RELEASE_NOTES

Release notes/change log for neuroConstruct

See also the README file


--------- Version 1.7.0 (April 2012) ---------

Moved codebase to GitHub: https://github.com/NeuralEnsemble/neuroConstruct


--------- Version 1.6.0 (August 2012) ---------

Improved 3D visualisation of cells and networks when all segments are located more than a few hundred microns away 
from the origin. Now 3D view centres on middle of visible cells. Origin is only included if "Show 3D axes" option
is selected. Also removed annoying clipping of back of 3D view when zooming out.

Added option to save cells in project in pure NeuroML v1.8.1 format in morphologies folder. Now all channels, synapses &
cells in a project can be stored natively in NeuroML. Also facilitates comparing versions of morphology files across
commits.

Added warning if a project contains multiple ChannelML files which have different values for reversal potential
but use the same ion (e.g. ek=-77 in one k channel, -87 in another). Pops up a warning dialog when such channels are
used together in one cell (without overriding the ChannelML files using an IonProperty in the cell).

A number of updates to the NeuroML 2 export of cells & channels in line with the developing specification at:
http://sourceforge.net/apps/trac/neuroml/browser/NeuroML2.


--------- Version 1.5.3 (Mar 2012) ---------

Fixed bug which gave problems saving RandomSpikeTrainSettings in projects on Java 1.7

Added option in GUI to edit/remove ion properties from cell & add more than one ion prop per group name.

Updated to use Jython 2.5.2

Added xlrd to Lib/site-packages to allow reading/writing Excel files from nC Jython scripts


--------- Version 1.5.2 (Jan 2012) ---------

Added anti-aliasing on 3D view for smoother renderings. Can be turned on/off via Settings -> Project Properties 
or when viewing in 3D, 3D Settings.

Allows multiple NeuroML files to be imported with: ./nC.sh -neuroml nml1.xml nml2.xml channelX.xml

Added option to plot multiple data files with: ./nC.sh -plot mydata1.dat mydata2.dat 

Fixed bug when compiling/running Neuron 7.2 on Windows. See templates\neuronUtils\mknrndll.sh

Improved integration of the NeuroML 2 and nC Ant build scripts. nC by default uses the copy of libNeuroML**.jar 
and lems**.jar in lib/neuroml2 to facilitate recompiling of downloaded copies of the code and to make sure nC has
a stable version of the LEMS/NeuroM 2 code.

Fixed bug in genesis export, whereby wrong rev pot of leak conductance was used, only if channelml file for leak 
cond was in SI units (which no project files used until now...) Put in check that all channelml files in project 
are in same unit system, either si or physiological. Throws warning at Validate if not the case. Important when 
exporting to single level 3 file.

Improvement of PyNN export from nC, supports NeuroML 2 based PyNN model descriptions, see Ex8_PyNNDemo, sim config
TestPyNN_NML2

--------- Version 1.5.1 (July 2011) ---------

Improvements to LEMS/NeuroML 2 integration. Added project at nCexamples/Ex10_NeuroML2/Ex10_NeuroML2.ncx
with some examples of NeuroML 2 channels and cells which can be run with the LEMS interpreter or NEURON

Made improvements to & added extra tests for saving & reloading continuous & spike train data in HDF5 format

Much more efficient reloading of data if a simulation only saves spike times. Now hundreds of thousands of
spike trains can be reloaded without filling memory (will max out memory if they're all plotted though)

Fixed bug in NetStimExt: Previously could fire outside of del/dur window if average firing rate was higher
than time window length, i.e. time of first spike was chosen as after end of duration.



--------- Version 1.5.0 (Mar 2011) ---------

Added preliminary export functionality for NeuroML 2. Morphologies can be exported to NeuroML v2 format, 
and some simple (e.g. HH Na & K) ChannelML files can be translated to the equivalent entities in NeuroML 
v2alpha. Networks files can be genenrated with simple <population> elements, and the temporary 
<explicitConnection> and <explicitInput> elements. The NeuroML 2/LEMS code which is being developed on 
the NeuroML SVN rep (see http://sourceforge.net/apps/trac/neuroml/browser/DemoVer2.0/lems) is included. 
This can be automatically updated when using nC from the SVN repository by running updatenC.sh/updatenC.bat. 

