CIF21 DIBBs: Middleware and High Performance Analytics Libraries for Scalable Data Science

Project: Research project

Project Details

Description

Summer REU: Simulation and analysis of large biomolecules will be hosted by the
Arizona State University, Department of Physics and Center for Biological Physics. The undergraduate student will carry out a research project in the computational biophysics group at Arizona State University (ASU). In the project the student will learn how to carry out molecular dynamics simulations of large biomolecular systems and how to analyze them. These simulations will provide challenging test cases for the analysis algorithms that are being developed as part of the SPIDAL project.The student will be mentored by the faculty PI, Beckstein, and a graduate student and will have regularly scheduled weekly meetings with the PI and informal meetings as necessary. The REU student will also participate in all
research group activities such as weekly group meetings and journal clubs. The student will present their work to the research group at ASU and at the virtual meeting of all the SPIDAL REU students. It is expected that the students work will become part of a publication, in which case the student will become an author on the paper. The impact of the research experience on the undergraduate student will be assessed by informal interviews at the beginning and at the end of research experience.

Description

Summer REU: Simulation and analysis of large biomolecules will be hosted by the Arizona State University, Department of Physics and Center for Biological Physics. The undergraduate student will carry out a research project in the computational biophysics group at Arizona State University (ASU). In the project the student will implement new analysis algorithms as modules in the MDAnalysis library http://mdanalysis.org. These modules will become entry points for the SPIDAL versions of these algorithms and will inform the user-interface design. The student will be mentored by the faculty PI, Beckstein, and a graduate student and will have regularly scheduled weekly meetings with the PI and informal meetings as necessary. The REU student will also participate in all research group activities such as weekly group meetings and journal clubs. The student will present their work to the research group at ASU and at the virtual meeting of all the SPIDAL REU students. It is expected that the students work will become part of a publication, in which case the student will become an author on the paper. The impact of the research experience on the undergraduate student will be assessed by informal interviews at the beginning and at the end of research experience.

Description

Summer REU: Simulation and analysis of large biomolecules will be hosted by the Arizona State University, Department of Physics and Center for Biological Physics. The undergraduate student will carry out a research project in the computational biophysics group at Arizona State University (ASU). In the project the student will use and implement BigData algorithms (e.g. from the SPIDAL library) and interface them with the MDAnalysis library (http://mdanalysis.org) with the aim to generate example cases for integrating the two libraries. The student will be mentored by the faculty PI, Beckstein, and a graduate student and will have regularly scheduled weekly meetings with the PI and informal meetings as necessary. The REU student will also participate in all research group activities such as weekly group meetings and journal clubs. The student will present their work to the research group at ASU and at the virtual meeting of all the SPIDAL REU students. It is expected that the students work will become part of a publication, in which case the student will become an author on the paper. The impact of the research experience on the undergraduate student will be assessed by informal interviews at the beginning and at the end of research experience.

Description

The Institution's contribution to CIF21 DIBBS: Middleware and High Performance Analytics Libraries for Scalable Data Science will be led by Oliver Beckstein. The scope of the work will involve the integration of applications, algorithms and abstractions to support data-intensive science in the biomolecular HPC community. Specifically:

1. Integrate the SPIDAL library with the MDAnalysis framework to produce a transparent big-data solution for the analysis of molecular dynamics trajectories.
2. Verify, document, and enhance performance of MDAnalysis/SPIDAL.
3. Produce documentation and tutorials for end users.

Deliverables
The specific deliverables/tasks and high level milestones are:

Item Description Institution Role

R3.0 Integrate with Applications Support
R3.1 Adapt MDAnalysis framework for SPIDAL Lead
R3.2 Run and benchmark MDAnalysis+SPIDAL Lead

Description

The Summer REU New analysis algorithms for biomolecular simulations will be hosted by the Department of Physics and Center for Biological Physics at Arizona State University. The undergraduate student will carry out a research project in the Computational Biophysics group. In the project the student will implement new parallel analysis algorithms as modules in the MDAnalysis pmda library (http://mdanalysis.org and https://github.com/MDAnalysis/pmda). These modules will become entry points for the SPIDAL versions of these algorithms and will inform the user-interface design. The student will be mentored by the faculty PI, Beckstein, and the graduate student working on the DIBBS project and will have regularly scheduled weekly meetings with the PI and informal meetings as necessary. The REU student will also participate in all research group activities such as weekly group meetings and journal clubs. The student will present their work to the research group at ASU and at the virtual meetings of the DIBBs SPIDAL group. It is expected that the students work will become part of a publication, in which case the student will become an author on the paper. The impact of the research experience on the undergraduate student will be assessed by informal interviews at the beginning and at the end of research experience.


StatusActive
Effective start/end date6/1/159/30/20

Funding

  • National Science Foundation (NSF): $175,402.00

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