Considerations for Strategic Positioning - Bioinformatics - University ...

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2 Οκτ 2013 (πριν από 4 χρόνια και 1 μήνα)

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1 September 2005

NSF EPSCoR Thematic Proposals

1

NanoToxicology and
Bioinformatics

2006 Arkansas NSF EPSCoR

Thematic Proposal

1 September 2005

NSF EPSCoR Thematic Proposals

2

Bioinformatics at UALR

Steve Jennings

Professor

Applied Science/EIT

SFJennings@UALR.Edu

(501) 569
-
8216/ETAS 505

http://Bioinformatics.UALR.Edu

1 September 2005

NSF EPSCoR Thematic Proposals

3

Intersection of Interests


Nanotechnology


Biosciences


Computational
Sciences

1 September 2005

NSF EPSCoR Thematic Proposals

4

Thematic Structure


Regional interests


and strengths


National/
international
impacts


Local economic
impact

1 September 2005

NSF EPSCoR Thematic Proposals

5

Theme Suggestion: NanoBioInfo


Toxicology of Nanoparticles


Understanding mechanisms


Abatement strategies


Strengths


Clear opportunity for combining
three cores


In addition to involving UAF, ASU
and UALR, it’s possible to draw
upon the research capabilities of
NCTR, UAMS and a number of
UGIs


Major funding opportunities over
the long term


not just EPSCoR

1 September 2005

NSF EPSCoR Thematic Proposals

6

Thematic Guidelines


Problem solution in
overlapping cores


Build upon the
strengths of each core


All efforts should be in
support of the overall
theme


Important to focus upon
the common objectives

1 September 2005

NSF EPSCoR Thematic Proposals

7

Participation Potential

NCTR

UALR

UAF

ASU

UGIs

Toxicology

X

X

X

X

Nanosciences

X

X

X

Biosciences

X

X

X

X

X

Bioinformatics

X

X

1 September 2005

NSF EPSCoR Thematic Proposals

8

Nanotechnology Grows Up

Science 6/18/04

“Carbon nanotubes,
quantum dots …, and
nanoparticles have
enticing electrical and
optical properties, but
toxicologists worry
that they might harm
organisms.”

1 September 2005

NSF EPSCoR Thematic Proposals

9

Nano Hazards: Exposure to
minute particles harms lungs,
circulatory system

Science News 3/19/05

“… new animal studies indicate that inhaling
these microscopic spheres and tubes could
cause big trouble, especially for workers
who manufacture and handle them.”

1 September 2005

NSF EPSCoR Thematic Proposals

10

Special Treatment: Tiny
Technology Tackles Mega Messes

Science News 4/23/05

“Unfortunately, risk assessments lag far
behind the pace of new
developments in nanotechnology.”







1 September 2005

NSF EPSCoR Thematic Proposals

11

Nanotechnology Grows Up

Science 6/18/04


“As funding for
nanotech skyrockets,
the U.S. National
Nanotechnology
Initiative devotes
11% of its budget to
health and
environmental
issues.”

1 September 2005

NSF EPSCoR Thematic Proposals

12

Toxicology


Collaboration with NCTR instantly gives
us the scientific credibility to compete
internationally


This is a new area of great interest to NCTR


NCTR has major animal study capabilities


ASU and UAPB have established
capabilities in undertaking toxicology
studies


Other UGIs and UAMS may also be
contributors as well

1 September 2005

NSF EPSCoR Thematic Proposals

13

Toxicology Research Areas


Assessing potential toxic effects of
nanoparticles


Abatement strategies for reducing harmful
effects


Manufacturing and disposal strategies


Understanding basic mechanisms


Appropriate use

1 September 2005

NSF EPSCoR Thematic Proposals

14

Nanosciences


UAF and UALR have major
investments in the nanosciences
including the unique capability of
producing high
-
quality nanoparticles
(i.e., of uniform characteristics)


This is critical for undertaking


toxicology studies


ASU has interest in collaborating in
this area

1 September 2005

NSF EPSCoR Thematic Proposals

15

Nanotechnology Research Areas


Production of high
-
quality nanoparticles
for toxicology testing


Experimental strategies for producing
particles with less toxic effects


Structural changes


Size changes


Encapsulation strategies


Delivery strategies

1 September 2005

NSF EPSCoR Thematic Proposals

16

Nanotechnology Collaborators


UAF


Greg Salamo and colleagues


UALR


Abhijit Bhattacharyya


Alex Biris


Malay Mazumder


Karin Pruessner


ASU


Robert Engelken

1 September 2005

NSF EPSCoR Thematic Proposals

17

Biosciences


All three universities have major
bioscience capabilities


Biology


Chemistry


Biochemistry

1 September 2005

NSF EPSCoR Thematic Proposals

18

Biosciences Research Areas


Understanding basic mechanisms


Developing appropriate biological
models

1 September 2005

NSF EPSCoR Thematic Proposals

19

Toxicology and Bioscience
Collaborators


UALR


John Bush


Jerry Darsey


QingFang He


Maurice Kleve


David Lindquist


XiaoDong Ma


Gary Thompson


HongLi Wang


UAPB


Andy Goodwin


Steve Lochmann


NCTR


Dan Buzatu


Yvonne Dragan


Paul Howard


Dwight Miller


ASU


Roger Buchanan


Carole Cramer


Maureen Dolan


Jerry Farris


Robyn Hannigan


Beth Hood


Malathi Srivatsan


1 September 2005

NSF EPSCoR Thematic Proposals

20

Bioinformatics


UALR/UAMS Joint Graduate Program in
Bioinformatics


40+

participating faculty


Including many NCTR adjunct faculty


10
current graduate students


Could double in next six months


Does not count UALR Applied Science graduate
students doing bioinformatics
-
related projects