Some simple models in NeuroML 2 can now be run through nC using the LEMS interpreter. Note the LEMS 
interpreter does not yet support multicompartmental cells. Try Ex4_HHCells for a network of 2 HH cells 
with a simple synapse. Results of a successful simulation on the LEMS interpreter should be listed in 
the Simulation Browser & can be reloaded/replayed in the usual way. 

More verbose warnings when launching external processes on Linux using konsole & gnome-terminal

Added a graphical tool for the analysis of action potential shapes. Plot a number of cell voltage traces, 
e.g. population in a network, and in the Plot Frame menu select tools -> AP shape analysis. This will align 
all spikes in the traces to the same trigger point (e.g. crossing 0mV), to compare shape of APs.

Updated simulation tree quick sim result plotter (button "Quick Plot..." at tab Visualisation). Now when 
e.g. 6 cell groups are plotted with "Plot is separate plot frame per cell group..." windows are arranged 
in grid to fit the screen.

Changed behaviour of input instance specific properties when multiple inputs are put onto individual cells: 
e.g. multiple synaptic inputs (or current clamps) on a cell's dendritic tree. This is only relevant when 
random synaptic firing rate/pulse amplitude/duration are used! Previously for e.g. input with random/gaussian 
amplitude etc. a different value of this was used for inputs on each cell, but the same values were used within 
a cell, e.g. if 4 were placed on dendrites of one cell. Now a different value will be used for each instance, 
including within one cell. 

Changed function doLoadNetworkMLAndGenerate() to doLoadNetworkMLAndRegenerateInputs() in ProjectManager as this 
is a more accurate name for its functionality (unchanged: loads positions, connections & inputs from a NetworkML 
file, OVERWRITES the inputs by starting the ElecInputGenerator and generates plot/saves). Added 
doLoadNetworkMLAndGeneratePlots() which loads & keeps all info from NetworkML, and generated PlotSaves for 
values found there.


--------- Version 1.4.1 (Aug 2010) ---------

Added option to import NeuroML Level 1-3 file with ./nC.sh -neuroml neuromlfile.nml, etc. and populate new project with cells/populations etc. found.

Added function to set all data traces in plot frame to same colour

Added beta version of saving NEURON simulation data in HDF5 format. Note: you need to be able to run "import tables" when NEURON started in Python mode for this
to work! Saved HDF5 data files can be reloaded in nC like text based saved simulation data.

When viewing a cell in 3D: added temporary highlight of section in cell 3D view  when Edit Group GUI open and section name is clicked on, facilitates choosing
which sections to add to a group

Updates in Validate function: Added warning if XSL files aren't latest version (e.g. NChannelML_v1.8.1_NEURONmod.xsl). Added option to clean
up old XSL files when Updating XSL mappings

Better visualisation of Simulation Configuration check boxes for large projects (text size reduced if >50 check boxes in Sim Config GUI)


--------- Version 1.4.0 (Jun 2010) ---------

Added 2 new projects in nCmodels: CA1Pyramidal & Thalamocortical which are discussed in the NeuroML paper in PLoS Comp Biol.

Improved general handling on Mac. Better interaction with simulators, execution of Python scripts etc. on the platform.

Improved behaviour of 'nC.sh -make' and 'nC.bat -make' to allow compilation without ant

Added functionality at tab Cell Types to compare cell to a cell in a different project (very handy when using multiple copies of a cell in different project)

Added "Compare simulations" in Simulation Browser interface. Lists different stored properties between two saved simulations (e.g. random seeds).

Adding new NEURON extra code location: -0.5, after all cells & network created but before run

General improvements to saving/loading NeuroML Level 3 files.

