Transcript Computational Core - University of Nebraska–Lincoln

COMPUTATIONAL CORE
Presented by
Hui Li
Department of Chemistry
University of Nebraska-Lincoln
Jan 16, 2009
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Necessity
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Computer and information technologies have grown
rapidly during the past few decades
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Created profound impact on biochemical research and
analysis
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Computer-aided collection, transfer, and processing of
large quantities of data
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Exploration of information from a variety of bioanalytical
databases
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Molecular modeling based on quantum chemical and/or
empirical force field methods
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Cyberinfrastructure
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A common cyberinfrastructure will significantly enhance
the accessibility, operation, management, and productivity
of projects that are performed in the NCRB
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This cyberinfrastructure will create a means by which
data can be directly input and shared from various new
and existing facilities, such as the Robotics & Automated
Sample Preparation Core and the MS and NMR facilities
at UNL, as well as the bioinformatics, functional analysis,
and nanoimaging facilities at UNL and UNMC
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Ready access to external connections and a means for
outreach and dissemination of research results to the
broader scientific community
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Computer-aided rapid bioanalysis
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The Computational Core will complement and enhance
the existing computing power at UNL and UNMC for work
in rapid bioanalysis
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Bioanalysis data obtained through modern analytical
instruments (e.g., those used in mass spectrometry or
NMR spectroscopy) will be important to many of the
projects comprising the NCRB’s research portfolio
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Significantly increase the ability of NCRB researchers to
use the established bioinformatics facilities at UNL and
UNMC
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Biomolecular simulation
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Theoretical and computational methods have been
increasingly employed in the study of biomolecules
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Quantum mechanics and molecular mechanics
calculations have reached a level of sophistication that
can provide valuable insights into complex molecular
systems, and often provide important guidance for
experimental studies
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The Computational Core will provide the processing
capability for such calculations, as will be required by
NCRB projects that involve either complex biomolecular
systems or simulations of bioanalysis methods
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Core support for NCRB projects
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This core will benefit all members of the NCRB
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Modeling of single molecule tracking/imaging (Project 2
Bashford)
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Creation of new data analysis methods (Projects 1 & 5
by Powers and Steinke)
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Support planned new hires involving the characterization
of complex biological systems through proteomics,
metabolomics or glycomics
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Existing faculty (Drs. Cerny, Du, Hage, Harbison,
Lyubchenko, Redepenning)
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Core support for NCRB projects
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Advanced quantum chemical calculations on
biomolecules and molecular mechanics simulations of
biomolecular systems will be immediately useful in
Project 1 (Powers).
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High-throughput drug screening, such as Projects 2 and
3 (Bashford and Cheung).
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Aims
The Computational Core will contribute to NCRB’s overall
success by completing the following specific aims:
Aim 1: Provide a cyberinfrastructure for the proposed
COBRE research and core facilities.
Aim 2: Provide computing power and software support for
analyzing data and simulating or optimizing new
bioanalysis methods.
Aim 3: Provide computing power and software support for
molecular modeling to be used to examine data from
bioanalysis methods.
Aim 4: Provide training to faculty, graduate students, and
post-doctoral fellows in use of the programs and
facilities hosted within the Computational Core.
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Hardware
Server
• 100 computer processors
• 400 gigabit memory
• 30,000 gigabit disk storage space
• A gigabit network for parallel computing
• Uninterrupted power source
User-end
• Five user-end workstations for NCRB investigators
• Graphics software necessary to visualize
protein/macromolecular structures
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Software
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Fortran and C compilers for researchers who wish to
develop their own computer programs for the
simulation or optimization of bioanalysis methods, as
well as for creating new programs for data analysis;
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Matlab with additional signal and image processing
toolboxes for use in the modeling and optimization of
bioanalysis methods;
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Software for examining protein/macromolecular
structures (e.g., AMBER, CHARMM, and Insight II) and
protein-ligand docking experiments (e.g., AutoDock 4) for
work involving proteomics, drug screening methods, or
biointeraction studies
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Software
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Software for use in calculations related to quantum
chemistry (e.g., Gaussian and Gamess) and molecular
mechanics software (e.g., AMBER and CHARMM) for
electronic structure analysis and dynamic simulations of
biomolecules, as could be used for work involving
proteomics, drug screening methods, or biointeraction
studies
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Other software packages required by users.
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Management
Director
Hui Li, Department of Chemistry, UNL
Research area: computational chemistry
Duty: User training and tutorials
System administrator
A full-time post-doctoral fellow
Formal system administration training
Duty: daily management
Location
Department of Chemistry, UNL
An existing computer room with heat exchange
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User friendly services
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No charge to all users associated with the NCRB;
A small fee to other users at UNL and UNMC
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Users will be provided with convenient, continuous
remote access
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Consultation and training regarding quantum electronic
structure calculations and molecular dynamics
simulations
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Tutorials on basic quantum chemistry, software use,
input decks, job submission, and output analysis will be
developed and/or posted by this core for use at the
NCRB website
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Specific daily functions
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Host the NCRB website, as updated and maintained by
the Administrative Core.
Work with the Center Administrator to create a facility
that will manage/share NCRB research reports and data.
Provide access to the other facilities at UNL and UNMC,
such as the mass spectrometry and NMR facilities.
Provide computing power for performing simulations of
new bioanalysis methods, as well as quantum
calculations on biomolecules, molecular mechanics
simulations for biomolecular systems, and drug-protein
docking experiments.
Provide consultation and training pertaining to advanced
computational chemistry methods
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