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So#ware/Science Co-‐Development: So%ware Engineering for Large-‐Scale in Silico Neuroscience Research

Prof. Felix Schürmann, Nenad Buncic, Dr. Fabien Delalondre, Stefan Eilemann, Jeffrey Muller [email protected]

EPFL/Blue Brain Project 1

Some Numbers on the Brain

•  Rat brain* ~200M (2x108) nerve cells

~130M glial cells

~O(1012) synapses

* Herculano-‐Houzel et al. 2006; **Herculano-‐Houzel 2009; *** Sims et al. 2007

•  Each cell – a universe*** ~O(10B) proteins/nerve cell

•  Human brain**

~90B (1011) nerve cells ~90B glial cells ~O(1015) synapses

QualitaIve Simulator Landscape*

3/3/14 EPFL/Blue Brain Project 3 * incomplete

Reac[on-‐Diffusion

Molecular Dynamics

Mean Field/Maps/Baysian

Neuron-‐based

NEST, BRIAN, CSIM, MVASpike, C2, …

NEURON, MOOSE, GENESIS, NCS, SPLIT, …

STEPS, MCELL, VCELL, NEURORD, CDS, …

LAMMPS, NAMD, AMBER, GROMACS, ESPRESSO, …

Gaussian, CPMD, CP2K, …

Topographica, MIIND, …

NEURON

•  Efficient, domain-‐specific simulator for mul[-‐compartment, conductance-‐based simula[ons of neurons and networks –  Efficient (Hines’ algorithm) –  Scriptable (python, hoc) –  Extensible (NMODL) –  Interac[ve (GUI)

•  Goes back more than 25 years •  Open source •  Ac[ve community •  Authored and ac[vely supported by Michael

Hines •  De-‐facto standard

–  More than 25 technical publica[ons on NEURON –  More than 1000 scien[fic publica[ons

men[oning NEURON

3/3/14 Blue Brain Project 4

The Blue Brain Project

•  pioneers a novel strategy to integrate fragmented biological knowledge into unifying models of brain 1ssue

•  develops a unique supercomputer-‐based pla7orm for crea[ng, simula[ng and evalua[ng unifying brain models

•  use the plamorm for simula[on-‐based research and tested on a rat’s neocor1cal microcircuit

•  Coordinator of the European Flagship Project: Human Brain Project hnp://humanbrainproject.eu

•  Funded by public sources •  Directed by Prof. Henry Markram


Modeling

Virtual Experiments Data Model

Analy[cs Visualiza[on

Simula[on

Neuroscience

NeuroinformaIcs

Microcircuit Ultrastructure Cell Experiment Mesocircuit Macrocircuit

Transcriptome

Organism Level Data

Cellular Level Data Predic[ve Reverse

Engineering

Parametric Geometry

Electro-‐dynamics

Connec[vity Rules Plas[city Macroscopic

Effects Physical Chemistry

Subcellular Level Data

Tissue Level Data

MathemaIc AbstracIon

Metabolome Channelome Connectome Genome Physiome Phenome Proteome Receptome

SimulaIon

3/3/14 EPFL/Blue Brain Project 6

Simula[on

..it’s really not just a simulaIon…

Goals for Development

•  Innova[on – Allow rapid prototyping – Mul[-‐language support

•  Sustainability – Test coverage, documenta[on, standardiza[on, backward compa[bility, etc.

– Needs: •  Infrastructure (standardiza[on & automa[on) •  Processes (SW lifecycle, development method, release strategy, …) •  Guidelines (coding standards, packaging, etc.)


InnovaIon & Sustainability

•  Worlds apart: Sandia TriBITS SW Lifecycle Model


Exploratory

Research Stable Produc[on Growth Produc[on Maintenance

*

* (Lean/Agile) (Lean/Agile) (Lean/Agile)

prototype

Works! Adopted in produc[on…

•  Neeeeeever seen this:

Legacy & Non SW Experts


-‐  Mandatory for prototypes with >1 user or >1 developer

-‐  Time limited (12 month) – up or out -‐  Migra[on path for exis[ng code -‐  Metrics & requirements adoptable

by scien[sts

Exploratory

Research Stable * (Lean/Agile)

Legacy Codes Non SW Expert

SW Expert Research Development *

<<refactor>>

<<stabilize>>

<<reimplement>>

Non SW Expert

*

Some Features of RD Class

•  Git repository •  CMake based on standard CMake config

•  Adhere to coding guidelines •  40% test coverage •  Doxygen •  Jira channel for bug tracking •  Con[nuous integra[on •  Ready for Gerrit code review •  Periodic code reviews


Need to make it suggesIve!

•  Pay coffee once in a while…. •  Provide templates for novel projects –  hnps://github.com/BlueBrain/Hello

•  Automate: – U[lize power of CMake

•  Tes[ng •  Documenta[on •  Dependencies check out buildyard for mul[-‐dependency builds: hnps://github.com/Eyescale/Buildyard.git

–  Provide stable and automated infrastructure/services •  CI services •  Puppe[za[on of infrastructure configura[on •  API to program infrastructure (PaaS)


Acknowledgements

•  Nenad Buncic – Sec[on Manager Core Services

•  Dr. Fabien Delalondre – Sec[on Manager High Performance Compu[ng

•  Stefan Eilemann – Sec[on Manager Visualiza[on

•  Jeffrey Muller – Sec[on Manager Plamorm Development

Contacts: Prof. Felix Schürmann Blue Brain Project Co-‐Director, Head of Compu[ng Division Email: [email protected]


hnp://bluebrain.epfl.ch hnp://humanbrainproject.eu

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