Improved the Python neuroConstruct utilities script at pythonNeuroML/nCUtils/ncutils.py which contains a convbenient simulationManager class for running multiple simulations,
e.g. a frequency versus input current curve as in nCmodels/GranCellLayer/pythonScripts/GranGolgiF_I.py


--------- Version 1.3.7 (Feb 2010) ---------

Updated import/export of NeuroML when an Ion concentration is present in cell. This is in line with recent conversations on neuroml-channels@lists.sourceforge.net
mailing list. Updated way GENESIS calculates "B" value for CaPool. Examples GranuleCell and GranCellLayer updated to reflect best practices of implementing CaPool/Ca
dep K chan, etc. Python scripts added to test these on NEURON/GENESIS/MOOSE

Minor bugfix: removed problem when generating code on Windows for NEURON when Cygwin is not installed locally. The 'date' system command was used to give textual
output of the simulation start/stop time. This is only available when Cygwin is installed. Code now checks existance of c:\cygwin or c:\Program Files\cygwin and
uses date if these are found, doesn't otherwise.

Bug fixed in 3d visualisation. Transparency checkbox now works as before.


--------- Version 1.3.6 (Jan 2010) ---------

Much improved MOOSE support. The very latest version of MOOSE from their Subversion repository should be used. The majority of projects which could run on
GENESIS should work fine on MOOSE too, but users are advised to double check any simulation results. MOOSE simulations are running 2-5 times faster than
GENESIS 2

Added new tree based simulation browser GUI to allow quick plotting of simulation results without viewing full network in 3D. Can be run from main GUI via
"Quick Plot..." button on Visualisation tab. Also can be run in standalone mode using: ./nC.sh -sims projectpath/projectname.ncx (or:
nC.bat -sims projectpath/projectname.ncx).

Added option in GENESIS tab to make spike transmission behave similarly to NEURON, or to use the usual GENESIS method based on abs_refract. Hover over the
checkbox on the GENESIS tab for more details. ***Using this may be crucial to getting NEURON & GENESIS network simulations to match***

Added option for GENESIS/MOOSE for reloading simulation if it finishes after a short time (e.g. 10 sec). Can be used for plotting results of short MOOSE
simulations as soon as they finish.

Updated to Jython 2.5.0, so most standard Python 2.5 modules should be available whn creating scripts to be run using './nC.sh -python'. Improved
Python scripting documentation. Online at http://www.neuroconstruct.org/docs/python.html

Added more 'GUI mode' options at NEURON & GENESIS tabs so that simulations can be run: in console with plots, in console without plots, or completely in background.
Very useful when running multiple simulations using Python scripts. See pythonnC/Ex5_MultiSimGenerate.py for example. Note: only works on Linux/Mac so far. The console
output is put into file: /tmp/logNEURON_Projectname_SimulationRef, etc.

Added simple script to allow neuroConstruct simulations to be loaded/plotted/analysed using NeuroTools (http://neuralensemble.org/trac/NeuroTools). Avaliable at 
pythonNeuroML/NeuroTools/LoadToNeuroTools.py

Updated many of the fonts used in the GUI & generated HTML views

Added option in nC.sh & nC.bat to build source without ant (using './nC.sh -make', etc.)

Different colours for gap junction connections in 3D view (orange-> orange, not green-> red)


--------- Version 1.3.0 (June 09) ---------

- Changed default project extension to ncx. Now it's easier to associate this file type with nC.bat/nC.sh for quick opening of neuroConstruct  
  projects by (double) clicking on project file in file explorer. However, it may still be better to start nC in a terminal/shell
  as any error console output will be caught if there is a problem and the application closes.

- Option in Plot Frame when one or more Data Sets being plotted to generate python files which will allow a high resolution PDF, ESP, png of 
  the data to be created. Requires install of matplotlib (http://matplotlib.sourceforge.net/).
 
- Added (long overdue) option for "silent mod file compilation", e.g. no pop up confirmation etc. when mod files are compiled on Windows.

- Improved import & export of NeuroML, incl Variable Parameters & inhomogenous channel densities. Added option File -> Import NeuroML Levels 1-3, to have all of the 
  cells, channels, synapses and networks found in a Level 1-3 file imported, possibly into a new project. Also added option (at tab Export -> NeuroML) to include in annotation 
  in Level 3 file details of neuroConstruct specific objects, to allow easy import of associates plots, sim configs etc. into a new nC project, using a valid Level 3 file 
  (note: other applications which parse this file will ignore this info, and just get the cell, populations, etc.)

