BIOINFORMATICS at USP
Junior Barrera
www.bioinfo.usp.br
Bioinformatics at USP
• Research activities
• Educational programs
Gene Structure
Nosso software
Dados para a estimação da expressão do gene
−3.5 −3 −2.5 −2 −1.5 −1 −0.5 0 0.5 1−1.5
−1
−0.5
0
0.5
1
1.5
2
phosphofructokinase, platelet
v−
erb
−b2 a
via
n e
ryth
robla
stic leukem
ia v
iral oncogene h
om
olo
g 2
LINEAR CLASSIFIER (DISPERSED−GAUSSIAN) w/ σ = 0.600
1−th (0.389593)
7−th (0.416607)
BRCA1 BRCA2/sporadic
the tumor sample from Patient 20
Interfase
Mitose
Division Steps
Cell Cycle Model
u1
I
u2
u5
v
vfp
w1
w2
w1fp
w2fp
w1f
w2f
x1
x6
y1
y2
z
x1f
x3f
x4f
x6f
x6fp
x1fp
y1fp
y2fp
.
.
.
.
.
.
z
Forward SignalFeedback to pFeedback to previous layer
y1f
y1f
y2f
y2f
p
Malaria parasite life cycle
Proteoma
Transcriptoma
Genoma
Metabolic pathways
Σ
Wet labWhat genes regulate a
pathway A->B->C->D ?
P1
P2
Pn
Pi : analytical procedures and data mining (parallel kernel )
Objected oriented database
E4000
E3500 V880
GRID Computer - DCC-IME-USP
Internet
and
Intranet
...
E4000:Databases and web application services
Processing services
(by SEFAZ)
10 processors
16 G-bytes main memory
1 T-bytes disk
(by CAGE-FAPESP)
4 processors
8 gigabytes
(by Malaria-FAPESP)
16 processors
32 G-bytes
V880?
(by eucalipto-CNPq ???)
16 processors
32 G-bytes
Educational Programs
• USP PhD program on Bioinformatics, with
the participation of seven USP Institutes:
Mathematics, Physics, Engineering,
Biology, Biochemistry,Medicine.
• Harvard-MIT-USP research and training
program, supported by NIH: 2004 - 2009
• Harvard-MIT-USP-IBM ???
• NIH + IBM ???
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