HBP CodeJam Workshop #7

11th-14th January 2016, Manchester, 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.

Organization

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.

Participants

• Kamal AbuHassan²¹
• Olivier Amblet⁶
• Jan Antolik^1,22
• 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 Gratiy^7,8
• Domenico Guarino³⁰
• Juan Hernando
• Juan Hernando Vieites⁶
• Michael Hines²⁰
• Detlef Holstein^1,18
• 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

Meeting Program

Mon. 11th Jan.
09:35	Model simplification
09:35	Eilif Muller	Phenomenological simplification of dendrites and synapses
09:55	Marmaduke Woodman	Simplifying brain activity: neural mass network models
10:15	Willem Wybo	Capturing dendritic computation using the Sparse Green's Function formalism
10:35	Christian Pozzorini	Characterization of single neurons by means of simplified spiking models
10:55	Nicolas Cain	DiPDE: A simulator for population density modeling [PDF]
11:15	Break
11:45	Standardisation of model representations
11:45	Padraig Gleeson	NeuroML, LEMS and Open Source Brain
12:10	Inga Blundell, Jochen Martin Eppler and Dimitri Plotnikov	NEST Modeling Language: A modeling language for spiking neuron and synapse models for NEST [PDF]
12:35	Sergey Gratiy	Model representation approaches for the Allen mouse visual column [PDF]
13:00	Lunch
14:30	Parallel tracks: tutorials and code sprints
14:30	Padraig Gleeson	Tutorial: The NeuroML and LEMS toolchain
16:00	Break
16:30	Parallel tracks: tutorials and code sprints
16:30	Inga Blundell and Dimitri Plotnikov	Tutorial: NESTML [PDF]
20:30-	Dinner
Tue. 12th Jan.
09:30	Simulation tools
09:30	Abigail Morrison	What's new with NEST
09:50	Michael Hines	NEURON + Python [PDF]
10:10	Eric Müller	The BrainScaleS neuromorphic system
10:30	Andrew Rowley and Alan Stokes	SpiNNaker: What's new [PDF]
10:50	Mikael Djurfeldt	MUSIC [PDF]
11:10	Break
11:45	Workflows in large collaborative projects
11:45	Olivier Amblet	HBP Collaboratory app development [PDF]
12:10	Bernd Schuller	UNICORE in the Human Brain Project [PDF]
12:35	Matteo Cantarelli	Tales of open collaboration - How to work with human beings
13:00	Lunch
14:30	Parallel tracks: tutorials and code sprints
14:30	Domenico Guarino	Tutorial: An introduction to scientific Python
14:30	Andrew Rowley and Alan Stokes	Tutorial: SpiNNaker
16:00	Break
16:30	Parallel tracks: tutorials and code sprints
16:30	Matteo Cantarelli	Tutorial: Geppetto
16:30	Olivier Amblet and Jeffrey Muller	Tutorial: the HBP Collaboratory
20:30-	Poster session, buffet dinner
Wed. 13th Jan.
09:30	Data integration and data analysis
09:30	Eilif Muller	The BBP data model, BluePy and friends [PDF]
09:55	Michael Denker	The Role of Elephants in Complex Workflows in Electrophysiology [PDF]
10:20	Adrian Stoewer	NIX: a file format for electrophysiology data and metadata
10:45	Kunal Lillaney	Neuro-visualization at the network edge [PDF]
11:10	Break
11:45	Validation suites for brain models
11:45	Jean-Denis Courcol	HBP Brain Simulation Platform validation automation [PPTX]
12:10	Jan Antolik	Mozaik as a brain model validation tool
12:35	Corinne Teeter	Generalized Leaky Integrate and Fire Neurons. Evaluating the contribution of different mechanisms in recreating the spike times of neurons
12:50	David 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
14:30	Alan Stokes	Tutorial: an introduction to Git and Github
14:30	Detlef Holstein, Vahid Rostami and Alper Yegenoglu	Tutorial: data analysis with Elephant
16:00	Break
16:30	Parallel tracks: tutorials and code sprints
16:30	David Feng	Tutorial: the Allen tools
20:30-	Poster session, buffet dinner
Thu. 14th Jan.
09:30	Neurorobotics / closed-loop systems
09:30	Matteo Cantarelli	Openworm: Building a digital organism
09:55	Petrut Bogdan	SpiNNaker meets silicon devices [PPSX]
10:20	Andrew Mundy	Spaun and SpiNNaker
10:45	Csaba Eroe	Point-neuron mouse brain in a closed-loop system
11:10	Philipp Weidel	ROS-MUSIC Toolchain
11:35	Break
12:05	Visualisation
12:05	Juan Hernando	Looking into the forest: Programmable visualization of neural networks with detailed morphologies
12:25	Lightning talks
12:25	Nicholas Cain	DiPDE, SpiNNaker, and Geppetto, Oh My! [PDF]
12:30	Andrew Davison	Reproducibility through environment capture: Docker and Sumatra [PDF]
12:40	Justas Birgiolas	Can we make computational neuroscience less "sticky": a newcomer's perspective [PPTX]
12:45	Kamal 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

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

Support

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.

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