CDP1 Components Report for SGA1 M13-M24

In this report Key Results of HBP Co-Design Project 1 (CDP1) - Development of Whole Mouse Brain Model and Mouse Brain Atlas- are presented. An HBP Mouse Brain Atlas has been obtained, based on the Allen reference atlas. An operational workflow going from experimental data and metadata submitted by data producers and modellers in HBP has been set up to extract data points and make them discoverable in the reference atlas space. Data delivered in the context of CDP1 (whole brain structural connectivity and cortical activity) have been used to test, adapt and complete the developed workflows. A data driven modelling network-level model (using point neurons) of an entire mouse brain has been pursued, that integrates whole-brain datasets from available atlases and sources, such as the Allen Institute for Brain Science. The model has been then refined for the thalamo-cortical pathway, that mediates the sensory information from the periphery to the cortex. Physical experiments before and after stroke demonstrated that the rehabilitation protocol has a plasticising role promoting the refocus of cortical output and the rewiring of interhemispheric connectivity. A virtuous approach of close-loop workflow between physical experiments and modelling and simulation has been used for validating models and co-designing the implementation of in silico experiments on HBP Platforms.