neuroConstruct is being developed in the Silver Lab in the
+
+ Department of Neuroscience, Physiology and Pharmacology at
+ UCL. neuroConstruct has been designed to simplify development of complex networks
+ of biologically realistic neurons, i.e. models incorporating dendritic morphologies and realistic cell membrane conductances.
+ It is implemented in Java and generates script files for a number of widely used neuronal simulation platforms
+ (including NEURON,
+ GENESIS, MOOSE,
+ PSICS and PyNN). It uses the
+ latest NeuroML specifications,
+ including MorphML, ChannelML
+ and NetworkML.
The latest version of neuroConstruct (v1.6.0, Aug 2012) is available for download
+ here.
+ The source code is included with this release under GPL.
+
+
+
A paper describing the latest stable version of NeuroML has recently been
+ published: NeuroML: A Language for Describing Data Driven Models of Neurons and
+ Networks with a High Degree of Biological Detail, P Gleeson, S Crook, RC Cannon, ML Hines, GO Billings,
+ M Farinella, TM Morse, AP Davison,
+ S Ray, US Bhalla, SR Barnes, YD Dimitrova,
+ RA Silver, PLoS Comput Biol 2010. It can be downloaded here and it
+ describes in detail the structure of version 1.x (Levels 1-3, MorphML, ChannelML, NetworkML), includes a
+ detailed discussion of the elements present at each level along with example NeuroML code (see the
+ supporting text
+ of the paper), outlines current simulator support, and presents a number of new cell and network models which have recently been
+ converted to the format.
+
+
+
A morphologically detailed CA1 pyramidal
+ cell model and a number of cells from the Traub et al. 2005 thalamocortical
+ network model are available here for download in NeuroML format or as complete neuroConstruct
+ projects for execution on a number of simulation platforms.
+ These models are also included with the latest version of neuroConstruct.
+
+
+
+
+
A recent Nature paper
+ (Jason S. Rothman, Laurence Cathala, Volker Steuber, R. Angus Silver,
+ Synaptic depression enables neuronal gain control. Nature 2009) has used neuroConstruct to investigate
+ a detailed layer 5 pyramidal cell model (Kole et al 2008) with dendritically distributed excitatory and
+ inhibitory synaptic input to look at the effects of short term plasticity on gain control (
+ see project on Open Source Brain).
+
+
+
+
+
The paper describing the application has been published:
+ P. Gleeson, V. Steuber and R. A. Silver, neuroConstruct: A Tool for Modeling Networks of Neurons in 3D
+ Space, Neuron 2007
+ It is available via Open Access here.
+
+
+
+
A more complete list of publications dealing with neuroConstruct and NeuroML can be
+ found here.
+
+
+
+
+
There is a mailing list for neuroConstruct related news (neuroconstruct@ucl.ac.uk).
+ Sign up here.
+
+
+
+
+
+
+
+
+
What is neuroConstruct?
+
+
+
+
Some of the key features of neuroConstruct are:
+
+
+
+
neuroConstruct can import morphology files in GENESIS, NEURON,
+ Neurolucida, SWC and MorphML format for inclusion in single cell or network models, or more abstract cells can also be built manually.
+
+
Creation of networks of conductance based neurons positioned in 3D
+
Simulation scripts can be generated for NEURON,
+ GENESIS, MOOSE, PSICS and
+PyNN based simulators (note: not every project can be generated for every simulator)
+
+
Biophysically realistic cellular mechanisms (synapses/channel mechanisms) can be imported from native script files (*.mod or *.g) or created from templates using ChannelML
+
+
+
Automatic generation of code to record simulation data and visualisation/analysis of data in neuroConstruct
+
+
+
Recorded simulation runs can be viewed and managed through the Simulation Browser interface
+
+
A Python based scripting interface can be used to control model generation and execution, allowing multiple
+ simulations to be run for cell and network model optimisation
+
+
+
+
+
+
+
+
+
+
What isn't neuroConstruct?
+
+
+
+
+
+
neuroConstruct is not a replacement for neural network simulators like NEURON or GENESIS
+
+
+
+
These packages have sophisticated environments for creating neuronal simulations from scratch,
+and controlling all aspects of the simulation run. neuroConstruct automates the generation of script files for
+these platforms, and provides a framework for creating conductance based neuronal models, creating, visualising and
+analysing networks of cells in 3D, managing simulations and analysing network firing behaviour.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
From a88fcf54c7d68cac7cc1f8ecaf922d7f5726e5a9 Mon Sep 17 00:00:00 2001
From: Padraig Gleeson
Date: Mon, 4 Apr 2022 10:25:15 +0100
Subject: [PATCH 02/13] Test add website
---
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rename docs/{XML/xmlForHtml/docs/python.xml => docs/python.html} (59%)
create mode 100644 docs/docs/python/Ex1_CreateNetworkML.py
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create mode 100644 docs/samples/downloads/Ex8_PyNNDemo.ncx.zip
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create mode 100644 docs/samples/downloads/Ex9_Synapses.ncx.zip
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create mode 100644 docs/skin/tigris.js
delete mode 100755 docs/stop.sh
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create mode 100644 docs/webapp/WEB-INF/logs/debug.log
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diff --git a/docs/.cvsignore b/docs/.cvsignore
deleted file mode 100755
index 0622adde..00000000
--- a/docs/.cvsignore
+++ /dev/null
@@ -1,4 +0,0 @@
-helpdocs
-.svn
-website
-api
diff --git a/docs/Dockerfile b/docs/Dockerfile
deleted file mode 100644
index 3ae750ee..00000000
--- a/docs/Dockerfile
+++ /dev/null
@@ -1,3 +0,0 @@
-
-FROM php:7.2-apache
-COPY website/ /var/www/html/
\ No newline at end of file
diff --git a/docs/README b/docs/README
deleted file mode 100755
index 0e5ea1fd..00000000
--- a/docs/README
+++ /dev/null
@@ -1,14 +0,0 @@
-This is the folder for the documentation of neuroConstruct
-
-Contents:
-
-XML: This is the XML source of the documentation. This is translated (via XSL and Forrest
- (http://forrest.apache.org/)) into HTML
-
-website: This is a version of the public website, generated from the contents of XML
-
-helpdocs: This is a version of the documentation with less graphics, used for the neuroConstruct
- internal help viewer
-
-api: This should conatin the Javadoc for the code. To generate this use "ant javadoc".
- See website/docs/install.html
diff --git a/docs/RELEASE_NOTES b/docs/RELEASE_NOTES
old mode 100755
new mode 100644
index 7bfa0076..8cf46262
--- a/docs/RELEASE_NOTES
+++ b/docs/RELEASE_NOTES
@@ -3,6 +3,29 @@ 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
diff --git a/docs/XML/Forrest/.cvsignore b/docs/XML/Forrest/.cvsignore
deleted file mode 100755
index c1d0ded1..00000000
--- a/docs/XML/Forrest/.cvsignore
+++ /dev/null
@@ -1,2 +0,0 @@
-tmp
-build
diff --git a/docs/XML/Forrest/README b/docs/XML/Forrest/README
deleted file mode 100755
index c23c6460..00000000
--- a/docs/XML/Forrest/README
+++ /dev/null
@@ -1 +0,0 @@
-This dir contains the Forrest files for generating the website
diff --git a/docs/XML/Forrest/forrest.properties b/docs/XML/Forrest/forrest.properties
deleted file mode 100755
index 7ab2d056..00000000
--- a/docs/XML/Forrest/forrest.properties
+++ /dev/null
@@ -1,112 +0,0 @@
-# Copyright 2002-2004 The Apache Software Foundation
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-##############
-# Properties used by forrest.build.xml for building the website
-# These are the defaults, un-comment them if you need to change them.
-##############
-
-# Prints out a summary of Forrest settings for this project
-forrest.echo=true
-
-# Project name (used to name .war file)
-project.name=neuroConstruct
-
-# Specifies name of Forrest skin to use
-project.skin=tigris
-#project.skin=pelt
-#project.skin=crust
-
-# comma separated list, file:// is supported
-#forrest.skins.descriptors=http://forrest.apache.org/skins/skins.xml,file:///c:/myskins/skins.xml
-
-##############
-# behavioural properties
-#project.menu-scheme=tab_attributes
-#project.menu-scheme=directories
-
-##############
-# layout properties
-
-# Properties that can be set to override the default locations
-#
-# Parent properties must be set. This usually means uncommenting
-# project.content-dir if any other property using it is uncommented
-
-project.status=${project.home}/status.xml
-project.content-dir=../xmlForHtml
-project.raw-content-dir=../rawHtml
-project.conf-dir=${project.content-dir}/conf
-project.sitemap-dir=${project.content-dir}
-project.xdocs-dir=${project.content-dir}
-project.resources-dir=${project.content-dir}/resources
-project.stylesheets-dir=${project.resources-dir}/stylesheets
-project.images-dir=${project.resources-dir}/images
-project.schema-dir=${project.resources-dir}/schema
-project.skins-dir=${project.content-dir}/skins
-project.skinconf=skinconf.xml
-project.lib-dir=${project.content-dir}/lib
-project.classes-dir=${project.content-dir}/classes
-project.translations-dir=${project.content-dir}/translations
-
-project.build-dir=${project.home}/../../website
-project.site-dir=${project.home}/../../website
-project.temp-dir=${project.home}/tmp
-
-
-
-
-##############
-# validation properties
-
-# This set of properties determine if validation is performed
-# Values are inherited unless overridden.
-# e.g. if forrest.validate=false then all others are false unless set to true.
-#forrest.validate=true
-#forrest.validate.xdocs=${forrest.validate}
-#forrest.validate.skinconf=${forrest.validate}
-#forrest.validate.sitemap=${forrest.validate}
-#forrest.validate.stylesheets=${forrest.validate}
-#forrest.validate.skins=${forrest.validate}
-#forrest.validate.skins.stylesheets=${forrest.validate.skins}
-
-# *.failonerror=(true|false) - stop when an XML file is invalid
-#forrest.validate.failonerror=true
-
-# *.excludes=(pattern) - comma-separated list of path patterns to not validate
-# e.g.
-#forrest.validate.xdocs.excludes=samples/subdir/**, samples/faq.xml
-#forrest.validate.xdocs.excludes=
-
-
-##############
-# General Forrest properties
-
-# The URL to start crawling from
-#project.start-uri=linkmap.html
-# Set logging level for messages printed to the console
-# (DEBUG, INFO, WARN, ERROR, FATAL_ERROR)
-#project.debuglevel=ERROR
-# Max memory to allocate to Java
-forrest.maxmemory=300m
-# Any other arguments to pass to the JVM. For example, to run on an X-less
-# server, set to -Djava.awt.headless=true
-#forrest.jvmargs=
-# The bugtracking URL - the issue number will be appended
-#project.bugtracking-url=http://issues.apache.org/bugzilla/show_bug.cgi?id=
-#project.bugtracking-url=http://issues.apache.org/jira/browse/
-# The issues list as rss
-#project.issues-rss-url=
-#I18n Property only works for the "forrest run" target.
