Twigger, Simon Ph.D.
Assistant Professor
Specialization: Bioinformatics, Model Organism Databases and
Data Mining
Tel: (414)456-8802 Dr. Twigger's CV
Email:
Computational biology consumes and generates data and managing
this effectively is a key thrust of much of current work. As part
of the NHGRI funded component of the Generic Model Organism Database
project (GMOD) we have created PubFetch, a webservice that provides
standardized access to popular literature databases PubMed and
Agricola. Access to literature is vital for model organism database
curation and the BioMOBY webservice approach we have used makes
this data accessible to any BioMOBY-compatible system. PubTrack,
another component of the GMOD project is a data tracking package
that allows researchers to follow their data and analyses as they
progress through the heterogeneous web lab and computational environments.
The NHLBI funded Rat Genome Database
(RGD) has established itself
as a primary source of rat genomic data. Our goal is to assist
the rat researcher in relating his or her results in the rat
to facilitate the development of disease treatments. However,
this
is a moving target and our latest challenge is to integrate the
rat genomic sequence and provide the database users with effective
ways to integrate the sequence with their own experimental research.
The NHLBI national proteomics center ties together many elements
of computational biology. We are developing a novel proteomic analysis
algorithm that is significantly faster than the existing state
of the art; we will be extending this package and adapting it to
run on in a parallel architecture. Effective use of high performance
computer clusters is another area of emphasis, and we will be making
use of BioMOBY and the PubTrack projects to assist in data management
and tracking in this distributed environment.
Twigger, S.; Smith, J.; Zuniga-Meyer, A.; Bromberg, S. Exploring phenotype data at the Rat Genome Database. Current Protocols in Bioinformatics. Hoboken, NJ: Wiley; 2006. pp. 1.14.1–1.14.27
Computational biology consumes and generates data and managing
this effectively is a key thrust of much of current work. As part
of the NHGRI funded component of the Generic Model Organism Database
project (GMOD) we have created PubFetch, a webservice that provides
standardized access to popular literature databases PubMed and
Agricola. Access to literature is vital for model organism database
curation and the BioMOBY webservice approach we have used makes
this data accessible to any BioMOBY-compatible system. PubTrack,
another component of the GMOD project is a data tracking package
that allows researchers to follow their data and analyses as they
progress through the heterogeneous web lab and computational environments. 
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