HBP CodeJam Workshop #8
13th-15th September 2017, Lausanne, Switzerland
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.
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.
Organization
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.
Participants
- 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
- 1UNIC, CNRS, Gif sur Yvette, France
- 2University of Manchester, Manchester, United Kingdom
- 3CNR, Palermo, Italy
- 4EPFL - Human Brain Project
- 5Blue Brain Project, EPFL, Switzerland
- 6University of Pavia, Pavia, Italy
- 7Yale University, New Haven, USA
- 8Forschungszentrum Jülich GmbH
- 9The University of Manchester, Manchester, UK
- 10Forschungszentrum Juelich GmbH, Juelich, Germany
Meeting Program
Wed. 13th Sept. | ||
| 09:30 | Welcome and introduction | |
| 09:30 | Jeffrey Muller | Welcome and introduction |
| 09:40 | From experiments to data repositories | |
| 09:40 | Samuel Kerrien | Blue Brain Nexus: a provenance based, semantic data management platform |
| 10:05 | Lyuba Zehl | Tracking complex workflows in neuroscience [PDF] |
| 10:30 | Break | |
| 11:00 | Data-driven modelling and validation | |
| 11:00 | B. Lungsi Sharma | What - Why - How of Validation [link to slides] |
| 11:25 | Luca Leonardo Bologna and Carmen Alina Lupascu | Optimization, Neuron Builder Pipeline |
| 11:50 | Stefano Masoli | Neuron Modeling: What's New? |
| 12:15 | Lunch | |
| 13:30 | Parallel tracks: tutorials and code sprints | |
| 13:30 | Allan 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 | |
| 15:30 | Lena Oden | Tutorial: the HBP HPAC platform |
| 15:30 | Code sprints and discussions | |
| 17:00 | Robert McDougal | Tutorial: NEURON + Python |
| 17:00 | Code sprints and discussions | |
Thu. 14th Sept. | ||
| 09:00 | Welcome for participants coming from the Young Researchers Event | |
| 09:00 | Andrew Davison | Welcome for participants coming from the Young Researchers Event |
| 09:15 | Building Bodies for Brains and Brains for Bodies | |
| 09:15 | Kenny Sharma and Axel von Arnim | The Neurorobotics Platform: the simulator to give brains a body and bodies a brain |
| 09:40 | Martin Pearson | Integrating Shrewbot and Miro in the NRP [PDF] |
| 10:05 | Terry Stewart | Using Nengo in the Neurorobotics Platform [PDF] |
| 10:30 | Break | |
| 11:00 | Next-generation simulation tools and hardware | |
| 11:00 | Andrew Rowley | The SpiNNaker Platform [PDF] |
| 11:25 | Marmaduke Woodman | TheVirtualBrain |
| 11:50 | Christian Mauch | BrainScaleS Hardware — Resource Management and Monitoring [PDF] |
| 12:15 | Johann Klähn | Mapping PyNN to BrainScaleS Hardware |
| 12:40 | Lunch | |
| 13:30 | Parallel tracks: tutorials and code sprints | |
| 13:30 | Akos Hencz and Carmen Alina Lupascu | Tutorial: Getting the most from the Jupyter notebook |
| 13:30 | Andrew 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 | |
| 15:30 | Emmanouil Angelidis and Hossain Mahmud | Tutorial: Neurorobotics Platform - setting up an experiment |
| 15:30 | Jean-Denis Courcol | Tutorial: Brain Simulation Platform |
| 15:30 | Code sprints and discussions | |
| 17:00 | Kenny 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 | |
| 09:00 | Matt Earnshaw | Open Source Brain and its Ecosystem [PDF] |
| 09:25 | Fabrice Gaillard and Jeffrey Muller | Under the hood of the Collaboratory platform [PDF] |
| 09:50 | Susie Murphy and Axel von Arnim | Neurorobotics Platform collaboratory features |
| 10:15 | Werner Van Geit | BluePyMM |
| 10:40 | Kevin Mader | Large scale Image processing with Spark |
| 10:40 | Break | |
| 11:35 | Lightning talks | |
| 11:35 | Martina Rizza | A Biophysically Detailed Cerebellar Stellate Neuron Model Optimized with Particle Swarm Optimization Algorithm |
| 11:50 | Alper Yegenoglu | Building packages with Conda [PDF] |
| 12:30 | Lunch | |
| 13:30 | Parallel tracks: tutorials and code sprints | |
| 13:30 | Johann Klähn, Christian Mauch and Eric Müller | Tutorial: BrainScaleS Neuromorphic Hardware — the DLS Prototype Chip |
| 13:30 | Mahmoud 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 | |
| 15:30 | Michael Denker and Alper Yegenoglu | Tutorial: Data analysis with Elephant [PDF] |
| 15:30 | Alessandro Ambrosano and Luc Guyot | Tutorial: Neurorobotics Platform - using multiple robots |
| 15:30 | Code sprints and discussions | |
| 17:00 | Code sprints and discussions | |
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. 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.