Transcript - Cal State LA - Instructional Web Server

The Wold Lab
BioHub
Cory Tobin
Collaborators
Brandon King
Joe Roden
Diane Trout
Dr. Barbara
Goal
•
Standardize the relationship between biological data
•
Integrate all of the data seamlessly
•
Provide novel methods to search for and analyze data
Adapted from http://woldlab.caltech.edu/biohub/
My Contribution
Implement a database for homology data
Background
Species A
Gene
Gene
Paralogs
The more general
term is “homology”
Orthologs
Species B
Gene
Requirements
•
Be more accurate and flexible than HomoloGene
•
Work in real time
•
Make sense of HomoloGene’s misleading data
Rationale
BioHub
HomoloGene
Gene
Gene
Gene
Gene
Gene
Gene
Gene
Gene
Gene
Gene
They are similar
They are related like this
Rationale Continued
Seq A
Seq B
Human Genome
BioHub
will BLAST
A BLAST
against
HomoloGene
wouldseq
BLAST
also
seq
mouse,
find
seq
C,
then
BLAST C
A against
seq
B against
mouse
mouse
and
and
determine
back
against
human
to an
see
that seq
detrmine
Cthat
is an
seq
ortholog
C is
of ifseq
there
areof
any
matches. It
A.
ortholog
seqbetter
B.
will find seq B to be better.
Seq C
Mouse Genome
Methods
•
Design data relationships that make sense biologically
•
Generate the low-level database interaction code
•
Parse and load HomoloGene’s data into our database
•
Write biologically useful functions
•
Create a web-based interface for easy use
Materials
•
ArgoUML – Design Aid
•
Pymerase – Design Implementation
•
PostgreSQL – Database
•
HomoloGene – Data Source
•
Python – Programming Language
Current State
•
Design data relationships that make sense biologically
•
Generate the low-level database interaction code
•
Parse and load HomoloGene’s data into our database
•
Write biologically useful functions
•
Create a web-based interface for easy use
Example Usage
Sequence of Interest
…GGATACAAAATTCCTC…
Are there any known genes in
this sequence?
acetyl - coenzyme A
dehydrogenase ( Human )
(cont.)
acetyl - coenzyme A
dehydrogenase ( Human )
Are there any homologs?
Mouse
Rat
Mosquito
Fruit fly
Nematode
(cont.)
How are those genes related?
Where do you
want to go?
More Info
BioHub
woldlab.caltech.edu / biohub
HomoloGene
www.ncbi.nlm.nih.gov
Python
python.org
Pymerase
pymerase.sf.net
PostgreSQL
postgresql.org