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 theme of this 9th installment is "co-design": scientists, students and engineers from different disciplines collaborating to build research infrastructure for computation-based neuroscience, and to use this infrastructure to model brain circuits, behaviour and learning, develop novel bio-inspired computing systems, and help discover new drugs for neurological disorders.

Programme

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.

Final programme

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.

Hippocampus, a brain area fundamental for learning and memory, is one of the most intensely studied brain areas world-wide. This means an enormous quantity of data, but also heterogeneity in terms of sources, methods, quality, etc. Integrating the available anatomical and physiological data in a unified model of hippocampus, and validating it broadly against known phenomena, is a challenging but feasible prospective given the HBP platforms roadmap.

In short, the aims of the workshop are two-fold. First, to engage the larger community of experimentalists and modelers working on hippocampus, and highlight existing modeling efforts and strategic datasets for modeling the Hippocampus. Second, to define and bootstrap an inclusive community-driven model and data-integration process to achieve open pre-competitive reference models of hippocampus, which are well documented, validated, and released at regular intervals (supported in part by IT infrastructure funded by HBP). Involvement from the community interested in characterization and modeling of hippocampus is highly encouraged.

The first day will be scientific presentations on modeling approaches, key datasets, problems and solutions, and some information on HBP activities relevant to the meeting. Instead of having regular research talks discussing the speaker's current research in detail, we aim to have shorter talks which either highlight important sources of experimental data (also discussing limitations etc.) or describe specific problems or solutions that are relevant to building a data-driven Hippocampus model. There will be ample time for discussion following talks. The second day will be highly interactive, and will have the objective of bootstraping a community process for planning, coordinating, reviewing, documenting, and validating regular releases of open integrative pre-competitive reference models of hippocampus. For this format to be effective, the meeting size has been intentially limited. There will be a poster session during lunches.

Preliminary List of Speakers

Bruce Graham (University of Stirling, UK)

Frances Skinner (University of Toronto, Canada)

Mariane Bezaire (Boston University, USA)

Giorgio Ascoli (George Mason University, USA)

Ivan Soltész (Stanford, USA)

Padraig Gleeson (UCL, UK)

Andrew Davison (UNIC-CNRS, Gif-sur-Yvette, France)

Marlene Bartos (University of Freiburg, Germany)

Nelson Spruston* (Janelia, USA)

Peter Somogyi* (University of Oxford, UK)

Jose Guzman (IST, Austria)

Javier Defelipe (Cajal Institute, Madrid, Spain)

Francesca Cacucci (UCL, London, UK)

To be confirmed - *

Organizers

Alain Destexhe, Katherine Fregnac, Szabolcs Kali, Audrey Mercer, Michele Migliore, Eilif Muller, Armando Romani, Katrien Van Look.

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.

Hippocampus CA1, a brain region fundamental for learning and memory, is one of the most intensely studied brain areas world-wide. This means an enormous quantity of data, but also heterogeneity in terms of sources, methods, quality, etc. Integrating the available anatomical and physiological data in a unified model of hippocampus CA1, and validating it broadly against known phenomena, is a challenging but feasible prospective given the HBP platforms roadmap.

In short, the aims of the workshop are two-fold. First, to engage the larger community of experimentalists and modelers working on hippocampus, and highlight existing modeling efforts and strategic datasets for modeling Hippocampal CA1. Second, to define and bootstrap an inclusive community-driven model and data-integration process to achieve open pre-competitive reference models of hippocampus CA1, which are well documented, validated, and released at regular intervals (supported in part by IT infrastructure funded by HBP). Involvement from the community interested in characterization and modeling of hippocampus CA1 is highly encouraged.

The first day will be scientific presentations on modeling approaches, key datasets, problems and solutions, and some information on HBP activities relevant to the meeting. Instead of having regular research talks discussing the speaker's current research in detail, we aim to have shorter talks which either highlight important sources of experimental data (also discussing limitations etc.) or describe specific problems or solutions that are relevant to building a data-driven CA1 model. There will be ample time for discussion following talks. The second day will be highly interactive, and will have the objective of bootstraping a community process for planning, coordinating, reviewing, documenting, and validating regular releases of open integrative pre-competitive reference models of hippocampus CA1. For this format to be effective, the meeting size has been intentially limited. There will be a poster session during lunches.

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 and code sprints.

