This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. Bacteria are living, chemical computers. By assembling together different genetic parts (refs), such as promoters, ribosome binding sites, and protein coding sequences, into a DNA molecule of a specific sequence, genetic programs are constructed that confer many useful functions to a bacterium, including the ability to manufacture biofuels and drugs from renewable sugars (refs). In the field of synthetic biology, a central goal is obtaining the ability to design genetic programs in a predictable fashion (refs). Currently, such genetic programs are constructed and tested using time-consuming trial-and-error techniques, such as random mutagenesis. We are developing the methodologies to design synthetic genetic systems in a predictive and systematic way. The methods combine biophysical models of genetic part function, DNA sequence optimization techniques, and design principles for genetic systems to convert a target biological behavior into a specific DNA sequence. We are also creating a user-friendly web-based interface where members of the genetic and metabolic engineering communities can specify a target biological function and receive the DNA sequence of a genetic program that carries out that function. We request 100 000 SUs to pursue the following research goals: (i) improve our recently developed design method for synthetic ribosome binding site by expanding it towards the optimization of entire protein coding sequences;(ii) allow users to request optimization jobs on their protein coding sequences of interest and off-load this computation onto TeraGrid resources;(iii) solve the RBS Minimax problem for a 22 enzyme metabolic network to maximize production of a chemical precursor to a biofuel. The computational resources are divided as: 40 000 SUs on Roaming TeraGrid and 60 000 SUs on Abe, Ranger, and/or Steele systems.

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Biotechnology Resource Grants (P41)
Project #
3P41RR006009-20S1
Application #
8364315
Study Section
Special Emphasis Panel (ZRG1-BCMB-Q (40))
Project Start
2011-09-15
Project End
2013-07-31
Budget Start
2011-09-15
Budget End
2013-07-31
Support Year
20
Fiscal Year
2011
Total Cost
$1,094
Indirect Cost
Name
Carnegie-Mellon University
Department
Biostatistics & Other Math Sci
Type
Schools of Arts and Sciences
DUNS #
052184116
City
Pittsburgh
State
PA
Country
United States
Zip Code
15213
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