NPACI Archive Page
The NPACI program ended on September 30, 2004. This site is presented for archival purposes only.
For current resources at each of the partner sites, please refer to the appropriate institution site.
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Project Leader: Wah Chiu (wah@bcm.tmc.edu)
Co-Project Leader: Steven Ludtke (sludtke@bcm.tmc.edu)
Project URL: http://ncmi.bcm.tmc.edu
The primary research goal of the National Center
for Macromolecular Imaging (NCMI) is to develop research infrastructure
for determining three-dimensional structures of large macromolecular
machines towards atomic resolution using electron cryomicroscopy
and computer reconstruction without crystals. Our specimens
typically range in size from hundreds of kilodaltons to megadaltons.
The three-dimensional reconstruction process involves merging
particle images in different orientations from hundreds of
micrographs. The algorithm and amount of data required is
determined by the specific symmetry of the particle being
investigated, but data requirements for a single project are
typically in the tens of gigabytes to terabyte range. Computational
requirements are also significant, with individual reconstruction
processes often using in excess of 100,000 CPU-hours on a
modern CPU. Planned projects are anticipated to require 10
to 100 times more computational resources than current projects.
We are actively developing three software packages
to enable this type of reconstruction: EMAN (Electron Microscopy
Analysis), for performing low-symmetry single-particle reconstructions,
SAVR, for reconstructions of icosahedral particles, and EMEN
(Electron Microscopy Electronic Notebook), an object-oriented
database and electronic notebook for comprehensive bookkeeping
and data mining of the entire reconstruction process from
purification to structure. EMAN is in active use in dozens
of electron cryomicroscopy labs worldwide, and has been used
to reconstruct a number of important structures such as Ca++
release channel from sarcoplasmic reticulum, IP3 receptor,
fatty acid synthase, F0F1 ATPase, and several others. SAVR
is also now being distributed outside of the NCMI, and has
been used on several recent virus structures, including P22
bacteriophage, rotavirus and cytoplasmic polyhydrosis virus.
EMEN has been in active use for ~18 months, and now archives
over 2.5 TB of data and metadata.
Through collaboration with the labs of Drs.
Ken Kennedy and Lennart Johnsson, the main refinement process
in EMAN has been ported to the GRADS Grid environment. Testing
basic functionality and characterization of the execution
profile of EMAN is underway. Through extensive discussions,
we have mapped out a path for future efforts to make EMAN
and SAVR fully Grid-capable. This aspect of our work will
make direct use of Globus, and indirect use of several other
NPACKage components including Ganglia, GSI-OpenSSH and MPICH-G2.
We are also investigating possible future use of Condor-G.
We are also in early implementation phase of
a local SRB installation for archival of the massive quantities
of data involved in this project. We hope to use SRB as a
storage mechanism for the raw data archived in EMEN.
NPACKage components will be used both on local
clusters and storage subsystems, as well as accessed on remote
resources.
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