Monday, February 18, 2013

How to Build a Neuron: The ultimate shortcut

We've gone through all the main steps for Building a Neuron, and  compiled them here. But there is one last shortcut that I absolutely have to tell you about. It's pretty much the ULTIMATE shortcut.

Full of Computational Models (source)
If you really want a computational model of a neuron, but just don't want to do the work to build one, even using the shortcuts I've already provided... you can use someone else's.

Model DB
 is a repository where scientists can upload their computational models for all to see and use. A README file is attached to each model and explains the basics of  the model. In addition, there is always a citation to the paper in which the model was first published, so you can read about how it was used. With these tools (and possible emails to the authors) you should be able to download and run a complete model and replicate the figures that someone uses in a paper. The model I mention is step 5 is there, and is an example of a complete and usable neuron with synaptic and intrinsic channels.

Model DB 

Model DB is helping advance the field of computational neuroscience in two ways.

First it allows for post-publication review, where people can make sure that the model does what the authors say it does. Having access to the actual code used to run the simulations is better than just reading the 'methods section' of a paper. As with all methods sections, you just can't explain everything well enough for it to be replicated
 exactly as performed.

Second, Model DB reduces the amount of overlapping work that scientists have to do. You've seen how tedious it can be to
 extract the Boltzmann curves of each intrinsic channel. Model DB allows you to see if someone has already done it for your cell type. You can use it just as it is, or you can follow the citations and re-extract it. In either case you have saved yourself valuable time.

One of the advantages of computational models is that they can be used to answer TONS of questions. Most of the time a huge amount of work is put into building the model, and then the model is used to answer a few questions, but the possibilities are endless. Having the models freely accessible allows for faster advancement in both computational neuroscience and the field of neuroscience in general. 

"ModelDB provides a resource for the computational neuroscience community that enables investigators to increase their understanding of published models by enabling them o run the models as published and build on them for further research. Its use can aid the field of computational neuroscience to enter a new era of expedited numerical experimentation." Migliore et al., 2003
Migliore M, Morse TM, Davison AP, Marenco L, Shepherd GM, & Hines ML (2003). ModelDB: making models publicly accessible to support computational neuroscience. Neuroinformatics, 1 (1), 135-9 PMID: 15055399

Hines ML, Morse T, Migliore M, Carnevale NT, & Shepherd GM (2004). ModelDB: A Database to Support Computational Neuroscience. Journal of computational neuroscience, 17 (1), 7-11 PMID: 15218350