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Project TitleGenomics in 3D: Overnight comparative studies of nucleosomes.
SummaryNucleosomes are the fundamental building block of chromatin, the bio-material that contains the genome in all higher organism. Given a four letter code for DNA (A,C,G,T) sequence complexity alone allow prevents exhaustive studies. For this reason we are developing tools for on-demand, comparative studies of ensembles of nucleosomes. Our goal is to integrate existing tools into a comprehensive work flow that bridges between the Desktop Environment and Blue Waters to yield comparative studies as an overnight exercise.
Job DescriptionThis project will be to port and enhance the workflow that we have developed for the on-demand study of mono-nucleosomes to Blue Waters. The workflow is for high performance high throughput all atom molecular dynamics. The workflow includes VMD tools for building a nucleosome with any sequence of DNA, amber for parameterization, NAMD for simulation and VMD for post processing and visualization. The work flow integrates these tasks with job management on local or remote supercomputers and data sharing via iBIOMES.
Each nucleosome simulation contains approximately 250,000 atoms and requires on the order of 250 core for reasonable throughput (depending on architecture). Even modest supercomputing resources allow ensembles consisting of 20 to 30 realizations of the nucleosome to run simultaneously, generating microseconds of sampling as an overnight run.
Our specific objective is to integrate our existing tools into a streamlined, robust workflow that unifies sequence selection, modeling, analysis, visualization and data sharing.
Conditions/Qualificationsstudents will be expected to learn to use our existing tools in (VMD, NAMD , Amber) to build nucleosome models, submit them for molecular dynamics optimization and sampling on Blue Waters and evaluate the success of the simulations based on results automatically extracted from the simulations.
Start Date06/01/2015
End Date06/01/2016
LocationLouisiana Tech University
Ruston, LA
Dr. Thomas C. Bishop's Theoretical Molecular Biology Lab
Departments of Chemistry & Physics
Ran Sun
Anik Karan