From: Yaroslav Halchenko Date: Tue, 30 Nov 2010 23:13:20 +0000 (-0500) Subject: adding a draft of a post to the mailing list summarizing initiation of electrophysiol... X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=bc9ecfb945bef9ccae818f24f9f3104641c09742;p=neurodebian.git adding a draft of a post to the mailing list summarizing initiation of electrophysiology effort --- diff --git a/sandbox/Makefile b/sandbox/Makefile new file mode 100644 index 0000000..6484429 --- /dev/null +++ b/sandbox/Makefile @@ -0,0 +1,3 @@ +all: electrophysiology_post.html +%.html: %.rst + rst2html $< $@ diff --git a/sandbox/electrophysiology_post.rst b/sandbox/electrophysiology_post.rst new file mode 100644 index 0000000..2d80c10 --- /dev/null +++ b/sandbox/electrophysiology_post.rst @@ -0,0 +1,102 @@ +Dear Electrophysiology Neuroscientists, +======================================= + +As you might know, during November 13-17, the NeuroDebian team ran its +first Debian booth at the annual meeting of the `Society for +Neuroscience`_ (SfN2010_) in San Diego, USA. Our generic report `is +available from NeuroDebian website `_. + +In this post we want to summarize our findings on the status of Free +and Open Source Software (FOSS) in the domain of +neuro-electrophysiology. + +- Majority of electrophysiology researchers are locked into software + platforms provided by the vendors of the used hardware +- There exist a number of FOSS platforms for all (?) stages necessary + for setting up the research workflow but their adoption in hindered + by difficulty to setup and maintain. That in turn results in the + absence of a set of commonly accepted and used ultimate FOSS + solutions in the field +- Majority of FOSS and some of the commercial data acquisition + solutions use Linux-based systems, relying on an additional stack + for real-time kernel support (e.g. RTAI_) and often the Comedi_ + library for interfacing with the (most often proprietary) hardware +- Some commercial companies are interested in sharing their products + as FOSS (e.g. Ripple LLC: Trellis-Neuro) and getting them ready for + inclusion into Debian +- Many labs develop their solutions and are willing to share but +- Nearly all researchers using Linux, already use Debian_ (or + Debian-derived such as Ubuntu_) Linux distribution as the platform + but primarily rely on manual deployment (download, build, install or + compose a custom Live media such as DVD or USB) of the 3rd-party and + their own products + +Existing Electrophysiology FOSS +------------------------------- + +We have initiated a `Debian Science Electrophysiology task page +`_ +to collect all relevant FOSS for the field and signal their status in +respect to inclusion in Debian distribution or presence of not (yet) +official Debian packages. The list is constantly growing (and +changing), so if you spot some relevant FOSS absent, please `let us +know `_. + +Here is a brief summary listing per application sub-domain: + +XXX may be listing is just not needed and duplicate of what could be +found on the tasks page, although there it is not very +structured... so may be it is better to come up with a verbal +description + +Data acquisition +~~~~~~~~~~~~~~~~ + +`Debian Science Data Acquisition task page +`_ +provides similar summary for software such as RTAI_, Xenomai_, Comedi_ +which enables data acquisition. + +- Nspike -- electrophysiological and behavioral data collection + +TODO: +- provide verbal summary on existing solutions +- mention RT-Preempt kernel images being available +- point to 'cooked' solutions on how to build using RTAI-patches + + +Online Frameworks +~~~~~~~~~~~~~~~~~ + +- Relacs -- framework for closed-loop neurophysiological experiments +- RTXI -- real-time data acquisition and control applications in biological research +- Trellis-Neuro -- interface to neurophysiology data acquisition and stimulation instruments + +TODO: + - pointers to the SfN posters for RTXI, Mehmet's setups + + +Offline data analysis +~~~~~~~~~~~~~~~~~~~~~ + +- Chronus -- Matlab toolbox for analysis of neural signals +- KlustaKwik -- spike sorting tool +- Neurodata -- Octave/Matlab suite to analyze data acquired from electrophysiology experiments +- Openelectrophy -- data analysis framework for intra- and extra-cellular recordings +- Sigviewer -- GUI viewer for biosignals such as EEG, EMG, and ECG +- Spike -- information-theoretic spike train analysis techniques +- Stimfit -- viewing and analyzing of electrophysiological data + + + +.. _chap_debian_booth_sfn2010: http://neuro.debian.net/booth_sfn2010.html +.. _blends_neuroscience_electrophysiology: http://blends.alioth.debian.org/science/tasks/neuroscience-electrophysiology + +.. _annual meeting: http://www.sfn.org/am2010/ +.. _SfN2010: http://www.sfn.org/am2010/ +.. _Society for Neuroscience: http://www.sfn.org/ +.. _RTAI: https://www.rtai.org +.. _Xenomai: http://www.xenomai.org +.. _Comedi: http://www.comedi.org +.. _Debian: http://www.debian.org +.. _Ubuntu: http://www.ubuntu.com