- Reset absolute refractory period for ***NETWORK CONNECTIONS IN GENESIS*** from 10ms to 1ms. May cause functionality change in some networks on GENESIS!!! 
  But should make net behaviour more similar to NEURON

- Added 2 new options for electrical input to cells: variable current clamp (e.g. ramped input current or sinusoidal input) & variable spike input rate. A generic 
  function of time can be provided for the input amplitude or the input spike rate. Both of these are only available for NEURON currently.

- Added warning every 10th startup if logging to file is turned on as it can lead to v big log file dir.

- Added some more expressions for equation parser incl sqrt(x) and Heaviside function

- Added option for minimum radius of segments displayed in 3D. Improves 3D display of large cells with thin dendrites

- Updated a number of the example files for controlling nC projects through Python. Generates/runs GENESIS projects now too.

- Added option to add all sections in existing groups (e.g. basal_dendrites, oblique_dendites) to new groups (e.g. basal_plus_obliques) as opposed to having
  to add all sections individually

- Allowed plotting of a specified max number of cells (e.g. 5# for up to 5 cells in a group)

- Added a number of other options for plotting Data Sets: crosses (x), thicker lines

- Added "MOOSE test mode" option in GENESIS tab. Note: there are known problems with this at the moment!

- Restructured how cell initial potentials are generated so when initial pot of cells in group != fixed num, NEURON & GENESIS use the same set of values

- Improved plotting of internals of ChannelML files when there is a tempreature dependence (q10/generic expressions)

- Improved PSICS export functionality. See nCexamples\Ex7_PSICSDemo for example

- Improved PyNN export functionality. See nCexamples\Ex8_PyNNDemo for example of what is currently supported. Only tested on Linux so far.

- Better support for running on KDE4 & Macs. Min Java version required is 1.5 again, doue to some lack of support for 1.6 on Macs. 


--------- Version 1.2.2 (Jan 09) ---------

-  Restructured main examples to 2 new dirs: nCexamples for non anatomical examples used to illustrate 
   core nC functionality; nCmodels for more biologically realistic examples, mainly based on published 
   models. Added Pyramidal cell model from Kole et al 2008/Rothman et al 2009.

-  Added preliminary mapping to PSICS. To use the PSICS functionality you will need to get a copy of 
   the jar file from the PSICS website, save it locally and set the location in Settings -> General 
   Properties and Project Defaults. The included example nCexamples\Ex7_PSICSDemo illustrates current
   functionality

-  Added one more Python interface example for loading morphologies by script (Ex6_LoadCells.py)

-  Added option to export project elements in single NeuroML level 3 file

-  Added option in MorphNetConn "Direct recurrent connections not allowed" for connections within a 
   cell group, so that if cell A is connected to B, B won't form a connection back to A. Useful for 
   electrical synapses

-  Fixed minor bugs in Morph Conn generator

-  Added option to have weights of syn connections function of radial distance between source & target. 
   Also can be function of soma to soma distances

-  Optimised viewing of parameterised groups in cells with a large number of segments

-  Updated channel templates to use v1.8.0 ChannelML examples, added gap junction template

-  Moved to GNU GPL v2 licence


--------- Version 1.2.0 (Dec 08) ---------

-  Added libraries for Java 3D, Jython and HDF5 in the standard distribution, making the download size larger, but meaning that no
   extra packages need be installed to use these with neuroConstruct. 

-  Renamed run.bat/run.sh to nC.bat/nC.sh and increased checks for 32/64 bit and win/linux to use correct libraries

-  Large networks in NEURON are more efficient/faster to load due to use of arrays of synapse objects as opposed to naming each individually

-  A number of optimisations have been added for random network connection, to speed up nets including conditions such as uniqueness of post 
   syn cells and max and min length. May slow smaller networks marginally, but most larger networks using these options will be faster to 
   generate.

-  Added warnings at generate tab when cell groups (in current sim config) are empty after generation, and if there are fewer than expected 
   network connections.

