SSCx Portal
Scientific Communication System · 2021–2023
Overview
The SSCx Portal is a comprehensive digital platform providing researchers with access to the Blue Brain Project's reconstructed rat somatosensory cortex — a circuit of 4.2 million morphologically detailed neurons connected by over 14 billion synapses. I led the development of the data processing and analysis pipeline that powers this portal.
The Challenge
How do you make a 4.2-million-neuron, 14-billion-synapse reconstruction accessible to researchers who aren't HPC specialists? The raw data is massive, the analysis pipelines are complex, and the scientific questions span multiple scales — from individual ion channels to entire cortical regions.
Multi-Scale Architecture
The portal organizes information hierarchically:
- SSCx mosaic — all 8 reconstructed subregions
- Brain regions — 100K to 1M+ neurons each
- Microcircuits — standardized 230μm radius columns for detailed analysis
- Cell types — morphological types (m-types), electrical types (e-types), and their combinations (me-types)
- Synaptic pathways — individual connections with anatomical and physiological properties
Data Pipeline
The portal is powered by two computational engines I developed:
- connsense-TAP — extracts and processes circuit data into analysis-ready HDF5 archives (see the TAP project for details)
- factology-LAB — generates "factsheets" characterizing circuit properties at each organizational level (see the SciTrails project)
Together, these systems transform petabytes of raw simulation data into structured, queryable, and visualizable knowledge that researchers can explore through the web interface.
Validation Framework
A critical aspect of the portal is scientific validation at every scale:
- Cellular — synthetic neuron populations validated against experimental distributions of morphology and electrophysiology
- Synaptic — connection probabilities and strengths compared with experimental measurements
- Network — spontaneous activity patterns and functional connectivity compared with in-vivo observations
The portal generates testable predictions, creating a feedback loop between modeling and experimentation.
Impact
- 170-fold scale increase over earlier microcircuit models — first mesoscale investigation of cortical circuit organization
- Served experimentalists, computational researchers, and method developers with interfaces tailored to their expertise
- Published as part of the Blue Brain Project's major SSCx reconstruction paper
Technical Stack
Python · HDF5 / SONATA data formats · HPC / SLURM · REST APIs · Web visualization · Multi-scale data management