-#project.i18n=true
diff --git a/docs/XML/Forrest/skinconf.xml b/docs/XML/Forrest/skinconf.xml
deleted file mode 100755
index 13cf8a44..00000000
--- a/docs/XML/Forrest/skinconf.xml
+++ /dev/null
@@ -1,407 +0,0 @@
-
-
-
-
-
-
-
-
-
-
-
- true
-
- true
-
- true
-
- true
-
-
- true
-
-
- false
-
-
- true
-
-
- true
- @
-
-
- true
-
-
- neuroConstruct
- Biophysical Neural Network Modelling Software
- http://www.neuroConstruct.org
- images/logoMain.png
-
-
-
-
-
-
-
-
-
- images/favicon.ico
-
-
- 2020
- UCL
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
- p.quote {
- margin-left: 2em;
- padding: .5em;
- font-family: monospace;
- }
-
- code {
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- Funding for this work was received from the Wellcome Trust
- http://www.wellcome.ac.uk/
- images/wct.png
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- Funding for this work was received from the Medical Research Council
- http://www.mrc.ac.uk/
- images/mrcsmall.png
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- Some of thei work took place as part of the EUSynapse Project
- http://www.eusynapse.mpg.de/
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diff --git a/docs/XML/Forrest/status.xml b/docs/XML/Forrest/status.xml
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- Initial Import
-
-
-
-
-
-
-
-
- Customize this template project with your project's details. This
- TODO list is generated from 'status.xml'.
-
-
- Add lots of content. XML content goes in
- src/documentation/content/xdocs, or wherever the
- ${project.xdocs-dir} property (set in
- forrest.properties) points.
-
-
- Mail forrest-dev@xml.apache.org
- with feedback.
-
-
-
-
-
-
diff --git a/docs/XML/README b/docs/XML/README
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-This directory contains the source for the documentation/webpages related to neuroConstruct.
-
-It's originally in the form of XML and is translated (via XSL and Forrest (http://forrest.apache.org/)) to HTML
diff --git a/docs/XML/glossary/Glossary.xml b/docs/XML/glossary/Glossary.xml
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-
-
-
-
-
-
-
-
-
- Cell Type
- A prototype cell containing information on its 3D morphology and the various Cell density mechanisms which determine its
- electrophysiological behaviour.
- Each Cell Group specifies a particular Cell Type and from these networks are built. Cell Types can be hard-coded (e.g. Simple Cell,
- Purkinje Cell)
- (which can form the basis of manually edited Abstract Cells) or ones based on imported morphology files, e.g. using GenesisMorphReader
- where a morphology file (ending in .p) as used in GENESIS is specified (more on importing morphologies). A Cell Type can be checked for
- validity. More on
- Cell Types in the main documentation
-
-
-
-
- Cell Group
- Cell Groups
- A number of cells of the same Cell Type positioned in 3D space.
- These will be laid out relative to a specified Region
- and arranged according to a Packing Pattern. Only Cell Groups
- included in the selected Simulation Configuration will be generated.
-
-
-
- Electrotonic length
- electrotonic length
- This measure of the length of dendrites, etc. as "seen" by electrical charge is dependent on the shape, axial
- and membrane resistance of the section. See the NEURON or GENESIS books for more details. It is important when
- simulating neurons with realistic morphologies that individually simulated points are not too far apart in terms
- of electrotonic length (a max of 0.1 is usually fine, though much smaller is needed if trying to match the behaviour of
- morphologically complex cells between simulators), i.e. a sufficiently fine-graned spatial discretisation
- should be used. Too short an electrotonic length can sometimes lead to problems in numerical integration, and
- neuroConstruct will perform validity checks for both of these (too long and too short). To correct the
- internal number of divisions in a Section to stay below a maximum electrotonic length,
- e.g. on an imported morphology, visualise the cell in 3D, showing all solids, click on any section,
- then Edit... and either manually set the parameter for each Section or select the Remesh option in the drop down function selector. See also the note
- about Compartmentalisations. Note that electrotonic length is dimensionless, and the term space constant
- is used for this measure in microns (see GENESIS book, or Rall's chapter in Koch and Segev 1989).
-
-
-
- Simulation Configuration
- Simulation Configurations
- Most neuroConstruct Projects will illustrate not just a single aspect of a cell
- or network, but will seek to show how the cells react under different inputs, or how a network behaves
- with different Cell Groups/cell populations present, etc. A particular Simulation
- Configuration has a number of Cell Groups, Network Connections, Electrical Inputs, and Plots
- associated with it, along with a simulation duration. As an example, a project accompanying a publication
- might have one Simulation Configuration for each figure in the paper. More on Simulation Configurations in
- the main documentation
-
-
-
- NEURON
- NEURON is a simulation environment for developing and exercising models of neurons and networks of neurons.
- The main tasks of actually simulating what goes on inside the neurons of a network built with neuroConstruct
- is done by simulation packages such as NEURON. The package is available for download here.
- More on importing NEURON models in the main documentation, and information on the interaction
- between neuroConstruct and NEURON on various platforms can be found here.
-
-
-
- Cvapp
- This Java application, developed by Robert Cannon, allows transformation between various morphology formats
- (e.g. from Neurolucida to NEURON or GENESIS), editing of loaded
- morphologies, along with other functions for cleaning up and optimising morphology files. It also has its own
- file format (stored in *.swc files). More information here.
- The Neuromorpho database uses SWC as the format for it's curated morphologies.
-
-
-
- SWC
- The file ending given to morphologies saved in the file format initially developed for Cvapp.
-
-
-
- ASC
- The file ending given to morphologies saved in the file format used by Neurolucida.
-
-
-
- Neurolucida
- A product by MicroBrightField Bioscience which is a system for "3D neuron reconstruction, serial section reconstruction, and anatomical mapping".
- It is a popular product for creating 3D morphological reconstructions of neurons with complex dendritic trees (although this is not the only functionality).
- A number of databases exist containing neuronal information in the file format used by these products (see Neuromorpho.org). neuroConstruct can import these files and extract the
- morphological information to use as the basis of detailed single cell models. See here for more information/limitations.
-
-
-
-
-
- Cell Mechanism
- A general term for an electrophysiological process (currently either a Channel Mechanism, a Synaptic Mechanism or an Ion Concentration) which is placed
- on modelled cell membranes or at the interface of two cells to alter their internal electrical and chemical state.
- More on Cell Mechanisms in the main documentation.
-
-
-
-
- Ion Concentration
- A term used for a mechanism describing how the internal concentration of an ion alters. An example would be a pool of calcium, which decays to a resting value.
-
-
-
-
-
- Action Potential Propagation Speed
- While the 3D structure of axons is important for creating the correct connectivity (e.g parallel fibers in cerebellar granule cells)
- the segments representing these axons need not necessarily be explicitly modelled, indeed physiological data on the channels
- present etc. can be quite difficult to obtain. Instead an average value for the speed of propagation of the Action Potential can
- be used for these segments, with the axonal propagation delay (calculated using the distance along the segments to the last fully modelled segment)
- added to the internal synaptic mechanism delay. To specify sections which should be modelled using Action Potential Propagation Speeds, select
- Cell density mechanism in the drop down box when viewing a single cell in the Visualisation tab. Note that reducing the number of
- explicitly modelled segments will reduce the simulation runtime.
-
-
-
- Cell density mechanism
- A term used to describe the mechanisms which can be applied to cell segments to allow simulation of electrophysiological
- mechanisms. Density refers to the fact that the effect of the mechanism is dependent on the physical size (surface area/length) of the segment. A
- Channel Mechanism is specified as a conductance per unit area, or alternatively an Action Potential Propagation Speed measures the
- rate of propagation of signals along a segment to synaptic connections. Specific capacitance and specific axial resistance can
- be specified on a per group basis also. To specify which cell density mechanisms are present on a cell, select
- Cell density mechanism in the drop down box when viewing a single cell in the Visualisation tab.
-
-
-
-
- Compartmentalisation
- Compartmentalisations
- Imported morphologies (e.g. Neurolucida files) may not always be in the most efficient spatial discretisation
- for a particular simulator (a number of 3D points/diameters can be specified along an unbranched dendrite to describe the structure,
- but these will lead to many segments in a simulator which maps all segments to individual compartments). A Compartmentalisation is a
- reorganisation of the structure of segments/sections to retain as many of the properties the cell which are important for electrophysiological
- simulations (total membrane area, total axial resistance along branches, total length etc.) but enables mapping on to a smaller number of
- simulated compartments. See GENESIS Compartmentalisation. The various Compartmentalisations can be visualised in 3D, see 3D View of Cells.
-
-
-
-
- nseg
- A NEURON section property. See Internal number of divisions.
-
-
-
- Internal number of divisions
- spatial discretisation
- internal number of divisions
- internal divisions
- A Section (in neuroConstruct) can consist of a long list of 3D point/diameters (Segments).
- Not all of this 3D information is relevant when modelling the Sections, sometimes just the surface area/axial resistance at a point
- is sufficient for modelling the dendrite. This is the approach NEURON
- takes modelling cables/sections. For long sections, it is possible to specify a number of internal divisions,
- and the membrane potential at each
- time step is calculated at the centre of each of these divisions (this is also known as setting the spatial discretisation of the
- morphology). The term nseg is used for this number in NEURON (see details in the NEURON book). It is also possible
- to set this parameter for Sections in neuroConstruct. View the cell in 3D (All solid),
- click on a segment, click Edit..., and in the second drop down box, select Section details.
- The number of internal divisions can be chosen automatically too (especially convenient for imported detailed morphologies, after
- the passive electrical properties are set), see electrotonic length. See information too on
- Compartmentalisations.
-
-
-
-
- Section
- Sections
- An unbranched part of a cell morphology, corresponding roughly to the concept of a section in NEURON.
- An example would be a non bifurcating dendritic section, or the soma.
- Each Section contains at least one Segment. The Section provides the start point and
- start radius, and each of the Segments has an end point and radius corresponding to the 3D points along the Section.
- Sections which have similar properties can be assigned to one or more Section Group. All of the Segments
- in a Section are also in these Groups. Note that a Section is referred to as a cable in MorphML. A Section is mapped
- to a section in NEURON, and the start point of this and endpoints of the Segments become the pt3d points along it. GENESIS
- only has the concept of a compartment, so the Segments are each mapped to a compartment as a default (but see GENESIS Compartmentalisation).
-
- See the NeuroML Level 1/MorphML paper for more details
- of the mapping to the different simulation environments.
-
-
-
- Segment
- Segments
- The basic unit of the morphological description of the cell. Segments correspond to the concept of a compartment as
- used in GENESIS. One or more Segments go to make up a Section, which maps to a cable in
- simulation environments using that concept (e.g. the section in NEURON, where the start point of the Section,
- and the Segment end points provide the pt3d points along the section). A Segment has a unique name, an end point, a pointer to
- its Section, a pointer to its parent Segment, and a value for the fraction (0 to 1) of the
- parent Segment's length at which it's connected. The first Segment in a Section can be connected at a point between 0 and 1 along
- its parent segment (which will be in another section) but all other segments need to be connected at the 1 point to their
- parent. Note: there is a difference with how NEURON handles sections, they specify the 0 to 1 point of connectivity along their
- parent section. When there are n Segments in a Section in neuroConstruct, this will translate to a NEURON section with n+1 pt3d points.
- See Section and the NeuroML Level 1/MorphML paper for more details
- of the mapping to the different simulation environments.
-
-
-
-
- GENESIS Compartmentalisation
- This Compartmentalisation for the GENESIS platform is needed since a simple mapping of each Segment in a detailed neuronal reconstruction
- to a compartment for running on GENESIS would lead to too great a spatial discretization. This Compartmentalisation maps the n Segments in each Section
- on to two CYLINDRICAL Sections each of half the original Section length, with the radii chosen to preserve total curved surface area and total axial resistance along
- the length. For sections with large electrotonic length, and which have an internal number of divisions (nseg)
- greater than 2, these cylinders will be split accordingly (e.g for num int divs = 7 or 8, the 2 cylinders will be split in 4 each).
