From p.gleeson at ucl.ac.uk Thu Dec 13 14:38:49 2007 From: p.gleeson at ucl.ac.uk (Padraig Gleeson) Date: Thu, 13 Dec 2007 14:38:49 +0000 Subject: [neuroConstruct] NeuroML v1.7 release, requirements for v2.0 and NeuroML workshop Message-ID: <476143F9.4090404@ucl.ac.uk> Hi, A new release of NeuroML has just been put live at: http://www.morphml.org:8080/NeuroMLValidator/index.jsp Details of the updates are at: http://www.morphml.org:8080/NeuroMLValidator/NeuroMLFiles/Schemata/v1.7/RELEASE_NOTES but in short: Minor updates to some of the schemas to incorporate special cases I've come across in some published models (Traub et al 2003, L2/3 cell), but the main addition is a list of possible requirements/changes for NeuroML v2.0. Most of these are rearranging some elements for greater consistency or brevity, but many could invalidate v1.x files. One major update would be to allow variability within populations in a network. We can discuss these over the next month, but if anyone has any other suggestions for major changes please let neuroml-technology at lists.sourceforge.net know. Incorporation of SBML like interactions might lead to some major changes in the structure of ChannelML, this will become clearer over the next few months. A beta of MOOSE in Jan will hopefully be informative... Some of the minor updates go hand in hand with updates of the files for NEURON v6.1 import/export to NeuroML found at: http://neuroml.svn.sourceforge.net/viewvc/neuroml/ Also in v1.7 is an initial version of a maping for MorphML and NetworkML to X3D (XML based follow up to the Virtual Reality Modeling Language (VRML)). There are some obvious shortcomings, but you should be able to put any compliant NeuroML Layer 1/2/3 cell morphology or NetworkML file into the application and generate a 3D view (with an X3D viewer locally installed). Unfortunately I've not got around to making any of the changes to synaptic mechanisms suggested recently, that's next on the cards... There are also plans taking shape for a 1 day workshop at the CNS meeting in July in Portland which would consist of a morning tutorial/introduction to neuroConstruct, and an afternoon session on NeuroML (introduction/plans for the future/models in this format). If anyone is interested in knowing more, or has any ideas for it please let Sharon and me know. Padraig From Nicolas.Debeissat at sophia.inria.fr Thu Dec 13 16:21:29 2007 From: Nicolas.Debeissat at sophia.inria.fr (Nicolas Debeissat) Date: Thu, 13 Dec 2007 17:21:29 +0100 Subject: [neuroConstruct] screencast of neuroConstruct simulation play In-Reply-To: <476143F9.4090404@ucl.ac.uk> References: <476143F9.4090404@ucl.ac.uk> Message-ID: <47615C09.50401@sophia.inria.fr> Hi, I recently tried to record a simulation play in a video file and I didn't succeed. It stays stuck on the first screenshot. I am on linux, I tried : - xvidcap - wink I removed the DRI support in xorg server. But I still don't have my video working. When I pass the mouse pointer in front of the animation, it refreshes the image where the mouse pointer passes, so I have the impression that the application doesn't know that the screen is being changed !! Has anybody succeeded in recording a simulation ? Thanks for the work on neuroConstruct. Regards Nicolas Debeissat From p.gleeson at ucl.ac.uk Fri Dec 14 16:24:50 2007 From: p.gleeson at ucl.ac.uk (Padraig Gleeson) Date: Fri, 14 Dec 2007 16:24:50 +0000 Subject: [neuroConstruct] screencast of neuroConstruct simulation play In-Reply-To: <47615C09.50401@sophia.inria.fr> References: <476143F9.4090404@ucl.ac.uk> <47615C09.50401@sophia.inria.fr> Message-ID: <4762AE52.8040103@ucl.ac.uk> Hi, Unfortunately I'm not familiar with a good screen capture tool under Linux to use to generate movies. There is one for windows at www.fraps.com, which will generate a large avi from just the 3D panel as you're playing a simulation back (the file can be recompressed later). Unfortunately the free version puts the web link at the top of the movie, but that could be trimmed with other editing software. If anyone finds a good package for doing similar under Linux, let me know.. Ideally, the movie generating functionality should be built in to neuroConstruct, and is likely to be possible with the Java Media Framework, although replaying large data sets and capturing video might be a strain on most systems. This is on the todo list for us and will hopefully be in a new release in ~Feb. Padraig Nicolas Debeissat wrote: > Hi, > > I recently tried to record a simulation play in a video file and I > didn't succeed. It stays stuck on the first screenshot. > I am on linux, I tried : > - xvidcap > - wink > I removed the DRI support in xorg server. > But I still don't have my video working. > When I pass the mouse pointer in front of the animation, it refreshes > the image where the mouse pointer passes, so I have the impression that > the application doesn't know that the screen is being changed !! > > Has anybody succeeded in recording a simulation ? > > Thanks for the work on neuroConstruct. > > Regards > Nicolas Debeissat > > > _______________________________________________ > neuroConstruct mailing list > neuroConstruct at ucl.ac.uk > http://www.mailinglists.ucl.ac.uk/mailman/listinfo/neuroconstruct >