Ohio Bioinformatics Consortium Research Infrastructure

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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

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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.

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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
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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

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Stable computational infrastructure to support
the research and innovation process
PRODUCTION COMPUTING

• Itanium2 Cluster
• 2.7 TF
• 596 processors 3x16 Alt
• 1 TBytes memory

• Intel P4 Cluster
• 2.46 TF
• 512 processors
• 1 TBytes memory

Gateway to User Science
Infiniband or Myrinet Interconnect

• 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

Mass Storage 470 TBytes disk 80 TBytes tape NFS,
PVFS, iSCSI
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Providing agile computational infrastructure to
support the research and innovation process
RESEARCH COMPUTING

• Visualization Cluster
• AMD Opteron
• 72 processors
• 144 GBytes memory
• nVIDIA Quadro 5600 graphics card(330 GF)

Gateway to User Science

• BALE Cluster
• AMD Athlon 64
• 110 processors
• 220 GBytes memory
• nVIDIA GeForce 6150 GPU

• Cell Blades
• 4 cell blade array
• Accessible from
• IBM e1350

Mass Storage 470 TBytes disk 80 TBytes tape NFS,
PVFS, iSCSI

• MATLAB/GRI Cluster
• AMD Opteron
• 164 processors
• 328 GBytes memory

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OSC supports a variety of software applications
for scientific research
Top 5 Software Applications by CPU Hours

• 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
Top 5 Software Applications by Projects
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
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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

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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)

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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

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OSC Instrumentation and Analytics Services

• Remote instrumentation uses OSCs state-wide
  resources
• Networking, Storage, HPC, Analytics (web service)

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Remote Instrumentation and Analytics with Miami
University
Brucker 850 Mhz NMR in Dr. Kennedys Miami Univ.
lab

• 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)

Joel TEM in the EM Facility at Miami Univ.
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MATLAB Distributed Computing Toolbox Architecture
Image source http//www.mathworks.com
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Common software services
E-Weld GridP Wordseeker MU NMR CAMM-VIM
Portal ? ? ? ? ?
LIMS (lab notebook) ? ? ? ?
Compute ? ? ? ?
Data Storage ? ? ?
Instrument Access ? ?
CSIDE ?
AAA ? ? ? ? ?