-  Allows setting of the version of NeuroML to use for validation, etc. via Settings -> General Properties

-  Renaming of groups in cells enabled in Edit Groups dialog

-  New method to specify segments for inputs, either: give a list of the segment ids to apply inputs to; or specify a group (e.g. dendrite_group)
   along with how many inputs to generate, and these will be randomly palced over the group. Can be used for adding multiple random synaptic 
   inputs over a dendritic tree.

-  Updated simulation replay to allow looping of simulation replaying, and "rainbow" shading of voltages

-  Added option to create distribution histogram over either X or Y values in a plotted Data Set (previously only Y). X distribution
   useful e.g. for plotting number of timesteps used per ms in NEURON variable time step simulation.

-  Updated import function for plotting of data files (now allows import of data in multiple columns). Added helper scripts nCplot.bat/nCplot.sh 
   with which data files (e.g. *.dat) can be associated, to allow double clicking of such files to plot them in neuroConstruct.

-  Added function for generating a *very simple* field potential from the activities of all somas in cell groups (in Analyse drop down box 
   when a simulation is reloaded)

-  Updated Volume based connections to allow such connections within a cell group.

-  Added support for new functions in parsable expressions (e.g. in expression for prob of connection in Volume based connections): H(x), 
   Heaviside function (=0 x<0, =1 otherwise); random(x) for a random number between 0 and x

-  Added links on main NEURON & GENESIS tabs directly to each of the extra code blocks

-  Extra support for gap junctions (no example yet, get in contact if you need one...)

-  Updated examples in pythonNeuroML for creating and for reading in the structure of NetworkML from Python scripts

-  Plotting of rate equations, etc. updated to support new ChannelML format as at: 
   http://www.morphml.org:8080/NeuroMLValidator/NeuroMLFiles/Examples/ChannelML/NaChannel_newFormat.xml

-  Added very provisional mapping to PSICS (get in contact for more info...)

-  Updated examples in pythonnC for controlling neuroConstruct projects via Python/Jython scripts

-  Added initial version of parameterisation over groups (e.g. 0 to 1 from soma to tips of dends) as step to allow inhomogeneous channel dists





-  



--------- Version 1.1.2 (July 08) ---------


-  Morphology based network connection now allows specification of which of the soma/axon/dendrites are allowed for the pre and 
   post synaptic points. This allows the possibility of axo-axonic and dendro-dendritic connections. Previously presynaptic 
   connections were on axons & soma, post were on soma & dendrites. Note though that the actual allowed locations are the 
   intersection of the groups set at Visualisation - View: <Cell> -> Synaptic Conn Locations and the selection of which of 
   soma/axon/dendrites are allowed for pre/post.

-  Autapses can be specifically allowed or disallowed for Morphology based network connections from a Cell Group to itself.

-  Updated to NeuroML version 1.7.2. Added drop down box at Setting -> General Properties where the version of NeuroML to use for
   validation, etc. can be set. If one (or all) of the Cell Mechanisms are selected at tab Cell Mechanims, and the Update
   ChannelML Mappings button is pressed, the XSL files for generating mod files/GENESIS scripts will be updated to the 
   mappings from this version of NeuroML. Note that there was a bug in the NeuroML v1.7.1 XSL mappings included with 
   neuroConstruct v1.1.0 which would lead to an error being thrown if used for synaptic mechanisms in GENESIS. Fixed in current
   specifications.

-  Optimisation of generation of network connections in cells with large morphologies. Also faster generation of NEURON code 
   for larger cells (e.g. Ex10-MainenEtAl).

-  Fixed bug when saving channel conductances in GENESIS. Included plotting/saving of Na & K conductances in Ex4-NEURONGENESIS.

-  Removed option for generating sequences of simulations with different pulse length/amplitude etc. at Input and Output.
   This functionality will be obsolete with the new Python scripting interface. Replaced with option to generate a range of 
   random/gaussian dist values of pulse amp etc. to allow variable input trains to cells in a cell group. These random values
   for the pulse amplitude/duration/delay will be the same in the generated NEURON and GENESIS simulations allowing direct comparison
   of simulations (when dt is small enough!).

