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 AbuHassan19
  • Olivier Amblet5
  • Jan Antolik1,20
  • Justas Birgiolas21
  • Inga Blundell8
  • Petrut Bogdan
  • Petrut Antoniu Bogdan9
  • Oliver Breitwieser17
  • Nicholas Cain6
  • Nicolas Cain
  • Matteo Cantarelli22
  • Matteo Cantarelli
  • Jean-Denis Courcol5
  • Benjamin Cumming23
  • Sergio Davies14
  • Andrew Davison1
  • Michael Denker11
  • Mikael Djurfeldt24
  • Jochen Martin Eppler25
  • Csaba Eroe5
  • David Feng6
  • Chris Fitzpatrick26
  • Sergio Emilio Galindo Ruedas27
  • Juan José Garcia Cantero27
  • Padraig Gleeson
  • Sergey Gratiy6,7
  • Domenico Guarino28
  • Juan Hernando
  • Juan Hernando Vieites5
  • Michael Hines18
  • Detlef Holstein1,16
  • Christian Jaques5
  • Samuel Kerrien29
  • Mitja Kleider17
  • Johann Klähn17
  • Susanne Kunkel30
  • David Lester
  • Kunal Lillaney13
  • Christian Mauch17
  • Abigail Morrison2
  • Eilif Muller3
  • Jeffrey Muller4
  • Andrew Mundy9
  • Eric Müller17
  • Paul Müller17
  • Eric Nichols31
  • Christian Pehle32
  • Alexander Peyser33
  • Dimitri Plotnikov34
  • Dimitri Plotnikov
  • Christian Pozzorini5
  • Vahid Rostami
  • Vahid Rostami10
  • Andrew Rowley14
  • Bernd Schuller10
  • Michael Sonntag35
  • Adrian Stoewer12
  • Alan Stokes14
  • Corinne Teeter6
  • Guido Trensch36
  • Werner Van Geit37
  • Stefano Vrizzi38
  • Philipp Weidel15
  • Marmaduke Woodman
  • Michael Woodman39
  • Willem Wybo5
  • Alper Yegenoglu10
  • Catherine Zwahlen5

Group photo from the HBP CodeJam Workshop #7

Meeting Program

Mon. 11th Jan.

07:35 Model simplification
07:35Eilif Muller Phenomenological simplification of dendrites and synapses
07:55Marmaduke Woodman Simplifying brain activity: neural mass network models
08:15Willem Wybo Capturing dendritic computation using the Sparse Green's Function formalism
08:35Christian Pozzorini Characterization of single neurons by means of simplified spiking models
08:55Nicolas Cain DiPDE: A simulator for population density modeling [PDF]
09:15 Break
09:45 Standardisation of model representations
09:45Padraig Gleeson NeuroML, LEMS and Open Source Brain
10:10Inga Blundell, Jochen Martin Eppler and Dimitri Plotnikov NEST Modeling Language: A modeling language for spiking neuron and synapse models for NEST [PDF]
10:35Sergey Gratiy Model representation approaches for the Allen mouse visual column [PDF]
11:00 Lunch
12:30 Parallel tracks: tutorials and code sprints
12:30Padraig Gleeson Tutorial: The NeuroML and LEMS toolchain
14:00 Break
14:30 Parallel tracks: tutorials and code sprints
14:30Inga Blundell and Dimitri Plotnikov Tutorial: NESTML [PDF]
18:30- Dinner

Tue. 12th Jan.

07:30 Simulation tools
07:30Abigail Morrison What's new with NEST
07:50Michael Hines NEURON + Python [PDF]
08:10Eric Müller The BrainScaleS neuromorphic system
08:30Andrew Rowley and Alan Stokes SpiNNaker: What's new [PDF]
08:50Mikael Djurfeldt MUSIC [PDF]
09:10 Break
09:45 Workflows in large collaborative projects
09:45Olivier Amblet HBP Collaboratory app development [PDF]
10:10Bernd Schuller UNICORE in the Human Brain Project [PDF]
10:35Matteo Cantarelli Tales of open collaboration - How to work with human beings
11:00 Lunch
12:30 Parallel tracks: tutorials and code sprints
12:30Domenico Guarino Tutorial: An introduction to scientific Python
12:30Andrew Rowley and Alan Stokes Tutorial: SpiNNaker
14:00 Break
14:30 Parallel tracks: tutorials and code sprints
14:30Matteo Cantarelli Tutorial: Geppetto
14:30Olivier Amblet and Jeffrey Muller Tutorial: the HBP Collaboratory
18:30- Poster session, buffet dinner

Wed. 13th Jan.

07:30 Data integration and data analysis
07:30Eilif Muller The BBP data model, BluePy and friends [PDF]
07:55Michael Denker The Role of Elephants in Complex Workflows in Electrophysiology [PDF]
08:20Adrian Stoewer NIX: a file format for electrophysiology data and metadata
08:45Kunal Lillaney Neuro-visualization at the network edge [PDF]
09:10 Break
09:45 Validation suites for brain models
09:45Jean-Denis Courcol HBP Brain Simulation Platform validation automation [PPTX]
10:10Jan Antolik Mozaik as a brain model validation tool
10:35Corinne Teeter Generalized Leaky Integrate and Fire Neurons. Evaluating the contribution of different mechanisms in recreating the spike times of neurons
10:50David Feng AllenSDK: automated, standardized, and reproducible single cell model optimization in the Allen Cell Types Database
11:15 Lunch
12:30 Parallel tracks: tutorials and code sprints
12:30Alan Stokes Tutorial: an introduction to Git and Github
12:30Detlef Holstein, Vahid Rostami and Alper Yegenoglu Tutorial: data analysis with Elephant
14:00 Break
14:30 Parallel tracks: tutorials and code sprints
14:30David Feng Tutorial: the Allen tools
18:30- Poster session, buffet dinner

Thu. 14th Jan.

07:30 Neurorobotics / closed-loop systems
07:30Matteo Cantarelli Openworm: Building a digital organism
07:55Petrut Bogdan SpiNNaker meets silicon devices [PPSX]
08:20Andrew Mundy Spaun and SpiNNaker
08:45Csaba Eroe Point-neuron mouse brain in a closed-loop system
09:10Philipp Weidel ROS-MUSIC Toolchain
09:35 Break
10:05 Visualisation
10:05Juan Hernando Looking into the forest: Programmable visualization of neural networks with detailed morphologies
10:25 Lightning talks
10:25Nicholas Cain DiPDE, SpiNNaker, and Geppetto, Oh My! [PDF]
10:30Andrew Davison Reproducibility through environment capture: Docker and Sumatra [PDF]
10:40Justas Birgiolas Can we make computational neuroscience less "sticky": a newcomer's perspective [PPTX]
10:45Kamal AbuHassan Bayesian inference in waveform signals based on BAYSIG [PPTX]
11:00 Lunch
12:30 Parallel tracks: tutorials and code sprints
14:00 Break
14:30 Code sprints
18:30- 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.