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Work at Zacharewski Laboratory
First Work Term: Jan-Apr, 2002
My work at the Zacharewski lab is bipartite: on one side, I
gained wet-lab experience by sequence-verifying a set of approximately
200 clones involved in Human Dioxin Responses. On the other
side, I'm involved in the Bioinformatics side of the lab - working
with Perl scripts, our Oracle back-end dbZACH, web interfaces
and general Windows administration of the computers in the laboratory.
The lab has found a significant reason to sequence-verify any
clones acquired from IMAGE distributors (see paper
for further details). I was involved in the sequence verification
of 192 human Dioxin Response Elements (DRE) clones - this procedure
involved purification of cultures, plasmid isolation, running
gels to isolate contaminants, their subsequent sequencing and
analysis. I proposed, designed, and tested an Access Database
to ease the processing of sequence, BLAST2 and NetBLAST data
- something that was previously done in Excel spreadsheets.
I was trained for sequence-verification work by graduate students
Darrell Boverhof and Kirsten
Fertuck.
On the Bioinformatics side, my projects for the term were:
- Building the Protocols subsystem for management and archival
of in-house protocols
- Creating, testing, and deploying a standard web-interface
design for the lab & dbZACH webpage, including the creation
of interfaces to query dbZACH data using Macromedia DreamWeaver
UltraDev
- Building a DB update script that would refresh dbZACH with
the latest information as retrieved from online databases
such as LocusLink, UniGene and Gene Ontology
- Ensuring that the NIA 15k clone set in the database was
also updated alongside the non-NIA clones
In addition to this, my responsibilities included general DBA
work for dbZACH, Windows administration for the lab network,
general troubleshooting and any ad-hoc requests from lab members.
I work in conjunction with the Bioinformatics group within
the lab, with support from Lyle
Burgoon and Yan Sun.
Second Work Term: Sep-Dec, 2002
This work term also saw a split in my efforts between the wet
lab and the Bioinformatics projects.
On the wet-lab side, I'm working under the direction of Cora
Fong and Darrell Boverhof
to prepare cDNA samples for microarray printing of new mouse
and human arrays. This task involves the PCR-amplification,
gel-verification, filtration, suspension (in spotting solution)
and final check of over 35 plates. Our team for this task also
has: Jigger Vakharia, Josh
Wallace, and Raeka Aiyar.
The Bioinformatics projects in the lab are now focussed on
developing a suite of Java interfaces that facilitate microarray
data analysis and interpretation. My major projects this term
include the development of the Java-based Clones interface and
JM-FIT - a Microarray Feature-Inspection Tool.
The Clones interface helps in batch data-retrieval of a variety
of clone-related information including (but not limited to)
in-house lab location, associated genes, NIA 15K information
(if the clone belongs to the NIA 15K set), and 3' and 5' sequence.
JM-FIT is a tool designed for microarray quality control; it
allows the user to look at microarray features of genes of interest
or to look at certain areas of the microarray to examine for
background problems. This interface uses extremely cool tiling
functionality made possible by Oracle9i's (our back-end database)
tools for media-rich applications and the Java Advanced Imaging
API.
If time permits, I may even get the chance to work on the preliminaries
for creating a Java version of GP3, our Gene-Pix Post Processing
Script (currently in Perl). Fellow Waterloo co-op Jigger
Vakharia and I collaborate on these Java projects.
Aside from the Java goodies, I work with Perl scripts - this
term has seen the crystallisation of the dbZach
update scripts into a suite of sorts, one that updates gene
annotation in the database on a weekly basis from online databases
such as NCBI and GeneOntology. I've also worked on a keyword
search script that returns comprehensive information from LocusLink
entries when provided with a list of keywords (Gene names, abbreviations,
RefSeq numbers).
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