-  Added new option in Segment Selector for modifiying the 3D end points of segments. A list of end points can be generated 
   which give a number of (x,y,z) integer value options which keep a specified integer length of the segment. Useful for quickly
   converting a cell to a more representative 3D shape and keeping segment length constant. Thanks to Michele Mattioni (EBI) for
   the suggestion/code.

-  Added option in Plot Frame to move Data Set to another open Plot Frame.

-  Updated run.bat & run.sh to set env variable NC_HOME, which is used to find location of directories for templates, etc. 
   as included with standard neuroConstruct distribution. Useful when starting neuroConstruct from commandline in dir other
   than the install directory.

-  Added Full Net Info button to Generate panel, for a view of all of the generated network info (contains the information
   which would go in a NetworkML file)

-  Fixed bug in NEURON template generation. Was only applicable when: soma is spherical AND (soma is not at origin OR first 
   child segs of soma are not cylindrical).

-  Added new 3D viewing functions. Added network 'slicer' button (button "|" beside buttons "0" and "^" in 3D network view).
   This renders transparent cells outside movable planes perpendicular to X, Y, Z directions. Useful for visualising dense
   networks. Another feature is in the rearranged Simulation Replay panel. When this panel is extended to full (press ">>") 
   a subset of cell groups (or parts thereof) can be specified as the ones to colour during the simulation replay (all other 
   cells black or transparent). Neither of these features are quite finished, but (with patience) can be used for generating 
   interesting screenshots/movies.

-  Initial version of Python scripting interface. To use type 'run.bat -python' or './run.sh -python'. No documentation at 
   the moment, but see test.py in the main directory

-  Added JUnit testing framework & a number of tests on cell structure & NeuroML compatibility. Cleared up minor bugs in 
   saving & loading NetworkML & MorphML

--------- Version 1.1.0 (based on 1.0.9beta) (May 08) ---------


- Added option of saving morphologies in smaller, more efficient format. Existing projects still use old method, 
  new ones use the smaller format by default. See "Morphology save format" in Glossary.

- Changed handling of mod file generation. Biggest practical change is now mod files are only compiled once (the first time 
  NEURON scripts are generated), unless any of the XML/XSL files are altered. An option "Copy sim files to results dir" is added,
  to either: (unselected) use mod files/compiled libraries in the location they're generated (generateNEURON dir, this is default now), 
  or (selected) copy the files to simulations/Sim_xx and use them there. This second option was the previous way of using accessing 
  the mods, and may have been the cause of some problems on Linux in the past. Another option "Generate all mod files" has been added, 
  to compile all mod files in project, even if the cell mechanism isn't used in this simulation configuration.

- NeuroML version 1.7.1 is used. Some of the proposed changes to NetworkML for v2.0 are now included as options, and the old format
  will be disabled in v2.0, see http://www.morphml.org:8080/NeuroMLValidator/ReqVersion2.jsp. The new format is used in the export of 
  NetworkML, but both formats can be loaded back in. 

- NeuroML export tab is slightly updated.

- Ability to translate & rotate child segments when the 3D endpoints of a segment are altered (allows you to rotate a cell to align it to the y axis,
  for example). View single cell in 3D (All solid), click on a segment -> Edit... Also added is function to split a long Section (e.g. 20 Segments)
  into multiple Sections (option in drop down box in Segment Selector dialog).

- Clickable links in panels giving cell info and network generation summary, i.e. cell group names can be clicked on to go to tab Cell Group, selecting that item.

- Cleaned up electrotonic length handling & updated docs/glossary.

- HDF5 support is added for importing plots/generic traces as 1D datasets in HDF5 files (Tools -> Import data for plot (HDF5 File)). 
  Also saving and loading of NetworkML structure in HDF5 (note: provisional structure, no electrical inputs saved, subject to change!)

- NetworkML import/export in XML format includes locations of electrical inputs

- Preliminary version of Python classes for generating network structure & saving in NetworkML (XML or HDF5 format) for loading into 
  neuroConstruct. This will allow network topologies of any given complexity to be built in Python, and saved in NetworkML for
  visualisation & use in nC projects. Will move to a PyNN friendly format over time.

