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Discussions about SimTracker, a tool for managing model development and execution

Moderator: neuromau

Welcome to the SimTracker Forum!

Postby neuromau » Mon Jun 06, 2016 11:01 pm

Welcome to the SimTracker Forum! This forum area is your place to receive support about the SimTracker tool (http://mariannebezaire.com/simtracker/) as well as the associated NEURON code template (https://senselab.med.yale.edu/ModelDB/showModel.cshtml?model=187604). Feel free to ask questions, report bugs, or offer suggestions and show how you use SimTracker in this forum. You may also log any bugs or enhancement requests at the BitBucket SimTracker repository: https://bitbucket.org/mbezaire/simtrackercode.

**Note: As of June 6, 2016 SimTracker is in the process of being rolled out now, so not all of the documentation and code is available yet.**

Useful Links:
ModelDB Entry for NEURON model: https://senselab.med.yale.edu/ModelDB/showModel.cshtml?model=187604
SimTracker Webpage (download compiled SimTracker here): http://mariannebezaire.com/simtracker/
SimTracker BitBucket repository (download MATLAB source code here): https://bitbucket.org/mbezaire/simtrackercode
SimTracker Instruction Manual: http://mariannebezaire.com/downloads/SimTrackerInstructionManual.pdf
SimTracker NEURON Code Template Instruction Manual: http://mariannebezaire.com/downloads/NEURONTemplateInstructionManual.pdf
SimTracker Issue (Bug & Enhancement) Tracker: https://bitbucket.org/mbezaire/simtrackercode/issues
Graphical Representation of Workflow using SimTracker: http://mariannebezaire.com/simtracker-workflow-and-context/

Longer Description of SimTracker:
SimTracker is a MATLAB-based simulation management tool, in a user-friendly GUI format. It was developed over the course of my graduate studies and grew along with my research and modeling work. SimTracker is meant to address common problems faced by modelers, especially new modelers, and to support the entire model development process for large scale, parallel NEURON models. That includes configuring new simulations, storing their parameters and code version used (to ensure reproducibility and complete documentation of each simulation), executing the simulations locally or on various supercomputers and then uploading the results in a standard format back to SimTracker. Additionally, SimTracker allows for easy organization of results and model configurations, standard and customized analyses of results, and publication or display of model results and analyses.

In addition to the tool, there is an associated NEURON model code template. You can plug in your own cell and ion channel types, customize the stimulation and connectivity, or just consult the template for ideas as to how to implement your own parallel NEURON model. The template can be used independently of SimTracker if you prefer to use another simulation management tool or process (see Subtopic Other tools for help with other simulation tools).

Citation:
Bezaire MJ, Raikov I, Burk K, Armstrong C, and Soltesz I. SimTracker: a tool and code template to design, manage and analyze neural network model simulations in parallel NEURON. Submitted, 2016.

- Marianne Bezaire
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