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 ???