HBP CodeJam Workshop #7

11th-14th January 2016, Manchester, UK

Shrigley Hall Hotel, Cheshire, UK

Shrigley Hall Hotel

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.

The 7th CodeJam was sponsored by the Human Brain Project.


The meeting was held at the Shrigley Hall Hotel, located in Manchester, UK. The meeting was organised by Andrew Davison, David Lester, Abigail Morrison, Eilif Muller and Jeffrey Muller.


  • Kamal AbuHassan21
  • Olivier Amblet6
  • Jan Antolik1,22
  • Justas Birgiolas23
  • Inga Blundell9
  • Petrut Bogdan10
  • Oliver Breitwieser19
  • Nicholas Cain7
  • Nicolas Cain
  • Matteo Cantarelli24
  • Matteo Cantarelli
  • Jean-Denis Courcol6
  • Benjamin Cumming25
  • Sergio Davies16
  • Andrew Davison1
  • Michael Denker13
  • Mikael Djurfeldt26
  • Jochen Martin Eppler27
  • Csaba Eroe6
  • David Feng7
  • Chris Fitzpatrick28
  • Sergio Emilio Galindo Ruedas29
  • Juan José Garcia Cantero29
  • Padraig Gleeson
  • Sergey Gratiy7,8
  • Domenico Guarino30
  • Juan Hernando
  • Juan Hernando Vieites6
  • Michael Hines20
  • Detlef Holstein1,18
  • Christian Jaques6
  • Samuel Kerrien31
  • Mitja Kleider19
  • Johann Klähn19
  • Susanne Kunkel32
  • David Lester
  • Kunal Lillaney15
  • Christian Mauch19
  • Abigail Morrison2
  • Eilif Muller3
  • Jeffrey Muller4
  • Andrew Mundy11
  • Eric Müller19
  • Paul Müller19
  • Eric Nichols33
  • Christian Pehle34
  • Alexander Peyser35
  • Dimitri Plotnikov36
  • Dimitri Plotnikov
  • Christian Pozzorini6
  • Vahid Rostami
  • Vahid Rostami12
  • Andrew Rowley16
  • Bernd Schuller12
  • Michael Sonntag37
  • Adrian Stoewer14
  • Alan Stokes16
  • Corinne Teeter7
  • Guido Trensch38
  • Werner Van Geit39
  • Stefano Vrizzi40
  • Philipp Weidel17
  • Marmaduke Woodman5
  • Willem Wybo6
  • Alper Yegenoglu12
  • Catherine Zwahlen6

Group photo from the HBP CodeJam Workshop #7

Meeting Program

Mon. 11th Jan.

09:35 Model simplification
09:35Eilif Muller Phenomenological simplification of dendrites and synapses
09:55Marmaduke Woodman Simplifying brain activity: neural mass network models
10:15Willem Wybo Capturing dendritic computation using the Sparse Green's Function formalism
10:35Christian Pozzorini Characterization of single neurons by means of simplified spiking models
10:55Nicolas Cain DiPDE: A simulator for population density modeling [PDF]
11:15 Break
11:45 Standardisation of model representations
11:45Padraig Gleeson NeuroML, LEMS and Open Source Brain
12:10Inga Blundell, Jochen Martin Eppler and Dimitri Plotnikov NEST Modeling Language: A modeling language for spiking neuron and synapse models for NEST [PDF]
12:35Sergey Gratiy Model representation approaches for the Allen mouse visual column [PDF]
13:00 Lunch
14:30 Parallel tracks: tutorials and code sprints
14:30Padraig Gleeson Tutorial: The NeuroML and LEMS toolchain
16:00 Break
16:30 Parallel tracks: tutorials and code sprints
16:30Inga Blundell and Dimitri Plotnikov Tutorial: NESTML [PDF]
20:30- Dinner

Tue. 12th Jan.

09:30 Simulation tools
09:30Abigail Morrison What's new with NEST
09:50Michael Hines NEURON + Python [PDF]
10:10Eric Müller The BrainScaleS neuromorphic system
10:30Andrew Rowley and Alan Stokes SpiNNaker: What's new [PDF]
10:50Mikael Djurfeldt MUSIC [PDF]
11:10 Break
11:45 Workflows in large collaborative projects
11:45Olivier Amblet HBP Collaboratory app development [PDF]
12:10Bernd Schuller UNICORE in the Human Brain Project [PDF]
12:35Matteo Cantarelli Tales of open collaboration - How to work with human beings
13:00 Lunch
14:30 Parallel tracks: tutorials and code sprints
14:30Domenico Guarino Tutorial: An introduction to scientific Python
14:30Andrew Rowley and Alan Stokes Tutorial: SpiNNaker
16:00 Break
16:30 Parallel tracks: tutorials and code sprints
16:30Matteo Cantarelli Tutorial: Geppetto
16:30Olivier Amblet and Jeffrey Muller Tutorial: the HBP Collaboratory
20:30- Poster session, buffet dinner

Wed. 13th Jan.

09:30 Data integration and data analysis
09:30Eilif Muller The BBP data model, BluePy and friends [PDF]
09:55Michael Denker The Role of Elephants in Complex Workflows in Electrophysiology [PDF]
10:20Adrian Stoewer NIX: a file format for electrophysiology data and metadata
10:45Kunal Lillaney Neuro-visualization at the network edge [PDF]
11:10 Break
11:45 Validation suites for brain models
11:45Jean-Denis Courcol HBP Brain Simulation Platform validation automation [PPTX]
12:10Jan Antolik Mozaik as a brain model validation tool
12:35Corinne Teeter Generalized Leaky Integrate and Fire Neurons. Evaluating the contribution of different mechanisms in recreating the spike times of neurons
12:50David Feng AllenSDK: automated, standardized, and reproducible single cell model optimization in the Allen Cell Types Database
13:15 Lunch
14:30 Parallel tracks: tutorials and code sprints
14:30Alan Stokes Tutorial: an introduction to Git and Github
14:30Detlef Holstein, Vahid Rostami and Alper Yegenoglu Tutorial: data analysis with Elephant
16:00 Break
16:30 Parallel tracks: tutorials and code sprints
16:30David Feng Tutorial: the Allen tools
20:30- Poster session, buffet dinner

Thu. 14th Jan.

09:30 Neurorobotics / closed-loop systems
09:30Matteo Cantarelli Openworm: Building a digital organism
09:55Petrut Bogdan SpiNNaker meets silicon devices [PPSX]
10:20Andrew Mundy Spaun and SpiNNaker
10:45Csaba Eroe Point-neuron mouse brain in a closed-loop system
11:10Philipp Weidel ROS-MUSIC Toolchain
11:35 Break
12:05 Visualisation
12:05Juan Hernando Looking into the forest: Programmable visualization of neural networks with detailed morphologies
12:25 Lightning talks
12:25Nicholas Cain DiPDE, SpiNNaker, and Geppetto, Oh My! [PDF]
12:30Andrew Davison Reproducibility through environment capture: Docker and Sumatra [PDF]
12:40Justas Birgiolas Can we make computational neuroscience less "sticky": a newcomer's perspective [PPTX]
12:45Kamal AbuHassan Bayesian inference in waveform signals based on BAYSIG [PPTX]
13:00 Lunch
14:30 Parallel tracks: tutorials and code sprints
16:00 Break
16:30 Code sprints
20:30- Dinner

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 and in particular the Neuromorphic Computing subproject. We also wish to express our great appreciation to the SpiNNaker team at Manchester University, to the HBP Education subproject, and to Björn Kindler at Heidelberg University for their considerable assistance with organisation and administration of the workshop.