HBP CodeJam Workshop #8

13th-15th September 2017, Lausanne, Switzerland

Le Centre-ville de Lausanne (Suisse) vu depuis le Lac Léman.

Lausanne seen from Lake Léman. Copyright Freeze750, CC-BY-SA licence.

The goal of the CodeJam workshops is to catalyze open-source, collaborative software development in computational and systems neuroscience and neuroinformatics, by bringing together researchers, students and engineers to share ideas, present their work, and write code together.

The general format of the workshops is to dedicate the mornings to invited and contributed talks, leaving the afternoons free for discussions, tutorials and code sprints.

Final programme

The 8th CodeJam was sponsored by the Human Brain Project. This year the CodeJam was preceded by the HBP Young Researcher Event in nearby Geneva.


The meeting was held at the EPFL, located in Lausanne, Switzerland. The meeting was organised by Alessandro Ambrosano, Luca Leonardo Bologna, Andrew Davison, Jeffrey Muller, Eric Müller, Lena Oden, Martina Schmalholz and Axel von Arnim.


  • Morteza Abbaszadeh
  • Mahmoud Akl
  • Alessandro Ambrosano
  • Emmanouil Angelidis
  • Shailesh Appukuttan1
  • Onur Ates1
  • Arthur-Ervin Avramiea
  • Harri Bendi
  • Cristian Rodríguez Bernal
  • Petrut Bogdan2
  • Luca Leonardo Bologna3
  • Stefano Casali
  • Jean-Denis Courcol
  • Andrew Davison1
  • Michael Denker
  • Jonathan Duperrier1
  • Michael Dupont
  • Matt Earnshaw
  • Hélissande Fragnaud1
  • Allan Francani4
  • Fabrice Gaillard
  • Andrew Gait2
  • Jie Gao
  • Pedro Garcia-Rodriguez1
  • Joffrey Gonin1
  • Luc Guyot
  • Akos Hencz
  • Diana Hoffmann
  • Julius Imbery
  • Jérémie Kalfon
  • Zhiqi Kang
  • Iurii Katkov
  • Samuel Kerrien5
  • Johann Klähn
  • Pramod Kumbhar
  • Daniel Kutny
  • Yan Lavryushev
  • Elodie Legouée1
  • Tianlin Liu
  • Carmen Alina Lupascu3
  • Kevin Mader
  • Hossain Mahmud
  • Stefano Masoli6
  • Christian Mauch
  • Robert McDougal7
  • Eilif Muller5
  • Jeffrey Muller4
  • Susie Murphy
  • Eric Müller
  • Lena Oden8
  • Sanja Pajic
  • Michael von Papen
  • Martin Pearson
  • Christian Pehle
  • Martina Rizza
  • Bogdan Roman
  • Armando Romani
  • Andrew Rowley9
  • Annapaola Iolanda Santarsiero
  • Martina Schmalholz
  • B. Lungsi Sharma1
  • Kenny Sharma
  • Terry Stewart
  • Alan Stokes2
  • Sara Summerton2
  • Mohameth François Sy
  • Matthieu Sénoville1
  • Werner Van Geit5
  • Marmaduke Woodman
  • Alper Yegenoglu10
  • Lyuba Zehl10
  • Axel von Arnim

Group photo from the HBP CodeJam Workshop #8

Meeting Program

Wed. 13th Sept.

09:30 Welcome and introduction
09:30Jeffrey Muller Welcome and introduction
09:40 From experiments to data repositories
09:40Samuel Kerrien Blue Brain Nexus: a provenance based, semantic data management platform
10:05Lyuba Zehl Tracking complex workflows in neuroscience [PDF]
10:30 Break
11:00 Data-driven modelling and validation
11:00B. Lungsi Sharma What - Why - How of Validation [link to slides]
11:25Luca Leonardo Bologna and Carmen Alina Lupascu Optimization, Neuron Builder Pipeline
11:50Stefano Masoli Neuron Modeling: What's New?
12:15 Lunch
13:30 Parallel tracks: tutorials and code sprints
13:30Allan Francani and Jeffrey Muller Tutorial: Collaboratory app development
13:30 Code sprints and discussions
15:00 Break
15:30-18:30 Parallel tracks: tutorials and code sprints
15:30Lena Oden Tutorial: the HBP HPAC platform
15:30 Code sprints and discussions
17:00Robert McDougal Tutorial: NEURON + Python
17:00 Code sprints and discussions

Thu. 14th Sept.

