Ohio Bioinformatics Consortium Research Infrastructure

underlingbuddhaBiotechnology

Oct 2, 2013 (4 years and 9 days ago)

86 views

Ohio Bioinformatics Consortium Research
Infrastructure

Ashok Krishnamurthy

Ohio Supercomputer Center

Michael Raymer


Wright State University

Zhong Hui Duan


University of Akron

Steven Gordon


Ohio Supercomputer Center

Lonnie Welch


Ohio University

2

What is the role of the Research Infrastructure
Group?


Premise: A vibrant research program is essential to drive
world
-
class education


Goals:


Facilitate interactions


Identify academic and industry researchers in Ohio


Create a website to highlight all known research expertise within
the State


Identify research opportunities for students to be supported by
undergraduate and graduate scholarships.


Assist in seeking external funding for education e.g., NSF
Research Experience for Undergraduate (REU) and Integrative
Graduate Education and Research Traineeship (IGERT)


Support inter
-
institutional summer research opportunities and
collaborative projects such as intra
-

and inter
-
collegial
competitions.


3

Ohio Bioinformatics Consortium members

Institution

No. of
faculty

Bowling Green State /University of Toledo

10

Case Western Reserve University (CWRU)

6

Central State University (CSU)

4

Miami University (MU)

10

Ohio State University (OSU)

3

Ohio University (OU)

10

University of Akron (UA)

4

Univ. of Cincinnati (UC)

8

Wittenberg University (WU)

4

Wright State University (WSU)

6

4

Ohio Bioinformatics Consortium research
expertise

Genome annotation, Comparative genomics, Pathway reconstruction,
RNA 3D structure
,
Genetic variation analysis, Network and systems
biology, Statistical and functional genomics
,
Metabolomics,

Biomedical
ontologies and image analysis
,
DNA sequencing, Ribotyping,
Microarray expression analysis
, Genome annotation and databases,
Signal recognition and modeling, Computational biology
,
Molecular
Evolution, Proteomics and Metabolomics, Structural genomics, Gene
and medical ontologies
,
Computational genomics, Regulatory
genomics, Proteomics and Disease research
,
Functional and
regulatory genomics, Proteomics, Disease research, Plant genomics,
Medical information/ cancer biology, Proteomics, Comparative
genomics, Computational biology, Medical informatics/ molecular
cardiology,

Evolutionary genetics
,
Medical informatics, Proteomics,
Computational biology
,
Marine biology, Environmental science, Health
information/ image processing
,
Metabolomics, Biomarker
identification/feature selection, Protein structure, Molecular evolution,
Forensic DNA


5

6

Stable computational infrastructure

to support the research and innovation process

IBM 1350


Opteron dual
-
core w/IBM Cell


4,000+ cores


8 TBytes memory


22+ teraflops


Blend of 4 core and 8 core nodes


Large processor count


Large memory SMP jobs

Intel P4 Cluster


2.46 TF


512 processors


1 TBytes memory

Itanium2 Cluster


2.7 TF


596 processors


3x16 Alt


1 TBytes memory

PRODUCTION COMPUTING

Mass Storage

470 TBytes disk

80 TBytes tape

NFS, PVFS, iSCSI

Infiniband or Myrinet Interconnect

Gateway to
User Science

7

Visualization Cluster


AMD Opteron


72 processors


144 GBytes memory


nVIDIA Quadro 5600
graphics card(330 GF)

Cell Blades


4 cell blade array


Accessible from


IBM e1350

Providing agile computational infrastructure

to support the research and innovation process

MATLAB/GRI Cluster


AMD Opteron


164 processors


328 GBytes memory

RESEARCH COMPUTING

Mass Storage

470 TBytes disk

80 TBytes tape

NFS, PVFS, iSCSI

Gateway to
User Science

BALE Cluster


AMD Athlon 64


110 processors


220 GBytes memory


nVIDIA GeForce
6150 GPU

8

OSC supports a variety of software applications
for scientific research

Center staff maintain more
than 30 software
applications, and we provide
access to more than 70
different software packages

Software

Area of Interest

CPU Hrs.

Gaussian
03

Electronic Structures, Chemistry, Chem.
Engineering, Biochem., Physics

942,103

VASP

Ab
-
initio Quantum
-
mechanical Mol. Dynamics,
Physics, Materials Science

768,019

Amber

Molecular Dynamics, Chemistry, Biochem.

515,661

Gromacs

Mol. Dynamics, Chemistry, Biochem.

265,507

LMF

Molecular Dynamics

195,302

Software

Area of Interest

Projects

Gaussian
03

Electronic Structures, Chemistry, Chem.
Engineering, Biochem., Physics

73

MATLAB

Higher Level Language

33

Amber

Molecular Dynamics, Chem., Biochem.

15

ADF

Molecular Dynamics, DFT

14

FLUENT

Fluid Dynamics, Engineering, Aerospace

14

Top 5 Software Applications by CPU Hours

Top 5 Software Applications by Projects

9

OSC CI Mission


OSC Cyberinfrastructure (CI) Mission


Participating in national CI initiatives (e.g., TeraGrid)


Hosting CI applications (e.g., GridChem)


Developing CI Applications


CI Software Development (CSD) Group created in July 2007


Vision: Connect people to supercomputing applications, large data
sets, research instruments, and virtual communities

10

OSC Cyberinfrastructure Applications


Web portal applications


Web
-
based access to cycles, data, software, expertise


Basis for OSC collaborations (E
-
Weld, GRIDP)


Enable research teams to create and plug in their own
portal


Instrumentation and Analytics Services


Web
-
based access to instruments, data sets and image
processing


MATLAB as analytics engine for rapid prototyping


Basis for OSC collaborations (CAMM, MU NMR)

11

Example 1: GRI Discovery Platform (GRIDP)


Collaboration between OSC,
the University of Cincinnati's
Genome Research Institute
(GRI) and the Ralph Regula
School of Computational
Science (RRSCS)


Designed to reduce the
technical hurdles associated
with modern computational
drug discovery with an intuitive
web
-
based user interface to
the software


High performance computing
(HPC) computational biology
programs are made available
as web services

12

OSC Instrumentation and Analytics Services


Remote instrumentation uses OSC’s state
-
wide resources


Networking, Storage, HPC, Analytics (web service)

13

Remote Instrumentation and Analytics with
Miami University


Remote Instrumentation Projects


NMR Spectrometer, Chemistry and Biochemistry
Dept.


Development of software for remote observation &
operation and for storage, retrieval and analysis of NMR
data. (under development, funded by OBR)


Unipulsed EPR Spectrometer, Chemistry and
Biochemistry Dept.


Development of software for remote operations and/or
observation


High Resolution TEM, Electron Microscopy Facility
(EMF), Geography Dept.


Development of software for remote operations and/or
observation


Biomarker discovery engine


Development of a web
-
portal for data hosting and
analytics in support of biomarker
-
based diagnostic
testing research (Frantz Biomarkers and MU, ODOD
BRCP Proposal, pending)

13

Brucker
850 Mhz
NMR in
Dr.
Kennedy’s
Miami
Univ. lab

Joel TEM
in the EM
Facility at
Miami
Univ.

14

MATLAB® Distributed Computing Toolbox
Architecture

Image source: http://www.mathworks.com