-
-
-
-
- Abstract Cell
- Abstract Cells
- A Cell Type which represents a real neuron, but whose morphology is described with a much reduced number of segments.
- These types of cells are useful for investigating basic electrophysiological properties of cells, or in large networks, where simpler individual cells
- are needed to reduce simulation time. These cells can be created manually by adding a Cell Type based on the included examples (e.g. SimpleCell), viewing in tab Visualisation,
- clicking on one of the segments, and pressing Edit....
-
-
-
- Abstracted Cell Mechanisms
- A Cell Mechanism which has been split between model template and parameters, allowing easy mapping onto
- each of the available simulation platforms. Note: This is a pre-ChannelML approach to implementing
- Cell Mechanisms and shouldn't be used anymore.
-
-
-
- File based Cell Mechanisms
- A Cell Mechanism whose functionality is hard coded in a native simulation environment's scripting language, e.g a mod file
- for NEURON or a GENESIS script file containing a single Cell Mechanism.
- Note: there can be a script for each simulation environment associated with the Cell Mechanism, but it is up to the modeller to ensure they
- produce the same results. Details on how to modify native script files for inclusion in neuroConstruct cells is available in the main documentation
-
-
-
-
- GENESIS
- GENESIS is a general purpose simulation platform which was developed to support the simulation of neural systems
- ranging from complex models of single neurons to simulations of large networks made up of more abstract neuronal components.
- The main tasks of actually simulating what goes on inside the neurons of a network built with neuroConstruct is carried out by simulation packages such as GENESIS.
- GENESIS is available for download here.
-
-
-
- Python
- Python is a scripting language which is becoming increasingly widely used in
- computational neuroscience. Details of the support for Python in neuroConstruct can
- be found here.
-
-
-
- Parallel computing support
- Support for generation of networks for execution in parallel computing environments is in development, concentrating on Parallel NEURON over MPI at present.
- As documentation for this is currently limited, please get in touch for more details.
-
-
-
- NeuroML
- NeuroML, the Neural Open Markup Language, is a model development language in XML
- that provides a common data format for defining and exchanging descriptions of neuronal cell and network models.
- Currently, there are three Levels of compliance to the NeuroML specifications:
-
-
-
Level 1 provides a common data format for neuronal morphology data and metadata. MorphML forms the main part of the specification at this Level.
-
Level 2 builds on Level 1 to include specifications for describing passive membrane properties, and the distributions of channels on neuron models.
- The dynamics of ion channels, synapses, and ion concentration mechanisms can also be described at this Level in ChannelML
-
Level 3 allows networks of cells to be described, either in template form (from which networks can be generated) or as explicit descriptions of
- cell placement and synaptic connectivity. The core of this Level is described in NetworkML. neuroConstruct can save generated networks in
- NetworkML, and load NetworkML files from any other application to use in simulations, provided the cell type/group/network connection names match those in the project.
-
-
- More information on NeuroML is available here, and a web interface for checking the validity of
- any NeuroML file is here. A description of the support
- for NeuroML in neuroConstruct is here.
-
-
-
- MorphML
- MorphML is an language which has been developed (using XML technologies) to allow data on cell morphologies to be
- easily transferred between neuronal simulation applications. More information is available here.
- It is a part of the NeuroML initiative, and is the core of NeuroML Level 1. Detailed specifications of the elements allowed in a MorphML document are
- available here.
- There has been a paper describing this part of the NeuroML language.
- A description of the current support
- for MorphML and NeuroML in general in neuroConstruct is available here.
-
-
-
-
- ChannelML
- ChannelML is a language (using XML technologies) for specifying the dynamics of various subcellular processes
- (Channel Mechanisms, Synaptic Mechanisms, etc.) which are present on biologically detailed model neurons.
- It is a part of Level 2 of NeuroML.
- The ability to model these types of mechanisms is one of the key features of platforms like NEURON or GENESIS, but the implementation
- of the mechanisms is far from trivial, requiring both knowledge of the physiological processes and of a low level programming language. ChannelML seeks to separate the
- electrophysiological data from any specific implementation, defining a template for numerous types of cellular mechanism, containing only the relevant biophysical parameters
- (e.g. reversal potentials, (in)activation rate equations) which can be automatically validated for completeness. These files can then be mapped to
- script files in the language of the target simulator for inclusion in cell models.
- The format for valid ChannelML files is described in an XML Schema document.
- Examples of valid ChannelML files and mappings to simulators can be found
- here, and detailed specifications of the elements allowed in a ChannelML document are
- available here.
- A description of the current support
- for MorphML and NeuroML in general in neuroConstruct is available here and
- details of the process to convert an existing channel script, e.g. a mod file, to ChannelML is outlined here.
-
-
-
-
-
- NetworkML
- NetworkML is a language (based on XML technologies and a HDF5 equivalent in development) to allow data on cell placement and
- connectivity in 3D to be
- easily transferred between neuronal simulation applications. More information is available here.
- It is a part of the NeuroML initiative, and is the core of NeuroML Level 3.
-
-
-
-
-
- HDF5
- HDF5 is a binary file format used for exchanging large amounts of structured data between software applications, widely used in the astrophysics community, among others.
- Libraries for development and an application, HDFView, for viewing the contents of HDF5 files can be obtained here here.
- This format is envisioned to be a useful alternative to text files or XML when exchanging voltage trace (or spike time) data, or network structure information (see NetworkML) between computational neuroscience applications.
-
-
-
-
- XML
- Short for eXtensible Markup Language, XML is a specification developed by the W3C. XML uses a similar tag structure to HTML,
- as used for Web documents. However, it allows designers to create their own customised tags, enabling the definition, transmission, validation,
- and interpretation of data between applications and between organisations. It is useful in the context of neuroscience when it comes to exchanging
- anatomical data, model descriptions, etc. between research groups and simulation environments and is the technology used in specifying the NeuroML language.
-
-
-
-
- NMODL
- Channel Mechanisms and Synaptic Mechanisms can be created in NMODL, and these can be placed in the cells in NEURON simulations.
- More info available here. See here for details on use of NMODL (*.mod) files in neuroConstruct.
-
-
-
- Region
- A volume in 3D space which can be filled with cells. These regions can be also used for specifying bounding regions for selecting cells, e.g. to
- selectively apply stimulations, or to aid in analysis of a subset of cells. In the current version of neuroConstruct, regions can be either rectangular
- boxes, spheres, cylinders or cones. More on Regions in the main documentation
-
-
-
- Channel Mechanism
- An implementation of a model of an electrophysiological process (e.g. a voltage gated ion channel, ion pump, etc.) which is placed
- on modelled cells' membranes to alter their behaviour. For NEURON these are usually implemented in NMODL.
- The preferred way to specify these in neuroConstruct is with a ChannelML file.
-
-
-
- Synaptic Mechanism
- An implementation of a model of synaptic transmission. This is a subtype of a Cell Mechanism. Usually this
- involves an event in one cell influencing the conductance at a point in another cell. For NEURON these are usually implemented
- in NMODL. Synaptic Mechanisms are needed to specify a Synaptic Connection Location on a cell.
-
-
-
-
- Packing Pattern
- When cells are placed in a Region, the somas need to be arranged in a particular pattern. In neuroConstruct, some of the available patterns are:
-
-
Random: Cells are placed in random locations in the Region
-
Cubic Close Packed: Cells are placed in Cubic Close Packed formation. A layer is placed in 2D first and the spheres in the next layer lie on top, at the center of the 4 spheres underneath, touching each. This is optimal packing of spheres in 3D
-
Simple Regular: The cells are placed in layers with cell centres directly above each other
-
Single Placed Cell: A single cell is placed in an exact location in the Region (or relative to the origin)
-
Hexagonal: The cells are placed in a single layer in a hexagonal pattern (each soma is surrounded by 6 other somas at equal angles)
-
One Dimensional Regular Spacing: The cells are placed at regular intervals in a straight line
-
- Note that for each of these packing patterns a number of variables need to be specified, besides the Region, e.g. the number of cells to place, extra cell spacing
- whether to avoid existing cells from this (or other) Cell Groups.
- New packing patterns can be added by extending the Java class CellPackingAdapter.
-
-
-
-
-
-
- Network Connection
- A connection between a number of points on cells in one Cell Group to points in another Cell Group.
- Some of the factors which need to be specified are:
-
-
Source Cell Group: (Presynaptic cells)
-
Target Cell Group: (Post synaptic cells)
-
Synaptic Properties: Which Synaptic Mechanism (under tab Cell Mechanism) defines the synapse, the delay, threshold and weight
-
Method of searching for a connection point (random, closest, etc.)
-
Maximum and minimum lengths of the connection
-
Various conditions on the number of connections to make between the Cells Groups
-
- There are two main types of Network Connection: Morphology Based Connection and Volume Based Connection
- More on Network Connections in this tutorial.
-
-
-
-
- Morphology Based Connection
- This type of Network Connection is appropriate for connecting cells where the axon of the presynaptic cell is well stereotyped
- and does not vary significantly between cells (e.g. parallel fiber of cerebellar granule cell). Cell axons can be created in 3D and a sub set of its sections allowing a certain type of Synaptic Mechanism
- can be specified. For single compartment cell models this type of Network Connection is most appropriate, Section Groupall can be used for
- each synapse.
-
-
-
-
- Arborization Defined Connection
- See Volume Based Connection.
-
-
-
-
- Volume Based Connection
- This type of Network Connection is appropriate for connecting cells where the axon of the presynaptic cell is known to make connections
- within a certain 3D region (e.g. axonal arborisation of cortical pyramidal cell). This region is defined relative to the cell body and dendrites of postsynaptic cells falling within this region allowing the same type of
- Synaptic Mechanism are candidates for connections. These regions are be specified at tab Visualisation in the single cell 3D view when a segment is being edited (select the appropriate function in the drop down box)
-
-
-
-
-
- Glomerulus
- Glomeruli are present in many areas of the CNS. Post synaptic connections from a number of cell types
- converge on a single point on a cell axon. An example would be the Mossy Fiber rosette in the cerebellum, where
- Granule cell dendrites, Golgi Cells axons and dendrites synapse on boutons on the Mossy Fiber axon.
-
-
-
-
-
- Simulation settings
- The main settings for the simulation. Default duration, time interval, default settings for biophysical properties, etc.
-
-
-
-
- Input/Output
- The inputs to the network, what to plot during the simulation run and what to record for playback in neuroConstruct
- can be defined here
-
-
-
-
-
-
-
-
- Finite volume Segment
- A Segment on a Cell in neuroConstruct, which for the purposes of packing
- is considered to take up space. Normally, only Segments in the soma are considered space filling, and will be packed to avoid each other.
- Dendrites and axons are ignored in packing as it would normally be impossible to get these well packed taking into account the dendritic arborisations.
- If large Sections in a specific cell need to be treated differently (e.g. a Glomerulus), these Segments can be specified as having
- finite volume
-
-
-
-
- Group
- See Cell Group or Section Group.
-
-
-
- Section Group
- Section Groups
- A group of Sections sharing some properties. These can be used to specify the Channel Mechanisms placed
- on areas of the cell (e.g. apical dendrites), or the locations where specific Synaptic Mechanisms are allowed (see Synaptic Connection Location).
