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NeuroManager: a workflow analysis based simulation management engine for computational neuroscience.

David B Stockton1, Fidel Santamaria2

  • 1Biomedical Engineering Program, The University of Texas at San Antonio San Antonio, TX, USA.

Frontiers in Neuroinformatics
|November 4, 2015
PubMed
Summary
This summary is machine-generated.

NeuroManager is a new software engine that automates computational neuroscience simulations. It simplifies managing complex workflows across different resources and improves tracking research data.

Keywords:
MATLABNEURONNeuroMLgrid computingparameter searchsimulation

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Area of Science:

  • Computational Neuroscience
  • Scientific Software Engineering

Background:

  • Computational neuroscience research relies heavily on complex simulations.
  • Managing diverse simulation workflows across various computational resources is challenging.
  • Tracking simulation parameters, results, and project evolution is crucial for reproducibility.

Purpose of the Study:

  • To develop an object-oriented software engine, NeuroManager, for automating computational neuroscience simulation workflows.
  • To enhance the flexibility and usability of simulation management across heterogeneous computational resources.
  • To improve the tracking and provenance of simulation data and research project evolution.

Main Methods:

  • Developed NeuroManager using an object-oriented approach in MATLAB.
  • Analyzed simulation submission workflows across various simulators, operating systems, and computational resources (22 stages identified).
  • Integrated features for progress notification, automatic data organization, labeling, time-stamping, and MATLAB analysis tools.

Main Results:

  • NeuroManager automates job submissions for heterogeneous computational resources, simulators, and tasks.
  • The object-oriented design enhances adaptability to different neuroscience simulators and simplifies resource management.
  • The software facilitates tracking of simulator/simulation evolution and automates daily tasks for researchers.

Conclusions:

  • NeuroManager provides essential infrastructure to streamline computational neuroscience workflows.
  • It enables efficient management of multiple simultaneous simulations and maintains data provenance.
  • The software supports individual researchers and principal investigators in managing and reproducing research projects.