09:00 Welcome for participants coming from the Young Researchers Event
09:00Andrew Davison Welcome for participants coming from the Young Researchers Event
09:15 Building Bodies for Brains and Brains for Bodies
09:15Kenny Sharma and Axel von Arnim The Neurorobotics Platform: the simulator to give brains a body and bodies a brain
09:40Martin Pearson Integrating Shrewbot and Miro in the NRP [PDF]
10:05Terry Stewart Using Nengo in the Neurorobotics Platform [PDF]
10:30 Break
11:00 Next-generation simulation tools and hardware
11:00Andrew Rowley The SpiNNaker Platform [PDF]
11:25Marmaduke Woodman TheVirtualBrain
11:50Christian Mauch BrainScaleS Hardware — Resource Management and Monitoring [PDF]
12:15Johann Klähn Mapping PyNN to BrainScaleS Hardware
12:40 Lunch
13:30 Parallel tracks: tutorials and code sprints
13:30Akos Hencz and Carmen Alina Lupascu Tutorial: Getting the most from the Jupyter notebook
13:30Andrew Rowley and Alan Stokes Tutorial: SpiNNaker
13:30 Code sprints and discussions
15:00 Break
15:30-18:30 Parallel tracks: tutorials and code sprints
15:30Emmanouil Angelidis and Hossain Mahmud Tutorial: Neurorobotics Platform - setting up an experiment
15:30Jean-Denis Courcol Tutorial: Brain Simulation Platform
15:30 Code sprints and discussions
17:00Kenny Sharma Tutorial: Neurorobotics Platform - using tensor flow in your experiment
17:00 Code sprints and discussions

Fri. 15th Sept.

09:00 Putting it all together - web portals and collaboration tools
09:00Matt Earnshaw Open Source Brain and its Ecosystem [PDF]
09:25Fabrice Gaillard and Jeffrey Muller Under the hood of the Collaboratory platform [PDF]
09:50Susie Murphy and Axel von Arnim Neurorobotics Platform collaboratory features
10:15Werner Van Geit BluePyMM
10:40Kevin Mader Large scale Image processing with Spark
10:40 Break
11:35 Lightning talks
11:35Martina Rizza A Biophysically Detailed Cerebellar Stellate Neuron Model Optimized with Particle Swarm Optimization Algorithm
11:50Alper Yegenoglu Building packages with Conda [PDF]
12:30 Lunch
13:30 Parallel tracks: tutorials and code sprints
13:30Johann Klähn, Christian Mauch and Eric Müller Tutorial: BrainScaleS Neuromorphic Hardware — the DLS Prototype Chip
13:30Mahmoud Akl Tutorial: Neurorobotics Platform - Virtual Coach: running batch experiments pools and post-processing with Jupyter Notebook
13:30 Code sprints and discussions
15:00 Break
15:30-18:30 Parallel tracks: tutorials and code sprints
15:30Michael Denker and Alper Yegenoglu Tutorial: Data analysis with Elephant [PDF]
15:30Alessandro Ambrosano and Luc Guyot Tutorial: Neurorobotics Platform - using multiple robots
15:30 Code sprints and discussions
17:00 Code sprints and discussions

Creative Commons License
Unless mentioned otherwise, all the downloadable talks are licenced under a Creative Commons Attribution-Noncommercial-No Derivative Works License.


The meeting organizers gratefully acknowledge the support of the European Union through the Human Brain Project. We also wish to express our great appreciation to EPFL for hosting the meeting, to the HBP Education Programme, and to Björn Kindler at Heidelberg University for their considerable assistance with organisation and administration of the workshop.