- There are four special groups:
-
-
all: every Section is included in this Group
-
soma_group: The Group containing only one Section, representing the soma
-
dendrite_group: The Group of dendritic Sections
-
axon_group: The Group of axonal Sections
-
- Every Section is part of one and only one of the last 3 Groups. Sections in groups whose names start with colour_, e.g. colour_Yellow,
- will be coloured as such in the single cell 3D view (these colourings may come from morphology files, e.g. Neurolucida format).
-
-
-
-
- Synaptic Connection Location
- A Synaptic Mechanism can be associated with a list of Section Groups. This means that any of the Sections in those
- Groups can be involved in a Network Connection involving the Synapse type.
- Note: Each of the Sections will also be a member of either soma_group, dendrite_group or axon_group. A PRE synaptic connection location is allowed on Sections in
- soma_group or axon_group while a POST synaptic connection location is allowed on a Section in soma_group or dendrite_group.
-
- See this tutorial for more on Synaptic Connection Locations and Network Connections
-
-
-
- Simply Connected cell
- A Cell where each Segment is connected to either the start of end point (0 or 1) of its parent
-
-
-
- Morphological validity
- For a cell with multiple Sections and Segments, to be considered valid i.e. in a form that will produce sensible,
- similar 3D morphologies in each of the simulators we deal with it should meet the following criteria (not a complete list):
-
-
Only one segment without a parent (root segment)
-
All segments have sections
-
All segments have endpoints
-
All Segment IDs unique
-
All Segment names unique
-
All Section names unique
-
Segments after the first in a section are only connected to 1 on parent
-
At most one segment is spherical and is in the Section Groupsoma_group
-
At least one segment present in cell
-
At least one soma section, i.e. section which is in group soma_group
-
Cell name present
-
- The following checks, when failed, lead to warnings (due to potential problems when packing, for example):
-
-
First soma segment is at origin
-
Start point matches point at specified fraction along parent
-
Cell is a Simply Connected cell
-
Each section is part of one of: soma_group, axon_group, dendrite_group
-
-
-
-
-
- Biophysical validity
- A number of checks can be carried out on the cells in a project to ensure they meet some minimum
- requirements for producing realistic results in the chosen simulators. It is not a complete list. At the moment these checks are:
-
-
At least one membrane mechanism on each segment
-
At least one passive conductance on each segment
-
Each section has an appropriate internal number of divisions for the specified maximum electrotonic length
-
-
- The following checks, when failed, lead to warnings:
-
-
At most one passive conductance on a segment (more than one can lead to erroneous calculations of Electrotonic length)
-
- The intention is to expand these checks to make it easier for non/new computational neuroscientists to catch some
- common errors when creating cell models. If there are any suggestions for checks to be made, please get in touch.
-
-
-
-
- Project validity
- To catch many, but not all, potential sources of error in a project a number of validity checks are performed. These include
- checks on the morphology and biophysical parameters of each of the cells in the project, and various global checks on the project
- settings, e.g. appropriate temperature, electrical input or network connection to all cell groups, etc.
-
-
-
- Validity checks
- validity checks
- Due to the large number of parameters present in a simulation of a network of realistic neurons, a number
- of automated checks have been created to help ensure sensible data is being given to the simulators. Note that these
- are *not complete* and there is still plenty of opportunity for "garbage in, garbage out". There are checks on:
-
-
Morphological validity: the structure of the cells in the project are valid
-
Biophysical validity: the cells in the project have minimal/sensible biophysical properties set
-
Project validity: the above two checks are performed on each of the cells in the project along with a number of other tests
-
- Note: projects/cells will work and native scripts can be generated even when not valid, but the simulation results should be treated as suspect.
-
-
-
-
-
-
- Project Info Tab
- General information on the project
-
-
-
- Cell Type Tab
- Add new Cell Types to the project here. These Cell Types can be based on the existing examples which come with neuroConstruct,
- or can be based on imported morphology files (e.g. GENESIS *.p, Neurolucida, MorphML files. etc.)
-
-
-
- Cell Groups Tab
- Cell Groups are sets of cells of a particular Cell Type, arranged in 3D space according to a pattern. They are the sources and
- targets of Network Connections
-
-
-
- Network Tab
- Specification of the various connections between the Cell Groups
-
-
-
-
- Input Output Tab
- Electrical inputs (e.g. constant current inputs) can be added to the network. Also, specified here are the plots of data to
- show during simulations
-
-
-
- Generate Tab
- Based on the settings in the previous tabs, the network structure, cell positions and synaptic connections can be generated here
-
-
-
- Visualisation Tab
- Single cell types or the whole generated network can be view in 3D here.
- The data saved from recorded simulations can also be visualised here.
-
-
-
-
- Export Tab
- After the network is generated by neuroConstruct, it can be translated to NEURON/GENESIS/etc. code, and the simulation data saved to file
-
-
-
-
-
-
-
-
-
- Tool Tips
- These appear when the cursor hovers over certain buttons, panels, checkboxes, etc. and provide hints on usage.
- They can be turned off via Settings -> General Properties & Project Defaults or by clicking on the button in the main toolbar.
-
-
-
- Project Description
- Enter a short description of the project
-
-
-
- Add New Cell Type
- Adds a new Cell Type from a number of prototype cells, e.g Simple Cell, Purkinje Cell or
- allows importation of a cell in a number of morphology formats, e.g. GENESIS, NEURON
-
-
-
-
- Add New Cell Type From Other Project
- Adds a new Cell Type from an existing neuroConstruct Project. Imports all the cell's Cell Mechanism too
-
-
-
-
-
- Edit Cell Biophysics
- Edit the cell's initial membrane potential, as shown above. Note: can have: 1) A fixed value,
- 2) a random value, between a max and min or 3) a value with a Gaussian distribution. If the value is
- variable, a new value is given to each member of the Cell Group when the simulation code is generated.
-
-
-
-
-
- Add New Region
- Specifies a named region of 3D space where Cell Types can be packed in Cell Groups
-
-
-
- View 3D
- Choose in the drop down box to view either the network created via tab Generate ->
- Generate Cell Positions and Connections or one of the Cell Types added to the project
-
-
-
- Previous Simulations
- If simulations have been run in NEURON/GENESIS, etc. and some parameters have been saved (as specified at the
- Input/Output tab), those simulations will be listed in the Simulation Browser here.
-
-
-
- Elec Input
- Various types of stimulation can be added to the Cell Groups, e.g. current clamp, random spike input
-
-
-
- Where to record
- The membrane potential can be recorded at 1) only the first soma segment, or 2) at every segment in every cell
-
-
-
- GENESIS 3D
- This shows a basic xcell/xdraw with the 3D Network. NOTE: very provisional version! Need to scale it for network
-
-
-
- GENESIS Symmetric
- Symmetrical or asymmetrical compartments. Generally asymmetrical is better as sims are faster. See GENESIS documentation for other details.
-
-
-
- GENESIS Units
- Which set of units to use in the GENESIS simulation (m/s/V or cm/ms/mV, see Help -> Units).
- Note: when simulations are loaded back into neuroConstruct, saved values are converted to neuroConstruct units (um/ms/mV etc.)
-
-
-
-
- GENESIS Num Integration method
- Which numerical integration method to use. See GENESIS documentation for full details.
-
-
-
-
- GENESIS reload
- Untick this checkbox and set a value >0 and neuroConstruct will try to reload a GENESIS/MOOSE simulation after this time.
- This is useful for short simulations which run for less than 10 secs or so.
- Can be used to plot MOOSE simulations, as there is no current native plotting functionality in that simulator.
- Note: neuroConstruct will hang while waiting for the simulation to finish!
-
-
-
- GENESIS abs_refract
- If this option is selected, the presynaptic object will pass spikes in a manner identical to NEURON, i.e. the spikegen will pass a
- spike event on crossing threshold, not pass any event while the presyn location stays above threshold, and resume listening for passing
- threshold once it has gone below again. There will be no extra refractory period.
- If this option is deselected and a value is entered for absolute refractory time, the behaviour will be the default spikegen object behaviour,
- i.e. once a spike event is sent, no more events will be sent for a time abs_refract, and after that time another event will be sent if the
- presyn location is above threshold, even if it has not stopped spiking. This can lead to undesirable behaviour if abs_refract is small or zero.
-
-
-
- NEURON 3D
- This creates a NEURON Shape plot during the simulation, so that the membrane potential of all cells can be visualised (Note: slows simulation)
-
-
-
-
-
-
- Netconngui Name
- The name of this specification of the parameters to generate a network connection
-
-
-
- Netconngui Source Cell Group
- The Cell Group on whose segments the presynaptic interfaces are formed
-
-
-
- Netconngui Target Cell Group
- The Cell Group on whose segments the postsynaptic interfaces are formed
-
-
-
- Netconngui Syn Props
- Properties of the synapse relevant for the NetConn object in NEURON. Which synapse type,
- the delay between reaching the threshold potential and firing, and the distribution of the
- weights for individual synapses.
-
-
-
- Netconngui Syn Props Button
- Click to change synaptic properties
-
-
-
- Netconngui Growth
- There are three options when generating the synaptic connections:
- 1) The cell morphologies remain the same and the synapses simply "jump" across the gap between
- the pre and post synaptic interfaces, with a delay determined by the above synaptic properties,
- 2) The dendritic sections of the target cellgroup are grown to meet the chosen points
- on the pre synaptic axonal sections,
- 3) The axonal sections are grow to meet the dendrites of the target cell group.
-
-
-
- Netconngui Growth Jump
- Cell morphologies remain the same and the synapses simply "jump" across the gap between
- between the pre and post synaptic interfaces, with a delay determined by the above synaptic properties
-
-
-
- Netconngui Growth Dend
- The dendritic sections of the target cellgroup are grown to meet the chosen points
- on the pre synaptic axonal sections
-
-
-
- Netconngui Growth Axon
- The axonal sections are grow to meet the dendrites of the target cell group
-
-
-
-
- Netconngui Search
- The target dendritic sections will be dispersed with respect to the source axonal sections.
- These options specify different ways to search out a corresponding dendritic section to connect to,
- given a fixed pre synaptic connection point on an axonal section
-
-
-
- Netconngui AP Speed
- This speed will be used to calculate the extra delay due to the propagation of the signal along the path
- between the pre and post synaptic connection points (green to red in 3D view) for each connection of this
- type. Typical values are 1000 um/ms (1 m/s) for unmyelinated axons and 100,000 um/ms for myelinated axons.
- NOTE: in most cases these values will result in a negligible extra delay as compared to the internal
- synaptic delay. To completely remove this effect, set the speed to MAX, resulting in zero delay
-
-
-
- Netconngui Inhomogenous Conn Prob
- Enter an expression for the connectivity probability for connecting to a given post synaptic location
- in terms of x,y,z and/or radial distance r, e.g. exp(-1*r/100), all relative to the origin of the cell
- (i.e. coords as used insingle cell 3D view). If this is not set to a uniform probability of 1, the synaptic
- location is calculated as usual, and then a probability of acceptance based on this expression, using the
- post synaptic position relative to the source cell is calculated. If the expression evaluates as negative
- it's rejected, greater than 1 it's accepted.
-
-
-
- Netconngui Search Random
- The post synaptic connection point will be picked completely at random from all allowed dendritic sections
- (quickest method)
-
-
-
- Netconngui Search Random Close
- A limited number of allowed dendritic sections will be selected and the closest of these will be chosen
- (takes longer to generate). Note, as the number gets larger this case will converge to the Closest case
-
-
-
- Netconngui Search Closest
- Every one of the allowed dendritic sections will be tested and the closest one picked
- (takes the longest time to generate)
-
-
-
-
- Netconngui Max Min
- The maximum and minimum distance between the pre and post synaptic connection points (i.e. the grown dendritic/axonal sections).
