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CodeJam #10 - Agenda

Tuesday, 26 November 2019

CodeJam #10

Venue:

Social Dinner:

Description:

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. While the mornings are dedicated to invited and contributed talks, the afternoons are free for discussions, tutorials and code sprints.

This year's theme is "Integration". It is aimed to gather scientists, students and engineers from different disciplines collaborating to build a highly integrated research infrastructure for computation-based neuroscience, and to show how this infrastructure can be used to model brain circuits, behaviour and learning, develop novel bio-inspired computing systems, and help discover new drugs for neurological disorders.

The CodeJm#10 agenda is aligned with the programme of other HBP events taking place before or in parallel so that participants of one event can also attend some sessions of the other events that are also interesting for them. Get the overview here.

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Opening Session
09:00-09:25
(25+5 min)
 Neuromorphic Computing and why it need CodeJams (show presentation.pdf)

Video recording of the talk

Johannes Schemmel (UHEI)

Session 1: Data organisation and collaboration tools
09:30-09:55
(25+5 min)
 New features of the Knowledge Graph (show presentation.pdf)

Video recording of the talk

Oliver Schmid (EPFL)
10:00-10:25
(25+5 min)
 Data and Models: curation and reuse (show presentation.pdf)

Video recording of the talk

Glynis Mattheisen (CNRS), Yann Zerlaut (CNRS)
10:30-11:00
(30 min)
 Coffee Break
11:00-11:25
(25+5 min)
 Data management and data integration - Analytical methods and workflow engine (show presentation.pdf)

Video recording of the talk

Kostis Karozos (AUEB), Thanasis Karabatsis (UoA)
11:30-11:55
(25+5 min)
 The Collaboratory, an extensible ecosystem (show presentation.pdf)Allan Francani (EPFL)
12:00-13:00
(60 min)
 Lunch Break

13:00-13:25
(25+5 min)
 Jupyter Notebooks in the Collaboratory

Video recording of the talk

Jonathan Villemaire-Krajden (EPFL)
13:30-14:25
(55+5 min)
 TUTORIAL: Integrating your app in the CollaboratoryAllan Francani (EPFL)
14:30-15:25
(55+5 min)
 TUTORIAL: Building a Tool in a NotebookJonathan Villemaire-Krajden (EPFL)
15:30-16:00
(30 min)
 Coffee Break
16:00-16:55
(55+5 min)
 TUTORIAL: fairgraph: a Python API for the Human Brain Project Knowledge GraphAndrew Davison (CNRS)
17:00-18:15
(75 min)
 Code sprints and discussionAll
18:45
End of the Meeting Day
19:30
Social Dinner @Kulturbrauerein (Heidelberg old town, see map)

Wednesday, 27 November 2019

Sesion 2: Simulators and Emulators
09:00-09:25
(25+5 min)
 NEURON Python Interface Strategies (show presentation.pdf)

Video recording of the talk

Michael Hines (Yale School of Medicine)
09:30-09:55
(25+5 min)
 NEST: News and features

Video recording of the talk

Dennis Terhorst (JUELICH)
10:00-10:25
(25+5 min)
 The architecture of TVB's simulationMihai Andrei (Codemart)
10:30-11:00
(30 min)
 Coffee Break
11:00-11:25
(25+5 min)
 Deep Learning on BrainScaleS-2 (show presentation.pdf)Philipp Spilger (UHEI)
11:30-11:55
(25+5 min)
 Running a cortical micro-column in real-time in SpiNNaker (show presentation.pdf)

Video recording of the talk

Andrew Rowley (UMAN)
12:00-12:25
(25+5 min)
 Lightning Talks
Lab visits are organised for Neuromorphic computing interested people
Diverse volunteer speakers (each 1 slide and max. 5 min.)
12:30-13:30
(60 min)
 Lunch Break
13:30-14:25
(55+5 min)
 TUTORIAL: PyNEST and NESTMLHåkon Mørk (NMBU)
14:30-15:25
(55+5 min)
 TUTORIAL: Using the web and scripting interfaces of TVB simulatorMihai Andrei (Codemart)
15:30-16:00
(30 min)
 Coffee Break
16:00-16:55
(55+5 min)
 TUTORIAL: SpiNNaker or BrainScaleS

Two tutorials in parallel - choose yours:

  • SpiNNaker tutorial - Andrew Rowley
  • BrainScaleS tutorial - Eric Müller
17:00-18:30
(90 min)
 Code sprints and discussionAll
18:30
End of the meeting day

Thursday, 28 November 2019

Session 3: Collaborative and integrative workflows
09:00-09:25
(25+5 min)
 Single cell modelling workflow (show presentation.pdf)

Video recording of the talk

Luca Leonardo Bologna (CNR)
09:30-09:55
(25+5 min)
 Cerebellar Network model reconstruction and simulation (show presentation.pdf)

Video recording of the talk

Claudia Casellato (UNIPV)
10:00-10:25
(25+5 min)
 Integrating virtual brains with virtual bodies. Simulated robots for closed-loop in-silico experiments (show presentation.pdf)

Video recording of the talk

Alberto Antonietti (UNIPV)
10:30-11:00
(30 min)
 Coffee Break
11:00-11:25
(25+5 min)
 Knowledge Graph - Neurorobotics Platform (NRP) Integration (show presentation.pdf)

Video recording of the talk

Axel von Arnim (FORTISS)
11:30-11:55
(25+5 min)
 SpiNNaker - Neurorobotics Platform Integration (show presentation.pdf)

Video recording of the talk

Lorenzo Vannucci + Daniel Zimmermann (SSSA)
12:00-12:25
(25+5 min)
 How modern software techniques can help the scientific process (show presentation.pdf)

Video recording of the talk

Christian Mauch (UHEI)
12:30-13:30
(60 min)
 Lunch Break
13:30-13:55
(25+5 min)
 Quality and testing for the Brain Simulation Platform (show presentation.pdf)

Video recording of the talk

Alexander Dietz (EPFL)
14:00-14:55
(55+5 min)
 TUTORIAL: SpiNNaker-NRP integrationLorenzo Vannucci (SSSA)
15:00-15:55
(55+5 min)
 TUTORIAL: Knowledge Graph - NRP IntegrationAxel v. Arnim (FORTISS)
Stefano Nardo (SSSA)
16:00-16:30
(30 min)
 Coffee Break

Wrap-up and outlook
16:30-16:40
(10 min)
 Stand-up 1Voluntary summary group 1
16:40-16:50
(10 min)
 Stand-up 2Voluntary summary group 2
16:50-17:05
(15 min)
 Stand-up 3Voluntary summary group 3
17:05-17:15
(10 min)
 Stand-up 4Voluntary summary group 4
17:15-17:30
(15 min)
 Stand-up 5Voluntary summary group 5
17:30-17:45
(15 min)
 Stand-up 6Voluntary summary group 6
17:45-18:00
(15 min)
 Closing remarksAndrew Davison (CNRS)
18:00
End of the CodeJam
Contact: martina.schmalholz@kip.uni-heidelberg.de