NCTR Center for Toxicoinformatics


1 September 2005

NSF EPSCoR Thematic Proposals

21

Bioinformatics Research Areas


Data management and data mining


Strong and active research programs at UALR


Leverage ties with Acxiom


Modeling and simulation of biosystems
and nanoparticles


Strong collaborations between UALR and
NCTR (and UAMS) in model development


Visualization of models and mechanisms


Major capabilities and investments in these
areas at UALR

1 September 2005

NSF EPSCoR Thematic Proposals

22

Bioinformatics Collaborators


Weida Tong and colleagues (NCTR)


UALR Bioinformatics Collaborators


Al Adams




Swaminadham Midturi


Coskun Bayrak



Fani Milanova


Yupo Chan




Jennifer Perkins


Chia
-
Chu Chiang



Peiyi Tang


Sean Geoghegan



Edi Tudoreanu


Kamran Iqbal



Xiaowei Xu


Steve Jennings



Kenji Yoshigoe

1 September 2005

NSF EPSCoR Thematic Proposals

23

Bioinformatics Resources


UALR MidSouth Bioinformatics Center


Bioinformatics Computing Facility


NCTR Center for Toxicoinformatics


UAMS Bioinformatics Centre


UALR Virtual Reality Center


Access Grids

1 September 2005

NSF EPSCoR Thematic Proposals

24

Bioinformatics Computing Facility


SunFire Servers


V880


Eight 900MHz UltraSPARC
-
III processors


32G memory with 438G disk space


Two 280Rs


Dual 1.2GHz UltraSPARC
-
III processors


8G memory, Fiber Channel Disk Array, SCSI tape drive


Free, open source software


bioPerl, EMBOSS, NCTR’s ArrayTrack


Commercial software packages as required


Oracle and S+/ArrayAnalyzer


1 September 2005

NSF EPSCoR Thematic Proposals

25

UALR’s Virtual Reality Center

1 September 2005

NSF EPSCoR Thematic Proposals

26

Visualizing Aphid Attacks on Plant Cells

Traditional View:

microscopy

3D Fungus
Attack

Cell wall

Immersed:

seeing 3D from

inside the cell

Interactive selection
and navigation

1 September 2005

NSF EPSCoR Thematic Proposals

27

Access Grid Conferencing

University of Arkansas at Little Rock

University of Arkansas at Fayetteville

Housed at Mullins Library

Arkansas State University

Housed at Dean B. Ellis Library

University of Arkansas for
Medical Sciences

University of Arkansas for Medical Sciences

Housed in the UAMS Library, 3
rd

floor

University of Arkansas at Little Rock

Funded through CyberCollege start
-
up

University of Arkansas at Little Rock

Funded by AR BRIN

1 September 2005

NSF EPSCoR Thematic Proposals

28

INBRE Funding Access Grid Executive
Stations for Seven AR UGIs

1 September 2005

NSF EPSCoR Thematic Proposals

29

Arkansas BRIN/INBRE Programs


In the midst of nine years of major
funding for UAMS, UAF, UALR and seven
UGIs to participate in biomedical research
infrastructure development


Funded initial bioinformatics efforts


Enabled strong working relationships
between these ten institutions


Intend to leverage these relationships in this
expanded program area of nanotoxicology

1 September 2005

NSF EPSCoR Thematic Proposals

30

MidSouth Nanotoxicology and
Bioinformatics Summit


Statewide meeting to be held on
Monday/Tuesday,
September 19/20


Monday afternoon
(NCTR): Welcome and
tours of NCTR facilities


Tuesday 8
-
5
(UALR): Keynote speaker,
Disciplinary working sessions, Action plan for
NSF EPSCoR white paper


Sponsored by NCTR, UALR Graduate School
and UALR CyberCollege


REGISTER AT
http://bioinformatics.ualr.edu/nanotox


1 September 2005

NSF EPSCoR Thematic Proposals

31

Dr. Anna Shvedova

National Institute for

Occupational Safety and Health

1 September 2005

NSF EPSCoR Thematic Proposals

32

NanoTox 2006

1 September 2005

NSF EPSCoR Thematic Proposals

33

Advisory Board


Board made up of senior scientific/
administrative representatives from:


ASU




UALR


NCTR




UAMS


UAF




UGIs


Responsible for overall project oversight,
inter
-
institutional coordination, and
assuring cohesiveness of sub
-
projects


Assist with long
-
term funding (post
-
EPSCoR submission)

1 September 2005

NSF EPSCoR Thematic Proposals

34

About EPSCoR

“EPSCoR’s goal is to
maximize the potential
inherent in a state’s S&T
resources and use those
resources as a foundation
for economic growth.”