- For this option to be ignored set max to MAX and min to 0. Note: This option cannot be used with the "Closest" option" above.
-
-
-
- Netconngui Max Min Max
- Any value >0. Set to MAX for no upper limit
-
-
-
- Netconngui Max Min Min
- Any value >0.
-
-
-
- Netconngui Max Min Num Attempts
- The number of failed attempts to allow before giving up. This is only needed with "Completely Random" option above.
- (The program chooses the source cell and searches this number of times for a match in the target cell group)
- For the "Random Close" option, the number to try above is used, but a max/min check is done on each of the chosen
- points before picking the closest.
-
-
-
-
-
-
- Netconngui Max Target
- The maximum number of source cells which can be connected to a target cell, when defining the connection from source to
- target. For example there may be 3 connections from each of source cell A and target cell B is limited to 4 post synaptic connections
-to prevent excessive innervation of any one target cell. The source/target above are reversed if the connection is defined target to source.
-Set to MAX if no restriction applies.
-
-
-
-
-
-
- Simulation def duration
- The default duration for new Simulation Configurations. Note: Simulation Configurations can have different durations.
-
-
-
- Simulation dt
- The time step used by the simulators for numerical integration of the equations governing channel dynamics, etc.
- 0.025 ms is commonly used. Note, this is ignored if a variable time step is specified for the simulation.
-
-
-
-
-
-
-
-
-
- Specify Reference
- If this is checked, the Simulation Reference used will be taken from the text box to the left, and so the same
- simulation directory will be used every time (and files overwritten). If unchecked, the application will automatically
- generate a new Reference every time (Note: this leads to generation of a lot of files)
-
-
-
- Simulation Reference
- A name to give to the stored simulation data. This data can be viewed afterwards via the Visualisation Tab -> Previous Simulations...
-
-
-
-
- NeuronNumInt
- Select this to use the basic variable time step in NEURON. dt will be ignored in this case.
- Note that this variable time step option is normally only useful for single (large) cell simulations.
- If there are multiple independently spiking cells, a small timestep will be needed almost always, and it's
- probably better to just use a small fixed time step.
-
-
-
- NeuronGenAllMod
- Select this to generate and compile all of the mod files that can be generated from the entries at
- the Cell Mechanisms tab. If unselected, only the mod files needed in this Simulation Configuration
- will be generated. Selecting this option is useful if you wish to add extra mechanisms in the
- 'Extra hoc code' blocks, which aren't present in the cell specification.
-
-
-
- NeuronCopySimFiles
-
- Selected: copy the hoc/mod files to simulations/Sim_XXX dir and run them from there
- Advantage: a copy of all files from the simulation are stored; files can be checked, simulation can be rerun at a later stage
-
- Unselected (default): run simulations in the directory the hoc/mod files/compiled libraries are generated in, i.e. generateNEURON
- Advantage: doesn't copy mod files to every simulations/Sim_XXX dir; saves space
- Advantage: more stable under Linux (problems copying the symbolic links generated by mod compilation)
-
- Both options save the results of the simulation in the simulations/Sim_XXX dir. The first option had been used prior to v1.0.7,
- and may have been the cause of some problems on Linux
-
-
-
-
- GenesisMooseMode
- Generate scripts compatible with MOOSE, and run using executable: moose (must be on PATH or present at ~/moose/moose)
-
-
-
- GenesisCopySimFiles
-
- Selected: copy the script files to simulations/Sim_XXX dir and run them from there
- Advantage: a copy of all files from the simulation are stored; files can be checked, simulation can be rerun at a later stage
- Advantage: multiple GENESIS simulations can be generated and run at the same time (doesn't block generateGENESIS dir)
-
- Unselected: run simulations in the directory the GENESIS scripts are generated in, i.e. generateGENESIS
- Advantage: doesn't copy script files to every simulations/Sim_XXX dir; saves space
-
- Both options save the results of the simulation in the simulations/Sim_XXX dir.
-
-
-
- NeuronForceCorrInit
- If this is selected, <initialisation> elements in ChannelML <voltage_gate> elements will be ignored, and the state variables
- will be initialised correctly (e.g. m=minf for v at t=0) as opposed to using this value. The <initialisation> element was introduced to
- test agreement of ChannelML files with incorrectly initialised original mod files.
-
-
- NeuronModSilent
- If this is selected, the mod files will be compiled in the background and not require any user feedback (e.g. Press any key to continue...)
-
-
-
-
-
-
-
- Parameters Tab
- These are parameters which don't usually change during the course of the simulation.
- They are usually set at the start of the simulation.
-
-
-
- Neuron Tab
- The entries for the NEURON block. The overall properties for the mechanism should be placed here.
-
-
-
-
-
-
- Neuron Tab Title
- A title for the mod file. This is completely optional, but is useful for anyone who wishes to reuse the file.
-
-
-
- Neuron Tab Curr Variable
- If there is a current specified, e.g. from an inbserted electrode, specify here
-
-
-
- Neuron Tab Range Variable
- Variables which vary over distance, which are a function of position
-
-
-
- Neuron Tab Global Variable
- Variables which are independent of position
-
-
-
-
-
-
-
- 3D Settings cell colour
- The colour of a single cell when a single cell is being displayed
-
-
-
-
-
-
- 3D Resolution
- A general guide as to how many polygons etc. to use for rendering objects in 3D. Used slightly differently for each
- object, 24 or so is fine normally, 12 generally gives a good rendering for large networks,>100 will result in very smooth
- spheres, etc.
-
-
-
-
-
-
- 3D Transparency
- Selecting this causes all cells to be rendered transparently (the degree of which can be set via 3D Settings)
- except for the selected cell(s) and the pre and post synaptically connected cells to it/them. The selected cell(s) are
- shown in their original colour as set at tab Cell Groups, and the connected cells are shown with a slight transparency
- and shaded with their original colour.
-
-
-
-
-
-
-
- 3D Gui Zoom
- Use this slider to zoom in and away from the image. The rate of zoom is inversely proportional to
- the speed, i.e. move it slowly and the zoom moves quickly. Also, the left and right mouse buttons can
- be used to move the image. If you have a middle button, hold this to zoom.
-
-
-
-
-
- Cell Type View Cell Info
- View a detailed text representation of the morphology of the cell
-
-
-
- Cell Type View Cell in 3D
- View this cell on its own in 3D, using the cell segments' (x,y,z) coordinates
-
-
-
- Cell Type View Memb Mechs
- Edit the Membrane Mechanisms of the cell, e.g. Channel Mechanism density on subsections of the cell,
- the passive properties such as capacitance or axial resistance, or specify an action potential propagation
- speed along axonal sections of the cell
-
-
-
- Cell Type Delete
- Delete from the project the cell type selected above. NOTE: This will render any previously recorded
- simulations using this Cell Type unusable!
-
-
- Cell Type Compare
- Compare morphology, cell mechanisms, synapses of this cell with another in the project
-
-
-
- Cell Type Copy
- Create an exact copy of this Cell Type with a different name
-
-
-
- Cell Type Move
- Moves the cell's internal positions so that the start of the first segment/section is at (0,0,0)
- This is important when the cells are packed together in 3D
-
-
-
- Cell Type Connect
- Moves the start point of sections so that they are connected the specified fraction along their parents.
- The relative positions of child segments is preserved. This may be needed after reading NEURON files which
- specify a connection point on the parent which is incompatible with the 3D info for the points on the segments.
- The electrical properties of the cell are not changed with this, but the cell will look better in 3D. This
- function is similar to calling the define_shape() function in NEURON
- NOTE: It might be wise to make a copy of the cell before changing the segment positions.
-
-
-
- Cell Type Make Simply Connected
- A Simply Connected Cell has each segment connected to either the start of end point (0 or 1) of their parent.
- Pressing this will split the parent segments at the point of connection resulting in 2 new colinear segments
- with the same total length as before, with the child segment connected at their connection point.
-
-
-
-
-
- Morphology save format
- There are two possible ways to save morphologies in neuroConstruct projects, both based on a mapping from the
-set of Java classes describing the cell internally in neuroConstruct:
-
-
XML based Java serialisation (*.java.xml files): a mapping to an XML file of the classes. Note: not any part of NeuroML.
-
Serialised Java object form (*.java.ser files): a serialised representation of the Java classes.
-
-The second of these is quicker to load and save and the files are smaller. The first however can be opened (and edited!)
-with a text editor. Change which format to use via Settings -> General Properties & Project Defaults/Project properties.
-
-Cell morphologies are stored in the morphologies directory of the project home directory. *.bak files in that dir backup
-the previously stored morphology before a new one is saved (if a problem occurs saving a morphology, close the application, remove
-the .bak from the name of the morphology file to use the previous structure of the cell when reloading the project).
-
-Note that the cells aren't currently stored in neuroConstruct projects in NeuroML/MorphML format, since new functionality
-is usually added to the neuroConstruct Cell class before it is supported in the specifications.
-
-
-
-
-
-
-
- Project
- Projects
- projects
- In neuroConstruct, a Project contains the specification of the Cell Types, Regions,
- Cell Groups and Network Connections in a model, along with the simulation parameters (duration, dt,
- etc.) and inputs into the network. A Project can be used to generate networks using combinations of these cells/connections etc. in different Simulation Configurations.
- Also associated with a Project are a number of Previous Simulations,
- i.e. recorded simulations run in a simulation environment (e.g. NEURON) which are available for replaying
- when the project is opened. The main project file (*.neuro.xml) is a proprietary XML file (not part of NeuroML), which should
- only be opened with neuroConstruct (though some minor manual edits are possible if you're careful...). A Project and all of its associated files (morphology files, simulation
- files, etc.) can be zipped up through the GUI for easy distribution.
-
-
-
- Open project
- Open existing neuroConstruct project
-
-
-
- Save project
- Save project and all morphologies
-
-
-
- Close project
- Close current project
-
-
-
- Copy project
- Create copy of main project file and all morphologies and channels (Note: doesn't copy previous simulations)
-
-
-
- Zipped Project
- All files in a neuroConstruct Project (morphology files, simulation data, etc.) can be zipped up into a
- single file for easy distribution/backup. To create a zipped neuroConstruct project select File -> Zip this Project... and to
- automatically unzip and open a file created in this way, select File -> Import Zipped Project...
-
-
-
-
- Import project
- Allows zipped neuroConstruct projects (created with menu item above) to be unzipped and used by the application
-
-
-
- Project properties
- Edit the properties specific to this project
-
-
-
- General properties
- Edit overall application properties, and some default values for new projects
-
-
-
-
- nmodlEditor menu item
- Launch nmodlEditor, used to produce mod files for NEURON channel mechanisms
-
-
-
- Project file source
- View readonly XML file containing project settings
-
-
-
- Condor monitor
- View GUI for checking state of Condor processes (Note: experimental state)
-
-
-
-
- Glossary menu item
- A glossary of some of the common terms in neuroConstruct
-
-
-
- Units menu item
- Outline of the units used by neuroConstruct and the main simulators supported
-
-
-
-
- No Graphics Mode
- Select this to temporarily disable all GUI objects (plots, etc.) even if they are included
- in the Simulation Configuration. Useful to generate an identical simulation but without the performance
- overhead associated with graphical elements.