The theme of the 6th BrainScaleS/ FACETS CodeJam was 'High-Performance Computing'.

More information

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 and code sprints.

The 5th BrainScaleS/FACETS CodeJam took place as a joint meeting with the NeuroML Development Workshop, with the theme "Convergence in Computational Neuroscience".

The NeuroML workshop was on 12th and 13th March with 14th March as a joint NeuroML-CodeJam day, including a Mini-workshop on Convergence, Interoperability and Reuse in Neuroscience Modelling Software.

The goal of the FACETS 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 and code sprints.

For the 4th FACETS CodeJam, the main theme of the meeting was workflows: what are the best practices for combining different tools (simulators, analysis tools, visualization tools, databases etc.) to ensure the efficient and reproducible flow of data and information from experiment conception to publication and archiving?

The first CodeJam focused on adding or improving Python support for different neuroscience simulators, and on the PyNN common simulator API.

The focus for the second CodeJam was expanded to include the next stages in the simulation workflow - analysis and visualisation of simulation results, and management of simulation projects to promote reproducibility and reliability.

The third CodeJam, aimed to catalyze development on a broad range of topics, including simulator interoperability, modeling langauge standardization, parallelizaion, Python tool-chain & abstraction development to further erode the complexity barrier facing computational neuroscientists, and much more ...

The general format of the workshop was to dedicate the mornings to invited and contributed talks on topics relating to simulation and collaborative software development in computational and systems neuroscience, leaving the afternoons free for discussions and code sprints.

Python is rapidly becoming the ''de facto'' standard language for systems integration. Python has a large user and developer-base external to the neuroscience community, and a vast module library that facilitates rapid and maintainable development of complex and intricate systems.

In this workshop, we highlighted efforts to develop Python modules for the domain of neuroscience software and neuroinformatics. Moreover, we sought to provide a representative overview of existing mature Python modules for neuroscience and neuroinformatics, to demonstrate a critical mass and show that Python is an appropriate choice of interpreter interface for future neuroscience software development.

There was a tutorial+demo session where visitors with laptops could install and get introduced and aquainted with the various Python software.

Many of these efforts have been featured recently in a special issue of Frontiers in Neuroinformatics on "Python in neuroscience ".

http://www.cnsorg.org/meetings/2009/workshops/CNS2009%20Python%20workshop.pdf

The first CodeJam focused on adding or improving Python support for different neuroscience simulators, and on the PyNN common simulator API. The focus for the second CodeJam was expanded to include the next stages in the simulation workflow - analysis and visualisation of simulation results, and management of simulation projects to promote reproducibility and reliability.

The general format of the workshop was to dedicate the mornings to invited and contributed talks on topics relating to simulation and collaborative software development in computational and systems neuroscience, leaving the afternoons free for informal discussions and code sprints.

Trends in programming language development and adoption point to Python as the high-level systems integration language of choice. Python leverages a vast developer-base external to the Neuroscience community, and promises leaps in simulation complexity and maintainability to any neural simulator which adopts it. As more and more simulators support Python, model development times can be drastically reduced by promoting code sharing and reuse across simulator communities. As a result, modelers can devote their software development time to innovating new simulation tools such as network topology databases, stimulus programming, analysis and visualization tools, and simulation accounting, to name a few. A multilateral effort to coordinate and organize these development efforts into a larger meta-simulator software system is a natural and alternate approach to incrementally address what is known as the complexity bottleneck, presently a major roadblock for neural modeling. While a solution here is arguably a necessary condition for resolving the present stalemate for understanding the complexities of brain-like computing, a successful initiative could also end up being a major innovation of the field for the larger computing community.

The goal of the CodeJam meeting was to bring together the core group of developers and modelers presently working towards such a common set of meta-simulator tools implemented in Python. As there was much to discuss, the meeting was partly parallelized into "Focus Groups". Code sprints were scheduled to address outstanding developer issues. A small number of technical talks were scheduled to promote discussion on recent innovations. We discussed how software already implemented can be improved and adopted, while trying to avoid arguing about specifications of unimplemented software, leaving this honor to the volunteer who risks to prototype it first. The focus of the meeting was on innovation, communication, convergence, multilateralism, and realization (from the german: Umsetzung).

The original meeting webpage: https://facets.kip.uni-heidelberg.de/tmp_course/course_wiki/index.php/CodeJam_Heidelberg_April2007