- Corrected bug in equation parser (used for plotting generic expressions for rate variables in ChannelML files). Expressions like
  exp ((-v - 40)/ 10) were being parsed as: exp ((-1 * (v - 40))/ 10)

- Solved bug when Input is placed on, e.g. seg id 0, but no seg id 0 is present in cell. Also resolved problem
  when new Input is added but there's no synaptic mechanism present to use for Random stim.

- Made generation of Matlab and IgorPro extra files for each simulation optional (via Settings. Default: don't generate these extra files)

- Added more options under Help menu item, including link to check for updates.

- For single compartment, spherical cells, the fract along is now always 0.5 in generated network connections

- Can now import GENESIS morphologies which use double_endpoint.

- Gap junctions & point processes (for integrate & fire mechanism) added as possible mechanism types (incomplete)

- Minor additions to project validation: checks if Cell Groups referred to in Elec Inputs and Plots are present in project



--------- Version 1.0.4.1 (Aug 07) ---------


- Only significant update is a bug fix for running NEURON from nC on a Mac (v1.0.4 ran fine on 
  Mac, but couldn't run the generated NEURON scripts). More warnings about installing Developer tools
  (XCode) after installing NEURON on the Mac are included too.



--------- Version 1.0.4 (Aug 07) ---------


- Uses NeuroML v1.6. Changes to that are listed at http://www.morphml.org:8080/NeuroMLValidator/NeuroMLFiles/Schemata/v1.6/RELEASE_NOTES. 
  Main change is addition of <status> element in ChannelML, which is picked up in nC when validating proj with non stable 
  ChannelML elements
  
- Allows user to change default location of new projects, from <user home dir>/nC_projects to wherever (note: no space allowed in dir name)

- Added phase plane plots (dV/dt versus V), for analysis of regular spiking cells, via Plot Info -> Spike Analysis

- Update to options for stimulations (tab Input and Output): pulses can be repeated. Required new version of IClamp.mod (CurrentClampExt)

- Updated import of SWC files. Fixed error of giving segments numbers as names (added suffix Comp_), added a number of options on import and
  now group compartments in unbranched dendrites into Sections with multiple Segments. Note: this will lead to fewer sections when run on NEURON
  but the nseg value will have to be increased in long dendrites (see next point).

- Added changable values for max and min electrotonic length at tab Export Network-> Common Simulation Settings. Added possibility to remesh morphology
  to ensure correct number of internal simulation points/divisions in sections (nseg). Visualise the cell in 3D, showing All Solids, click on any 
  section, then Edit... and select Remesh option in drop down function selector.

- Added more information in network generation summary on total synaptic conductance for post synaptic cells

- Updated import of NeuroML morphologies, to ease NEURON ModelView exported files. 
  See http://neuroml.svn.sourceforge.net/viewvc/neuroml/nrn2NeuroML/ to export cells from NEURON in Level 1 & 2 NeuroML.

- Some extra tool tips added, along with warnings/advice, e.g. info on getting extra memory in run.bat/run.sh. Updated Glossary and added a number of
  new entries.

- Fixed minor bug where project file modified date is changed on loading of project; now reflects when proj last saved

- Caught most (but not all) sources of problems for NEURON/cygwin GENESIS when spaces are present in a
  Windows file/directory name, e.g. C:\Documents and Settings\Padraig Gleeson\nC_projects. Will give specific warnings 
  when spaces are present in a directory name: this can cause errors when file names are handed to the process running NEURON, 
  for example. If an error is thrown, the project should be copied (Save as..) in a dir without spaces in the name.
  
- Added dialog box choice when a previous simulation has been reloaded and generate NEURON/GENESIS is requested.
  Had been a problem that no plots were generated in that case, as no info on plots is stored with simulation structure.
  
- Made generated GENESIS more portable between directories: one variable targetDir specifies where all sim data will be stroed

- Removed use of the NEURON system() calls in generated scripts when running under Windows, to deal with some instability there. 
  Was mainly used for recording of hostname, date, etc.



--------- Version 1.0.1 (Apr 07) ---------


Basically the same as v0.9.8, but with examples outlined in paper included.



--------- Version 0.9.8 (Mar 07) ---------


The first full public release, just before publication of the paper. Uses NeuroML v1.5