hammer, code written for this project will be
available for non-profit scientific use (and citing me is always
appreciated!).
Current Research
I am the lead bioinformaticist for the
Hominid Project. I have built, with the help of Olga Savina, a Phred-Phrap-Consed pipeline
specifically designed to handle complex, highly variable regions of the genome
(GUI-fied and everything). I'm also the designer and administrator of the
Hominid database (PLOP - polymorphism and linkage organizational platform).
On top of this, I also take care of many of the various bioinformatics fires
that arise when you try and sequence and organize waaayyy to much DNA (30 million
bases and counting).
Edjumacation:
It has been alledged that I have a BS in Biology from Marlboro College.
Because I love self-flagellation, I am also a part-time Computer Science major here
at the University of Arizona.
Popular and Portable Scripts:
Wallop.pl
Creates a table of polymorphisms, based off of a fasta/nexus file,
optionally with the genomic coordinates of said SNPs (Simple/Single
Nucleotide Polymorphisms).
IM_going_crazy.pl
Reads in a fasta file, and returns either the largest, non-recombining
block (by removing data), or it returns multiple non-recombining blocks
(without removing data). This was originally written for the IM
program, although it has other uses as well.
Fasta2phase/Phase2fasta
Creates Phase 2.1.1 compatable files from an aligned fasta file, and vice versa.
Other Stuff:
I enjoy games way too much as well. If you are reading this, play bridge,
and live near Tucson, contact me. I have been without for too long! I also play Quiddler, Set, Boggle, Scrabble, Hearts, Euchre, and, well,
pretty much anything.
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