-
-
-
-
- Generate comments
- Select this to have extra comment lines in the generated scripts, to facilitate readability. Unchecking this
- option keeps the generated files short, and also supresses most of the console output when running the simulation
-
-
-
-
-
- Click sim config
- Click on any Simulation Configuration name to generate that network
-
-
-
-
-
-
- Data Set
- Set of x, y values which can be plotted in a Plot Frame, saved in the Project (for reloading through the Data Set Manager), exported, etc.
- The x values do not have to be evenly spaced, unique or sequential. See here for information on what variables can be saved/plotted during a simulation run.
-
-
-
-
- Plot/Graph
- These terms are used in various ways by NEURON and GENESIS for a) the frame/window showing a number of sets of data and
- b) the individual sets of points in each trace. In neuroConstruct, Data Set is used for a set of points which can be plotted, and
- Plot Frame is used for the window in which a number of these can be viewed. In the Input/Output tab, the second table lists the values to
- to be plotted during a simulation run. For example, the membrane potential of a subset of cells in each group could be plotted. Note that here too is where variables
- to be saved during the simulation are specified, e.g. all cells' membrane potential could be saved but just one specified to be plotted, etc. The names to use for variables
- to plot and/or save are given here
-
-
-
-
-
- Variables to plot/save
- Variables which change during the simulation can be specified to be plotted and/or saved for later display in neuroConstruct via
- the Input/Output tab. Variables have different names in each of the simulation environments (e.g. v or Vm), so a set of
- generic names of the most common interesting values has been defined:
-
-
VOLTAGE for the membrane potential (v in NEURON, Vm in GENESIS)
-
SPIKE can be used to record spike trains, as opposed to voltage at every timestep, e.g. SPIKE:-20 sets the spike threshold to -20mV
-
- To plot a value present on a Cell Mechanism, use a colon, e.g. NaConductance:m. Note, as the gate activation
- variables are a special case, GENESIS will search through the list of gates (only if the Cell Mechanism is defined by a
- ChannelML file), search for a gate with the specified name, and plot that variable. See Ex4-NEURONGENESIS for an example.
- Other named variables that can be plotted for Cell Mechanisms are:
-
-
CONC for the concentration of an ion, e.g. CaPool:CONC:ca
-
REV_POT for the reversal potential of an ion, e.g. NaConductance:REV_POT:na
-
CURR_DENS for the current density through a channel, e.g. NaConductance:CURR_DENS:na
-
COND_DENS for the conductance density of a channel, e.g. NaConductance:COND_DENS:na
-
-
-
-
-
-
- Graph
- See Plot/Graph
-
-
-
-
- Axes in 3D
- A set of axes can be added in 3D (either when a single cell is being displayed or a generated network). The green axis represents
- the x direction, the yellow the y direction and the red the z direction. The axes measure 100 microns from the origin in positive
- and negative directions, the arrow on the positive. The ticks are at 10 micron intervals. Due to perspective the axes should only be
- used for getting bearings/a concept of scale in the 3D scene.
-
-
- Anti Aliasing
- If anti-aliasing is turned on, 3D renderings of both solid compartments and line segments will be smoother. This may have some performance overhead on some video cards,
- or may prevent the 3D view from displaying, and so should be turned off.
-
-
-
-
- Plot Frame
- The window in which a number of Data Sets can be viewed. Each Plot Frame has a name and new Data Sets can be added to existing Plot Frames.
- The Data Sets can be viewed in a number of different ways: all graphs using the same axes, graphs stacked vertically, zoomed in to user selected area, etc. Each Data Set is
- listed and can be individually analysed (e.g. for mean/std dev values, spiking rates calculated) or the format (colour/point type) edited. See here
- for information on what variables can be saved/plotted during a simulation run.
-
-
-
- Data Set Manager
- A number of Data Sets can be stored in a neuroConstruct Project, showing a concept illustrating a point about the model,
- e.g. an I-F curve derived from a number of simulation runs. When a Data Set is viewed in a Plot Frame the points can be saved
- to the project. The Data Set Manager allows these saved Data Sets to be viewed, edited, and redisplayed in a new (or any open) Plot Frame
-
-
-
-
-
- Initial Membrane Potential
- Potential of membrane of all segments at t=0
- Units: mV (typical value for squid: -70 mV)
-
-
-
- Global Membrane Leakage Potential
- Potential of membrane with no other currents as t->infinity
- Units: mV (typical value for squid: -59.4 mV)
-
-
-
- Global specific axial resistance
- Specific cytoplasmic resistance. Multiply by length, divide by cross sectional area for total axial resistance of segment
- Units: Kohm um (typical value for squid: 300 Kohm um)
-
-
-
- Global specific membrane capacitance
- Capacitance of membrane per unit area. Multiply by surface area for total capacitance of segment
- Units: uF/um2 (typical value for squid: 1e-8 uF/um2)
-
-
-
- Global specific membrane resistance
- Specific resistance of membrane. Divide by surface area for total resistance of segment
- Units: Kohm um2 (typical value for squid: 3.3e8 Kohm um2)
-
-
-
- Simulation Temperature
- Temperature at which the simulation is run. Usually only used to change the time course of activation/inactivation
- in HH like channels. Units: celsius
-
-
-
-
-
-
-
- Zoom function
- Zoom in and out of the scene. It's also possible to zoom by holding middle mouse button
- Note: left mouse button rotates scene, right button translates
-
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- 3D View mode
- Choose whether to view the segments as solid, lines, etc. Also a number of views of how the
- morphology can map to NEURON, GENESIS, etc.
-
-
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- 3D Find one cell
- View the cell (and the origin) from a point looking back along the z axis
-
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- 3D Find Regions
- View all the regions from a point looking back along the z axis
-
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- Transparent view
- When multiple cells are present and one is selected all others are made transparent for clarity,
- except for cells to which the selected cell is attached pre or post synaptically
-
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- Find cells
- Refresh the 3D visualisation and relocate the viewpoint at a reasonable distance from all cells
-
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- Reload Simulation List
- Refreshes the list of simulations above. This is in case any simulations finish, and write to file while this window is open
-
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- Highlight pick section/segment
- Allows examination of sections and segments within the cell and editing of the positions, etc.
-
-
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- Highlight channels
- Shows location of channels (active conductances, e.g. Na channels) on the sections
-
-
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- Highlight section types
- Shows which sections are dendrites/axons and which have finite volume (important for packing)
-
-
-
-
- Highlight groups
- Shows which sections are defined to be in groups together. Note all segments in the section are in the group
- and so all segments in one section are assumed to have the same biophysical properties
-
-
-
- Highlight param groups
- Shows the groups which have associated parameter values (e.g. length from soma) which change according to position along sections.
- Used as basis for describing how parameters vary with position for channel mechanisms (e.g. max conductance density varies along dendrites).
- Implementation based on Parameterized Domain Specification in Cell Builder in NEURON.
-
-
-
-
- Highlight syn conn location
- Shows locations of sections where synaptic connections of different types are allowed.
- Note: for each type of synapse, sections also in axon_group or soma_group can have presynaptic
- connection points, while those in dendrite_group or soma_group can have postsynaptic connection points
-
-
-
- Plot View
- Select how the plots should be drawn (stacked, all visible, etc.)
-
-
-
- Plot Difference
- Subtract each of the Data Sets from one another. NOTE: only works if all the Data Sets have the same X values!!
-
-
- Plot Average
- Generate a single graph of the average of each of these graphs at each X value. NOTE: only works if all the Data Sets have the same X values!!
-
-
- Analyse AP shape
- Superimpose the APs made by the selected cells in a given time window for a quick comparison.
-
-
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- Plot Tools
- Some useful tools for generating new Plots based on these Data Sets
-
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- Plot points only
- Fix the axes so every point contained in each Data Set is visible
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- File Based ChannelML
- Adds a ChannelML based Cell Mechanism specifying manually the XML file and an XSL file for each simulator mapping
-
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- Template Based ChannelML
- Adds a ChannelML based Cell Mechanism based on one of the supplied examples
-
-
-
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- Update ChannelML Mechanism
- Updates the mapping files (*.xsl) for each of the simulators to the latest supported NeuroML version for the selected Mechanism
-
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- Reload Cell Mechanism file
- Reloads ChannelML file implementing cell mechanism. Useful if file has been externally edited.
-
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- Save NetworkML
- Saves the generated network (cell positions and network connections) in NetworkML format in the savedNetworks
- folder of the project.
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-
-
- Compress NetworkML
- The saved NetworkML file is zipped when this is selected. This can be opened as normal with gzip, Winzip, etc.
- There should be approx a 90% reduction in file size for a small overhead on saving and reloading time
-
-
-
- Plaintext NetworkML
- The saved NetworkML file will be a plaintext XML file (can be opened in any text editor).
-
-
-
- Extra comments NetworkML
- Some extra information is added as comments in the NetworkML file if this is selected. This information could
- be calculated from the info in the file (e.g. synaptic locations worked out from cell morphology and cell placement)
- but can also be included here for convenience.
-
-
-
- HDF5 NetworkML
- The saved NetworkML file will be in HDF5 format, structured similarly to the XML version.
- Note 1: BETA implementation!! Subject to change!!
- Note 2: File size should reduce when compression is used when saving the HDF5 file.
-
-
-
- HDF5 NEURON Save
- BETA implementation!! Data can be saved after a NEURON simulation (and reloaded in nC) in HDF5 format.
- Note: you need to be able to run "import tables" when NEURON is started in Python mode for this. Install numpy and pytables.
- neuroConstruct has HDF5 reading/writing included as standard.
-
-
-
- Load NetworkML
- Loads a network structure (cell positions and network connections) from a (compressed) file in NetworkML format. The file does not have to
- have been generated by neuroConstruct, but the cell group names, synapse types, etc. should match those in the project.
-
-
-
-
-
- Cell Group Priority
- Specifies the order in which Cell Groups are placed. Higher priority Cell Groups are always placed first.
-
-
-
- 3D View of Cells
- When a single cell is viewed in 3D (at tab Visualisation, select the name of the Cell Type in the drop down box and press View)
- there are a number of actions possible:
-
-
Left click anywhere in the view and drag to rotate the cell
-
Right click anywhere and drag to translate the cell
-
Clicking the middle mouse button and dragging (or turning the middle wheel) will zoom the view. Note that if there
- is no middle button, there is a zoom slider bar on the GUI
-
Pressing the 0 button will reset the view, usually centering on the cell
-
Pressing the ^ button will open a window in full screen with just the 3D objects (good for capturing screenshots)
-
Left clicking on one of Segments will highlight that segment (red) and any other segments in the same Section (yellow) (only when All solid is selected)
-
When a Segment is selected, a summary of the 3D information on it appears, and the endpoints, etc. can be altered by pressing the Edit... button
-
- Specifying Section Groups allows different subsections of the cell to be assigned as dendrites, etc. and can be used to colour regions of the cells.
- When multiple cells are being displayed (e.g. when Latest Generated Positions is selected, or a simulation is reloaded) the following options are also possible:
-
-
Clicking on part of a cell highlights that cell. Note this is easiest when the level of detail displayed is All Solid (see below). Selecting cells can also be
- difficult is other objects are close, e.g. transparent regions, synaptic endpoint spheres, 3D axes (turn some of these off via 3D Settings). If a cell can't be selected by clicking, the cell group and cell number can be selected in the drop down boxes.
-
Multiple cells in a cell group can be selected too via the drop down boxes (e.g. all cells, a percentage of cells, etc.). These can then be plotted together as a group if a previous simulation has been loaded.
-
When one or more cells are selected, checking the Transparent mode box keeps that/those cell opaque, makes cells it is/they are connected to partially transparent and turns other cells almost completely transparent.
