"Collaboration and Validation in Model of Cells and Circuits"

Rick Gerkin is an assistant research professor at Arizona State University with a research program in neuro- and bioinformatics.  His main focus is the development of approaches and tools to systematically validate computational biology models against a wide range of experimental data, and to make validation a major part of the model development and model sharing process. 

Padraig Gleeson is a senior postdoc at University College London and works on infrastructure for building, standardising and sharing models in computational neuroscience. He is the developer of neuroConstruct (http://www.neuroconstruct.org) and is one of the main contributors to the NeuroML language for model specification (http://www.neuroml.org). He has recently been leading the development of the Open Source Brain repository (http://www.opensourcebrain.org) for collaborative model development.

Biological models are increasingly complex, but the building blocks of complex models are ubiquitous and increasingly well-supported.  How can we use these building blocks to collaboratively develop complex models without reinventing the wheel?  How can we make sure that the models we build -- and the components they rely on -- are true to the empirical data about the system we want to model?  Here we present two tools for model development in neuroscience that solve these challenges.  Open Source Brain is a collaborative model development platform for both creating and extending models of neurons and neural circuits using software development tools such as GitHub as well as popular standards for expressing, visualizing, and simulating models.  NeuronUnit is a library for the validation of neurophysiology models against experimental data harvested from a wide range of published and unpublished sources, which builds upon the discipline-agnostic and pythonic SciUnit model validation framework.  We show examples of these tools in use by the community, including in the international C. elegans simulation project Open Worm. 

Comments:

from Rick Gray to Everyone:

first one is the "must read" paper

http://rsfs.royalsocietypublishing.org/content/6/2/20150103

last two are examples of functional curation

https://www.ncbi.nlm.nih.gov/pubmed/21704062

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0135699

from Lou Gross to Everyone:

This is all from the perspective that the model is the code. But the model is not the implementation to many of us - it is the underlying assumptions and their mathematical formulation.  {Need to encode/document the assumptions underlying the model as well as the criteria for assessment!}

from Rick Gray to Everyone:

agreed...FDA has just published a Guidance for models in submissions ONLY ON REPORTING in which we ask for that info  http://www.fda.gov/ucm/groups/fdagov-public/@fdagov-meddev-gen/documents/document/ucm381813.pdf

from Bill Cannon to Everyone:

Lou, I think you are talking about the model of the physics more or less. What about models of different processes as well that use the same physical model? (I use the word 'physics' loosely in this case)

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