From 61daf4f12938f33bead01608841512b1ad669153 Mon Sep 17 00:00:00 2001 From: Michael Hanke Date: Mon, 2 Apr 2012 11:20:58 +0200 Subject: [PATCH] G-Node blog post. Not awesome, but was getting outdated -- so pushed. --- .../blog/2012/2012-04-02_gnode_workshop.rst | 104 ++++++++++++++++++ 1 file changed, 104 insertions(+) create mode 100644 sphinx/blog/2012/2012-04-02_gnode_workshop.rst diff --git a/sphinx/blog/2012/2012-04-02_gnode_workshop.rst b/sphinx/blog/2012/2012-04-02_gnode_workshop.rst new file mode 100644 index 0000000..621c0d6 --- /dev/null +++ b/sphinx/blog/2012/2012-04-02_gnode_workshop.rst @@ -0,0 +1,104 @@ +:date: 2012-04-02 00:00:00 +:tags: G-Node, neuroscience, software, electrophysiology, neuroshare + +.. _chap_gnode_packaging_workshop_2012: + + +Exciting new software for electrophysiology -- NeuroDebian@G-Node +================================================================= + +Upon an invitation by `Thomas Wachtler`_, on Feb 28 2012 NeuroDebian visited +the German INCF_ node -- `G-Node`_ for a short workshop on Debian packaging. +G-Node drives a number of software projects primarily focused on +electrophysiology research -- ranging from server-side data storage to data +access and analysis tools for workstations. None of those are part of +(Neuro)Debian yet, so all participants had high hopes to change this as soon as +possible. + +During the workshop we looked into various projects and discussed how they +could be packaged for Debian. Fortunately, it turned out that the majority of +the necessary packaging work will be fairly straightforward and there are no +obvious show stoppers, such as licensing problems, that would prevent inclusion +into Debian in a rather near future. This is especially exciting as no less than +three key infrastructure problems of electrophysiology research, and +electrophysiology on Linux machines in particular will be tackled with the new +packages. + + +Access proprietary data formats +------------------------------- + +Maybe one of the most pressing issues is data access. There are numerous +hardware vendors for data acquisition devices that all have their own +proprietary data formats. This is a serious obstacle when it comes to data +sharing efforts or collaborative work in general. To access such data, one +depends on the vendor to provide support for a particular computing +environment. However, not surprisingly this support is typically limited to the +Windows platform, or other commercial systems, such as Matlab. + +For many years these hardware vendors could not agree on a common data format, +but instead came up with a standardized API to access vendor specific IO +libraries to ease the life of developers trying to add support for a data +format to their software. This standardization initiative is called +Neuroshare_. Unfortunately, it does not address the core of the problem, as it +still requires the vendors-specific libraries implementing the Neuroshare-API +to access a proprietary data format -- and of course the vast majority of these +libraries is closed-source and Windows-only. + +G-Node has developed a Wine_-base solution that behaves like a Neuroshare +library on the Linux platform and internally passes library calls on to one of +the vendor libraries. This nswineproxy_ can be used as a drop-in replacement +for any Neuroshare library and therefore allows for access to all +Neuroshare-compliant modules. While this solution admittedly lacks the +performance of a native implementation, it still makes a huge difference to be +able to access a particular data format at all, and is perfectly suitable for +one-time data conversion -- for example into the open HDF5 data format. + +In addition to the Wine-proxy, G-Node also provides `python-neuroshare`_, +a Python package to access any Neuroshare-library. + + +Comprehensive data description and sharing +------------------------------------------ + +Plain data access is not sufficient for collaborative work and data sharing. +In addition, it requires a comprehensive description of data, including +information on data origin, acquisition parameters, and applied processing. +G-Node offers several software packages that offer important functionality in +this regard. ODML_ is a markup language to create comprehensive meta +information for a particular dataset (Python and Java bindings are provided). +datajongleur_ is a Python package to create data views that combine plain data +with meta information, such as physical quantities, or more detailed meta data. +It allows injecting these enriched datasets in SQL databases for efficient +storage, querying, and retrieval. Finally, G-Node also develops a server-side +database solution that aids multi-site data-sharing efforts. Clients for +various environments, such as Matlab and Python are either being developed or +are already available. + + +Real-time data analysis +----------------------- + +The third topic for software development at G-Node are closed-loop real-time +systems for online stimulus creation, data acquisition, and data analysis, such +as Relacs_. The upcoming Debian release (wheezy) will offer a Linux kernel with +real-time capabilities which should make it easier to offer out-of-the-box +solution for this type of research. + +If you are interested in any of these software packages and would like to see +them integrated into the Debian system quickly, please do not hesitate to +:ref:`contact us `, so we can coordinate the effort. + +.. _Thomas Wachtler: http://neuro.bio.lmu.de/research_groups/res-wachtler_th/index.html +.. _INCF: http://www.incf.org/ +.. _G-Node: http://www.g-node.org/ + +.. _Neuroshare: http://neuroshare.sourceforge.net +.. _nswineproxy: http://github.com/G-Node/nswineproxy +.. _python-neuroshare: http://github.com/G-Node/python-neuroshare +.. _ODML: http://www.g-node.org/projects/odml + +.. _datajongleur: http://github.com/G-Node/Datajongleur +.. _Relacs: http://relacs.sourceforge.net/ + + -- 2.39.2