-
-
- There are a number of settings which can be changed by pressing the 3D Settings button:
-
-
The background colour and preferred cell segment colour
The resolution of 3D elements. Note for better 3D performance when viewing large cells/networks this should be set low (<12)!
-
A number of items can be excluded or included from the 3D view, e.g. Regions (when viewing generated networks), Inputs, Synaptic Endponts (green for presynaptic location, red for post), etc.
-
The level of detail to display (see below)
-
- The default view for 3D cells is to show all the segments in full solid detail (spheres or cylinders/truncated cones). However this can be too much detail to show on many
- machines for large cells. The following options allow different views of the cells, either at reduced details, or transformed for a particular simulator:
-
-
All solid: all segments are seen in 3D detail. Note the resolution of these can be increased or decreased under 3D Settings
-
Soma solid, neurite lines: segments in the soma group are solid, all other segments are lines through their centres
-
Soma solid, no neurites: just the soma segments are shown in 3D
-
All lines: all segments are represented by lines
-
Original Compartmentalisation: a transparent view of the cell, showing the segments in 3D, white lines through their centres, blue spheres
- for their end points, and yellow lines linking segments which are electrically connected, but not physically linked. There will be a red sphere in
- the middle of each of the internal divisions, with small blue spheres connecting them. These red spheres correspond to the simulated
- points in NEURON as defined by the nseg value.
-
GENESIS Compartmentalisation: this is a Compartmentalisation of the cell which converts it to a smaller number of compartments for GENESIS
- but retains the section groups, total surface area, total dendritic length and total axial resistance.
-
-
- Note: see points on allocating extra memory for the application here, which will be important when displaying large networks in 3D. Also,
- there is sometimes excessive flickering when showing 3D on Windows (a common problem when mixing Java3D and Swing, see here), try updating the drivers for your graphics card, or adding -Dsun.java2d.noddraw=true to the command in nC.bat.
-
-
-
-
-
-
-
diff --git a/docs/XML/glossary/Glossary.xsl b/docs/XML/glossary/Glossary.xsl
deleted file mode 100755
index 0e7a86fb..00000000
--- a/docs/XML/glossary/Glossary.xsl
+++ /dev/null
@@ -1,131 +0,0 @@
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- This XML file was automatically generated from the entries in XML/glossary/Glossary.xml
- and the stylesheet XML/glossary/Glossary.xsl. To add entries to the glossary, edit that original file
- AND NOT THIS ONE!!
-
-
-
-
-
-
- Glossary of the main terms used in neuroConstruct
-
-
-
-
-
-
-
-
-
- #
- -
-
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-
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A Cell Mechanism (previously referred to as Cell Process), as used in neuroConstruct is an abstraction of an electrophysiological mechanism present on a cell.
-
-
The three main types are Channel Mechanism,
- Synaptic Mechanism and Ion Concentration
- (although 2 more: Point process and Gap junction are being added).
- The Cell Mechanisms available in a neuroConstruct project are
- listed under tab Cell Mechanism. New Cell Mechanisms can be added, and the existing ones edited/deleted here.
-
-
There are two ways to create Cell Proceses in neuroConstruct:
-
-
-
ChannelML based Cell Mechanism: The parameters of the Cell Mechanism are stored in a ChannelML file
-
File based Cell Mechanism: The core of the Cell Mechanism is contained in files written in the native language of simulators (e.g. NMODL)
-
-
-
-
The Abstracted Cell Mechanism was an older approach to implementing simulator independent Cell Mechanisms without XML. It is no longer in use.
-
-
Each Cell Mechanism will have:
-
-
-
A unique Mechanism Instance Name by which the Mechanism Model coupled with a specific Parameter Set is known
A Mechanism Model: the conceptual model behind the Cell Mechanism. A Synaptic Mechanism could be modelled as a Double or
- Single Exponential Synapse, for example. ChannelML based Cell Mechanisms have Mechanism Model: Template based ChannelML file
-
A Description, which is a short text description of the Cell Mechanism
-
A Parameter Set for the variables in the model (e.g. a Double Exponential Synapse will have
- rise/decay time of conductance, etc.) In ChannelML based Cell Mechanisms these
- are contained in an XML file
-
Templates containing the mapping to the scripting language of one or more simulation environments (e.g. NEURON, GENESIS)
- for which implementations of the Cell Mechanism are available.
-
-
-
-
- Mapping to simulation environments
-
-
How neuroConstruct creates the native script codes implementing the Cell Mechanisms (mod files/GENESIS scripts) is as follows:
-
-
When the files for a simulation environment (e.g. NEURON) need to be generated, neuroConstruct first checks which
- Cell Mechanisms are included on each of the Cell Types in the network (see below). If there is not an implementation
- of that Cell Mechanism for the simulation environment (i.e. a template of the scripting code is present) an error will be thrown.
-
-
In the case of a File based Cell Mechanisms, the core of the script
- implementing the Cell Mechanism is already present, e.g. an almost complete mod file is specified for a mapping to NEURON. All that
- needs to be replaced in the file is the Cell Mechanism name and a maximum conductance (density), as outlined here.
-These parameters are inserted into the file, a complete native script is generated (and, if needed, compiled) and so the
-Cell Mechanism can be used by other files which define the cells.
-
-
For a ChannelML based Cell Mechanism all of the important parameters are present in the XML file.
-The mappings to native scripts takes place by transforming the XML using an XSL (EXtensible Stylesheet Language) document.
-XSL allows easy transformation of an XML file into another format, basically restructuring the information present in the file.
-XSL documents are present for each simulation environment, which take the values in the ChannelML file (e.g. maximum conductance density)
-and place them in the correct location in partially written native script files. Examples of valid ChannelML files and mappings to simulators can be found
-here, or opening a ChannelML based Cell Mechanism in neuroConstruct
-will allow inspection of the XML, editing of the parameters, validation of the file and preview of the mapping to NEURON or GENESIS
-
-
-
-
-
- Placing Cell Mechanism on Cells
-
-
Cell Mechanism need to be placed on cells before the native script files are generated.
-
-
Inclusion of Synaptic Mechanism on cells is outlined in the Network Connections tutorial.
-
-
To place Channel Mechanisms on cells, go to the tab Visualisation, select the cell
-name in the drop down box and press View.
-
-
Note that Channel Mechanisms, like Synaptic Connection Locations, are associated with
- Section Groups as opposed to sections. Therefore the Groups of Sections which have similar channel densities should be
- constructed first by selecting Groups in the bottom right drop down box. Click Edit Groups,
- or for a simple cell, use the existing Groups. Now select Cell density mechanisms in the drop down box, and
- click Edit Density Mechanisms. In the drop down box of the dialog, all the Cell Mechanism of Mechanism Type:
- Channel Mechanism will be listed (if there are none, go to tab Cell Mechanisms, click Add ChennelML
- from Template and add at least a Leak conductance). Select one of these and for each Group with this Channel
- Mechanism add it to the list. The Max Conductance Density of the channel needs to be specified. NOTE: This overwrites the
- Max Conductance Density as specified in the Parameter Set/ChannelML file. All other parameter values remain the same.
-
-
-
Once a number of channels are added, the densities can be seen back in the Visualisation view.
-For a Channel Mechanism with different densities on different Groups, a shaded colour between the maximum and minimum is shown.
To copy a Cell Mechanism present in one project to another, go to the directory
- cellMechanisms in the project's home directory, and copy the folder named after the cell mechanism into the
-cellMechanisms directory of the target project. That project should now have the cell mechanism listed under the
-tab Cell Mechanisms. Note: make sure there was not already a mechanism with that name before pasting. Also,
-problems may be caused if the project is under version control (CVS or Subversion); remove any CVS or .svn directories from the
-pasted directory.
A prototype cell from which networks are built. There are 3 ways to get new Cell Types into the project:
-
-
Use a hard-coded Cell Types as included with the code. There are a number of simple example cells which (e.g. Simple Cell, Purkinje Cell)
-can be added to the project. Select tab Cell Type -> Add New Cell Type to Project... and choose the
-prototype cell.
-Their initial morphology is hard coded in Java, but they can be edited in tab Visualisations
--> (select the Cell Type in the drop down box) -> View. Select any Segment and press More... to edit (Note:
-it is best to display the cell with segments All solid, to make it easier to select individual segments)
-
-
Cells based on imported morphology files, e.g. GenesisMorphReader where a morphology file (ending in .p) as used in GENESIS is specified.
-Select tab Cell Type -> Add New Cell Type to Project... and choose the morphology importer
-
Cells imported from other neuroConstruct projects: Cell Type -> Add Cell Type from another Project...
Outlined here are the various morphology file importation options available in neuroConstruct.
-
-
Note: it is essential to examine the imported cell
- carefully before using it in any simulation.
- Two potential problems which should be checked are:
-
-
Point of connection of dendritic branches to the soma, e.g. in Neurolucida, there is no explicit soma, but usually an outline.
- There will normally be a root segment added and this can serve as a basis on which to manually build the soma
-
Zero length sections, NEURON is fine with consecutive pt3d points being equal (i.e. segment length zero)
- but the standard mapping of this will result in an error in GENESIS. A check on the
- Cell Validity will reveal any problem segments. (Note that only the first soma segment should be spherical, which is specified by making start point = end point)
-
-
To reiterate, just because a morphology file is successfully imported doesn't mean it is immediately suitable
- for use in a neuronal model. Bear in mind that whoever created the file may have had different goals from creation
- of a single cell model (as with Neurolucida files), or may have created it specifically for a particular simulator, with the
- eccentricities of that platform in mind.
-
-
To import a morphology file: Open a new or existing project, go to tab Cell Types, click on Add New Cell Type... and select one of the
- format specific readers, e.g. GENESISMorphReader.
-
-
- GENESIS
-
-
-
GENESIS morphology files can be imported. These are *.p readcell compatible files. The proper
-format for these files is specified here.
-
-
-
This is a well described format and there exists a number of models containing cells specified in this way.
-However, the whole specification is not supported in neuroConstruct, an inexhaustive compliance list follows:
-
-
Each line is included in the target cell as a Segment with it's own
-Section, i.e. no cables are automatically built
-
Relative or absolute coords are supported, but only cartesian, not polar coords
-
RM, RA, ELEAK, etc are ignored as they usually refer to variables set outside the file
-
When a *compt statement is encountered, a Section group is created for all subsequent segments, until another *compt is encountered
-
*spherical will result in a zero length segment
-
Channel densities after the coords in segment lines are not imported (however, as Section Groups are created
-from the *compt statements, these should be easy to add later)
-
-
-
Note that cells specified in this way assume the target platform is GENESIS and compartmental modelling,
-as opposed to cable modelling, will be used. Therefore the compartmentalisation will not be ideal for platforms such as NEURON.
-This issue has been addressed with the introduction of Compartmentalisations
-
-
-
-
- NEURON
-
-
-
A subset of NEURON files can be imported. In contrast to GENESIS, there is no fixed format in
- NEURON for specifying morphologies (note however, MorphML export is being implemented in a new vesion of NEURON, see
- here) However, a number of models exist with the
- cellular morphology in separate files, many of which were created by the ntscable program. These files are usually characterised
- by a large number of lines of coordinates (lines of 4 floats) containing information accessed previously in the file by the fscan()
- command.
