Workflows

Each step in every workflow is supported by dedicated software tools and workflows. The key steps are:

  • Neuroscience: systematic collection of experimental data making it possible to describe all possible levels of structural and functional brain organization from the subcellular, through the cellular, to the micro-circuit, meso-circuit and macrocircuit levels;
  • Neuroinformatics: automated curation and databasing of data, prediction of unknown data from interdependencies in the data that is available;
  • Mathematical abstraction: definition of parameters, variables, equations, algorithms and constraints representing the structure and functionality of the brain at different levels of organization;
  • Digital Reconstruction: building geometric and computational models representing different levels of the structural and functional organization of the brain;
  • In silico experiments: use of digital reconstructions for in silico experiments and exploratory studies requiring configuration of the experiment to exactly define stimulation and recording protocols, initial conditions, and measurement protocols;
  • Simulation: simulation of the evolution of the state of virtual brain tissue over time (firing dynamics, voltages, synaptic strengths etc.); replication of previous in vivo experiments (application of specific patterns of simulation, knock-out and lesioning experiments, administration of drugs etc.), design and implementation of new experiments;
  • Visualization: use of advanced techniques to display the structure and dynamics of simulations and (in the medium-long term) to interactively “steer” and “navigate” the simulation;
  • Analysis: analysis of simulation results, initially for model validation, subsequently for simulation-based investigations of brain function and dysfunction, diagnostic tools and possible treatments.

The Blue Brain Project (BBP) has implemented prototype versions of the software applications needed to support the different steps in the workflow. Each application or component is composed of a steadily expanding set of sub-components (e.g. a sub-component to collect a specific class of data).

Sub-components are developed in a well-defined three-stage process, beginning with exploration (identification of required data, estimation of data volumes, study of data availability), continuing with research (definition of data representations and their integration in the model, automation of the data acquisition process) and concluding with prototype development (definition of software architecture, implementation of software, implementation of required workflows). In the rest of this report, we will clearly indicate the stage of development reached by different components and subcomponents.

The Blue Brain Project has adopted an incremental development strategy in which the capabilities of the facility are gradually enhanced through step-by-step addition of new subcomponents. The end result will be a completely transformed facility with the capability to model and simulate:

  • The brain or any region of the brain of any species, at any stage in its development;
  • Specific pathologies of the brain;
  • Diagnostic tools and treatments for these pathologies. The geometric and computational models of the brain produced by the facility will reproduce the structural and functional features of the biological brain with electron microscopic and molecular dynamic level accuracy .