G-Node blog post.

Not awesome, but was getting outdated -- so pushed.

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+: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 <support>`, 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/
+
+