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Open Collaboration in Computational Neuroscience

By
Level
Intermediate

Neuroscience has traditionally been a discipline where isolated labs have produced their own experimental data and created their own models to interpret their findings. However, it is becoming clear that no one lab can create cell and network models rich enough to address all the relevant biological questions, or to generate and analyse all the data required to inform, constrain, and test these models. The success of the open source software development movement suggests that both model building and data collection/curation would be greatly enhanced by public, collaborative efforts to solve these problems. This workshop will highlight several examples of such efforts taking place in neuroinformatics today, and will present open tools and resources that can be instrumental in facilitating further efforts.

Course Features
Videos
Lectures
Slides
Lessons of this Course
1
1
Duration:
8:34
Speaker:

In this opening lesson, you will hear from the chair of the workshop (Neuroinformatics 2014 in Leiden, Netherlands), who gives an introduction and motivating argument underscoring the importance of collaboration in computational neuroscience.

2
2
Duration:
23:26

This lesson gives an introduction to OpenWorm: an open-source project dedicated to creating a virtual C. elegans nematode in a computer.

3
3
Duration:
25:32

The Open Source Brain (OSB) initiative (http://www.opensourcebrain.org) has been created to address the issues of poor accessibility, transparency, validation, and reuse of models in computational neuroscience.This lecture covers the aims of the Open Source Brain initiative, the current functionality of the website, and the range of models already available, and future plans for the project.

4
4
Duration:
17:21

This lecture covers NeuronUnit, a library that builds upon SciUnit and integrates with several existing neuroinformatics resources to support validating single-neuron models using data gathered by neurophysiologists.

5
5
Duration:
17:41

This lesson provides an introduction to the NeuroElectro project, which aims to organize information on cellular neurophysiology.

6
6
Duration:
29:56

In this lecture, the speaker demonstrates Neurokernel's module interfacing feature by using it to integrate independently developed models of olfactory and vision LPUs based upon experimentally obtained connectivity information.