ISyMAB
From HP-SEE Wiki
Contents |
General Information
- Application's name : Integrated System for Modeling and data Analysis of complex Biomolecules
- Virtual Research Communities : Computational Chemistry Applications
- Scientific contact : Ionut Traian Vasile, itvasile@nipne.ro
- Technical contact : Ionut Traian Vasile, itvasile@nipne.ro
- Developers : Ionut Traian Vasile, IFIN-HH, Department of Elementary Particles and Informational Technologies, Romania
- Web site :
Application and Short Description
We aim at providing an efficient tool for data analysis in the framework of the simulation and modeling of large biomolecular systems by means of parallel molecular dynamics codes designed for high-performance computing (NAMD). The main focus is in the modeling of the G Protein-Coupled Receptors, which are found in a wide range of species, and are involved in signalling from the outside to the inside of the cells.
Generally, large biomolecule simulations with NAMD involve many steps which are not always easy and/or within the reach of the researchers. The proposed application provides an integrated solution that will help them solve these problems instantly.
The application builds a remote access framework on NAMD clusters which offers the users an integrated interface with analysis tools, which will make possible fast data analysis of complex simulation outputs directly on the remote systems. The users provide the initial parameters of the MD simulation, launch jobs, and make various dataanalysis on the output files.
The application will generate the inputs needed for the batch system, the inputs for the MD simulation, will help manage simulation jobs, make various data-analysis on the outputs obtained, visualize the biosystem after the job, and make graphs on the selected data. Besides this, the application will ensure the secure connection of the user with the cluster.
Problems Solved
The application facilitates the interaction between the scientists and the NAMD cluster, making the simulation work on clusters much easier and user-friendly. Also, the system will provide and integrate an extensive list of publicly available tools that are used in many research centers which simulate large biomolecules using NAMD.
Scientific and Social Impact
The integrated system will increase the user productivity, defined as the ratio between the actual simulation time and the total time spent for running the simulation. Also, it will accelerate research, the scientists getting relevant results sooner.
The application will help the workers/students in biophysics and biochemistry to perform faster research and discovery, by optimizing the time needed for MD simulations.
Collaborations and Beneficiaries
The integrated system will be used in the research collaborations started with the Faculty of Physics and the Faculty of Biology of the University of Bucharest.
Technical features and HP-SEE implementation
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Usage Example
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Publications and Presentations
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