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 AbuHassan15
  • Olivier Amblet7
  • Jan Antolik1,4
  • Justas Birgiolas3
  • Inga Blundell16
  • Petrut Bogdan
  • Petrut Antoniu Bogdan17
  • Oliver Breitwieser11
  • Nicholas Cain10
  • Nicolas Cain
  • Matteo Cantarelli8
  • Matteo Cantarelli
  • Jean-Denis Courcol7
  • Benjamin Cumming18
  • Sergio Davies12
  • Andrew Davison1
  • Michael Denker19
  • Mikael Djurfeldt20
  • Jochen Martin Eppler21
  • Csaba Eroe7
  • David Feng10
  • Chris Fitzpatrick2
  • Sergio Emilio Galindo Ruedas22
  • Juan José Garcia Cantero22
  • Padraig Gleeson
  • Sergey Gratiy10,23
  • Domenico Guarino24
  • Juan Hernando
  • Juan Hernando Vieites7
  • Michael Hines13
  • Detlef Holstein1,5
  • Christian Jaques7
  • Samuel Kerrien25
  • Mitja Kleider11
  • Johann Klähn11
  • Susanne Kunkel26
  • David Lester
  • Kunal Lillaney27
  • Christian Mauch11
  • Abigail Morrison28
  • Eilif Muller9
  • Jeffrey Muller29
  • Andrew Mundy17
  • Eric Müller11
  • Paul Müller11
  • Eric Nichols30
  • Christian Pehle31
  • Alexander Peyser32
  • Dimitri Plotnikov33
  • Dimitri Plotnikov
  • Christian Pozzorini7
  • Vahid Rostami
  • Vahid Rostami14
  • Andrew Rowley12
  • Bernd Schuller14
  • Michael Sonntag34
  • Adrian Stoewer35
  • Alan Stokes12
  • Corinne Teeter10
  • Guido Trensch36
  • Werner Van Geit37
  • Stefano Vrizzi6
  • Philipp Weidel38
  • Marmaduke Woodman
  • Michael Woodman39
  • Willem Wybo7
  • Alper Yegenoglu14
  • Catherine Zwahlen7

Group photo from the HBP CodeJam Workshop #7

Meeting Program

Mon. 11th Jan.

08:35 Model simplification
08:35Eilif Muller Phenomenological simplification of dendrites and synapses
08:55Marmaduke Woodman Simplifying brain activity: neural mass network models
09:15Willem Wybo Capturing dendritic computation using the Sparse Green's Function formalism
09:35Christian Pozzorini Characterization of single neurons by means of simplified spiking models
09:55Nicolas Cain DiPDE: A simulator for population density modeling [PDF]
10:15 Break
10:45 Standardisation of model representations
10:45Padraig Gleeson NeuroML, LEMS and Open Source Brain
11:10Inga Blundell, Jochen Martin Eppler and Dimitri Plotnikov NEST Modeling Language: A modeling language for spiking neuron and synapse models for NEST [PDF]
11:35Sergey Gratiy Model representation approaches for the Allen mouse visual column [PDF]
12:00 Lunch
13:30 Parallel tracks: tutorials and code sprints
13:30Padraig Gleeson Tutorial: The NeuroML and LEMS toolchain
15:00 Break
15:30 Parallel tracks: tutorials and code sprints
15:30Inga Blundell and Dimitri Plotnikov Tutorial: NESTML [PDF]
19:30- Dinner

Tue. 12th Jan.

08:30 Simulation tools
08:30Abigail Morrison What's new with NEST
08:50Michael Hines NEURON + Python [PDF]
09:10Eric Müller The BrainScaleS neuromorphic system
09:30Andrew Rowley and Alan Stokes SpiNNaker: What's new [PDF]
09:50Mikael Djurfeldt MUSIC [PDF]
10:10 Break
10:45 Workflows in large collaborative projects
10:45Olivier Amblet HBP Collaboratory app development [PDF]
11:10Bernd Schuller UNICORE in the Human Brain Project [PDF]
11:35Matteo Cantarelli Tales of open collaboration - How to work with human beings
12:00 Lunch
13:30 Parallel tracks: tutorials and code sprints
13:30Domenico Guarino Tutorial: An introduction to scientific Python
13:30Andrew Rowley and Alan Stokes Tutorial: SpiNNaker
15:00 Break
15:30 Parallel tracks: tutorials and code sprints
15:30Matteo Cantarelli Tutorial: Geppetto
15:30Olivier Amblet and Jeffrey Muller Tutorial: the HBP Collaboratory
19:30- Poster session, buffet dinner

Wed. 13th Jan.

08:30 Data integration and data analysis
08:30Eilif Muller The BBP data model, BluePy and friends [PDF]
08:55Michael Denker The Role of Elephants in Complex Workflows in Electrophysiology [PDF]
09:20Adrian Stoewer NIX: a file format for electrophysiology data and metadata
09:45Kunal Lillaney Neuro-visualization at the network edge [PDF]
10:10 Break
10:45 Validation suites for brain models
10:45Jean-Denis Courcol HBP Brain Simulation Platform validation automation [PPTX]
11:10Jan Antolik Mozaik as a brain model validation tool
11:35Corinne Teeter Generalized Leaky Integrate and Fire Neurons. Evaluating the contribution of different mechanisms in recreating the spike times of neurons
11:50David Feng AllenSDK: automated, standardized, and reproducible single cell model optimization in the Allen Cell Types Database
12:15 Lunch
13:30 Parallel tracks: tutorials and code sprints
13:30Alan Stokes Tutorial: an introduction to Git and Github
13:30Detlef Holstein, Vahid Rostami and Alper Yegenoglu Tutorial: data analysis with Elephant
15:00 Break
15:30 Parallel tracks: tutorials and code sprints
15:30David Feng Tutorial: the Allen tools
19:30- Poster session, buffet dinner

Thu. 14th Jan.

08:30 Neurorobotics / closed-loop systems
08:30Matteo Cantarelli Openworm: Building a digital organism
08:55Petrut Bogdan SpiNNaker meets silicon devices [PPSX]
09:20Andrew Mundy Spaun and SpiNNaker
09:45Csaba Eroe Point-neuron mouse brain in a closed-loop system
10:10Philipp Weidel ROS-MUSIC Toolchain
10:35 Break
11:05 Visualisation
11:05Juan Hernando Looking into the forest: Programmable visualization of neural networks with detailed morphologies
11:25 Lightning talks
11:25Nicholas Cain DiPDE, SpiNNaker, and Geppetto, Oh My! [PDF]
11:30Andrew Davison Reproducibility through environment capture: Docker and Sumatra [PDF]
11:40Justas Birgiolas Can we make computational neuroscience less "sticky": a newcomer's perspective [PPTX]
11:45Kamal AbuHassan Bayesian inference in waveform signals based on BAYSIG [PPTX]
12:00 Lunch
13:30 Parallel tracks: tutorials and code sprints
15:00 Break
15:30 Code sprints
19:30- 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.