-
-
The following is a summary of what can be imported from a given NEURON morphology file:
-
-
create statements, followed by section (array) names, e.g.: create soma, dendrite_1[31]
-
connect statements, e.g. soma connect dendrite_1[0] (0), 0.5
-
simple for loops
-
pt3dclear() and pt3dadd()
-
fscan() will attempt to retrieve the next float on a line not recognised as one of the previous commands
-
Comments are ignored, forward slashes, used to spread single commands over a number of lines, are recognised as such
-
-
-
This functionality has been tested for a handful of files, but if there are examples of files which you feel are in a
-format which could easily be imported please get in touch
-
-
-
-
-
- Cvapp (SWC files)
-
-
-
The file format used by Cvapp (extension SWC) is also supported. It was developed to
-cover most of the information common between in Neurolucida,
-NEURON and
-GENESIS formats. This format is pretty straightforward, but as mentioned,
-care must be taken with the first soma segment. Check the morphology when imported and ensure the root segment
-is as intended. Note that as of v1.0.4, there was a change in the import of SWC format files, to automatically create
-Sections from the 3D points between splits in the dendritic morphologies, resulting in a
-lower number of Sections but the same number of Segments. See the note on
-Electrotonic length before using those morphologies in simulations.
-
-
-
-
-
- MorphML
-
-
Files can be imported and exported in MorphML format.
-
-
Normally the most recent version of the MorphML specifications will be used by neuroConstruct, but to check compliance,
-this web service should be used.
-
-
There is a close relation between the internal model of a cell in neuroConstruct and the information present in a MorphML file,
-so exporting and importing a cell in this format should lead to identical cells (though the names need to be different
-if they are in the same project).
-
-
-
-
- Neurolucida
-
-
-
The Neurolucida file format is used by MicroBrightField products to store information
-on neuronal reconstructions. Both binary and ASCII format files can be generated by these products, and at this time neuroConstruct can import
-ASCII (*.asc) format V3 files (a heirarchical file structure with "CellBody", "Dendrite", etc). The format allows recording of various anatomical features, not only neuronal processes such as dendrites and cell bodies, but
-can record other microanatomical features of potential interest to anatomists. Not all of these features will be relevant when constructing
-a single cell computational model. Go to Cell Types -> Add New Cell Type and select NeurolucidaReader in the first drop down box.
-Specify the location of the morphology file and choose a name for the Cell Type. A dialog box will be presented with some options as mentioned below.
-
-
-
The main points to note when importing Neurolucida files are:
-
-
-
The soma is normally specified in ASC files as an outline in 2D. An import option is presented for whether to include this information
-in the neuroConstruct cell, to give a visual guideline of where the real soma should be placed. Obviously this will not
-represent a sensible construct to be simulated, and so should be removed before using the morphology (View the cell in 3D with solid Segments,
-select the first Segment in the outline and click on the Edit... button. The whole Section can now be deleted).
-
-
Another import option concerns how to handle the radii of daughter sections.This is important for example when a small dendrite branches off
- from a thick main dendrite. The first point on the small dendrite will have a smaller radius than the thick dendrite, and there are two
- ways to deal with the segment which connects them. The first is to have a truncated cone starting with the larger radius tapering to the
- radius of the first point on the small dendrite. This probably will lead to more surface area on the small dendrite than intended.
- The second option is to have the start radius equal to the end radius on this connecting segment. The choice of which approach to take
- is presented at import of a new Neurolucida file and cannot be changed later.
-
-
-
A root Segment is added to form the basis of the real soma. This can be edited to produce a spherical segment filling the soma outline
-or can be the start of a multi Segment Section representing a soma with complex shape.
-
-
-
Trees will normally be considered dendrites (and so added to the group
-dendrite_group), unless the property (Axon) is found at the start of the tree.
-
As the tree is descended, each line of coordinates will be added as a new Segment. The same Section will be used until
-a branch point is encountered. At this point a child Section will be created. All new Sections will be specified as connected at point 1
-along parent. If the first point on a new Section is equal to the parent endpoint, this point will be used as the start point of a new Section
-and the next line will specify the end point of the first Segment. If the first point on the new Section
-is different from the parent endpoint, a Segment will be added connecting the endpoint to this first point.
-
-
-
Statements such as (Color Red) will cause the following segments to be added to the
-groupcolour_red, etc.
-
All (FilledCircle) type statements highlighting boutons, etc. are ignored.
-
If more than one cell is present in a single ASC file, all info on the dendrites of each cell will be imported, along with
-each soma outline, and a single root Segment will be created. Select which of the cells to save and based on proximity to the soma outline,
-and possibly the colouring, remove all dendritic trees not associated with the chosen cell. In the future,
-a more automated way of separating the cells can be added, if required.
-
-
-
This functionality uses the bulk of the information in Neurolucida files which might be needed for neuronal modelling.
-Please get in contact if there you have example files, some of the information in which you feel could be useful
-in other modelling scenarios.
First you'll need to get the application installed. Click here for instructions
-on the system requirements and installation instructions for neuroConstruct
Details on most of the main terms used in the application are provided in a glossary,
-which provides links to more details on the key concepts used (e.g. Cell Group, Cell Mechanisms)
The source code for the application, as well as instructions for installation can be found: on GitHub.
-
-
-
-
-
-
NOTE: The instructions below are out of date, but may be useful for reference/troubleshooting.
-
-
-
-
-
- Requirements
-
-
neuroConstruct has been tested on on WinXP/NT, Red Hat Linux and openSUSE and Mac OS (please let us know
- if you've any other experiences on other systems).
-
-
A local installation of NEURON,
- GENESIS, MOOSE,
- PSICS or a PyNN compliant simulator
- will be needed to execute the simulation scripts generated by neuroConstruct.
-
- Details of the interaction with these environments is available here.
-
-
-
neuroConstruct will run on most machines which can run Java and Java3D. For networks/cells with >5000 total segments,
- you'll need a fairly modern machine, and the more RAM and graphics memory, the better; 1GB RAM and 128MB graphics is usually fine, higher is better.
- See here for tips on improving graphics performance on slower machines.
-
-
Approx. 130MB of disk space is required for the installation.
-
-
-
Install Java J2SE 5 or higher. Available here. It's better to download the JDK
- (Java Development Kit), which includes command line tools for Java.
-
-
-
From version 1.2.0 the libraries for Java3D are included with the neuroConstruct download.
- There is no need to install this separately. Also, jar files and binaries for HDF5 and
- Jython
- are included with the standard release.
-
-
-
-
- Installation on Windows
-
-
Make sure you have the correct version of Java installed (see above). Open a command prompt (Start -> Programs -> Accessories ->
- Command Prompt) and type java -version. The version should be 1.5 or higher.
-
-
There are 2 options available for installation on a Windows machine: automatic installer or zip file.
-
Automatic installer
-
-
-
-
Download the windows installer from the neuroConstruct download page.
- Note: this is not currently recommended for Vista, Windows 7 or 64bit Windows machines. It's better to use the zip file below instead.
-
-
-
Double click on the downloaded neuroConstruct_windows_1.x.x.exe file (where 1.x.x represents the current version number).
-
-
Select the install location. NOTE: it's best **not** to use a directory with a space in the name (though C:\Program Files on
- 32bit Windows is fine).
- By default the Windows installer puts the code into C:\Program Files\neuroConstruct_1.x.x.
-
-
On Vista and Windows 7, the installed files under C:\Program Files\neuroConstruct_1.x.x have read/write permissions designed
- to make modification of installed files difficult. This has an
- impact on the examples which are under this directory. These problems can be solved by browsing to the folder, and recursively setting
- Full access control for the current user to all files in that directory via right click -> Properties -> Security -> Edit....
-
-
The application can be launched via the desktop icon, or via Start -> Programs -> neuroConstruct_1.x.x -> neuroConstruct_1.x.x.
- There is also a link to the documentation in this menu, or the HTML files which are available at:
- C:\Program Files\neuroConstruct_1.x.x\docs\website\docs.
-
-
neuroConstruct can also be run/rebuilt using the nC.bat script. See points 3, 4 and 5 below. Note also the information there
- about running neuroConstruct with extra RAM.
-
-
-
-
-
Zip file install
-
-
-
Download neuroConstruct_1.x.x.zip from the download page.
- This contains a directory tree from neuroConstruct_1.x.x, containing the main jar file and directories with the examples, documentation, etc.
-
-
Unzip this to a convenient location e.g. to C:\neuroConstruct_1.x.x.
-
-
-
There is a precompiled jar file, (neuroConstruct_1.x.x.jar) present.
- neuroConstruct can be run using this by executing nC.bat, either at the command prompt in the installation directory or
- by double clicking on it in the file explorer. NOTE: you will have to open nC.bat for editing first and change the value
- of NC_HOME to the installation directory.
-
-
The NC_MAX_MEMORY=450M used in this file changes the maximum amount of memory available to the Java Virtual Machine.
- Alter this according to your machine's capabilities (use approx 50% of max memory available).
- NOTE: it's been found that requesting too much memory for neuroConstruct under Windows can result in the application crashing when
- the graphics card is required to display large networks; aim for less than half the available RAM. See points on displaying
- large 3D networks here.
-
-
-
The Java source code of neuroConstruct is included in the src directory. This can be recompiled using: nC.bat -make.
- You'll need the Java compiler at command line (try typing javac -version, and if this fails add the bin
- directory of the installed JDK to the PATH environment variable).
- It is also possible to install Apache Ant and compile (type ant) and run (type ant run)
- the code using the settings in build.xml.
-
-
-
-
-
-
- Installation on Linux
-
-
-
Make sure you have the packages gcc, ncurses and ncurses-devel installed to allow compilation of NEURON mod files. More tips on interaction with NEURON here.
-
-
Make sure you have the correct version of Java installed (see above). Open a terminal window and type java -version.
- The version should be 1.5 or higher. neuroConstruct has to date been developed using Sun's Java SE, as opposed to OpenJDK, and some of the GUI elements
- might look different if using OpenJDK, which is the default option on many Linux distributions. If you find buttons disappearing or labels too large for
- the dialog boxes, try using the Sun JDK instead.
-
-
There are 2 options available for installation on a Linux/Unix machine: automatic installer or zip file.
-
Automatic installer
-
-
-
-
Download the Linux installer from the neuroConstruct download page.
- Note: this is not currently recommended for 64bit Linux machines. It's better to use the zip file below instead.
-
-
-
- Click on the downloaded neuroConstruct_unix_1.x.x.sh file (where 1.x.x represents the current version number), or open a terminal, go to the install
- directory and type ./neuroConstruct_unix_1.x.x.sh. You may need to give exectue permissions to the file first: chmod u+x neuroConstruct_unix_1.x.x.sh.
-
-
-
Select the install location. NOTE: it's best **not** to use a directory with a space in the name.
- A suggested location is /home/username/neuroConstruct_1.x.x.
-
-
-
The application can be launched via the desktop shortcut, though this is not guaranteed to work on all distributions.
- It may be better to open a terminal, go to the install directory and run ./neuroConstruct_1.x.x.
-
-
-
neuroConstruct can also be run/rebuilt using the nC.sh script. See points 3, 4 and 5 below. Note also the information there
- about running neuroConstruct with extra RAM.
-
-
-
-
-
Zip file install
-
-
-
Download neuroConstruct_1.x.x.zip from the download page.
- This contains a directory tree from neuroConstruct_1.x.x, containing the main jar file and directories with the examples, documentation, etc.
-
-
Unzip this to a convenient location e.g. to /home/username/neuroConstruct_1.x.x.
-
-
-
There is a precompiled jar file, (neuroConstruct_1.x.x.jar) present.
- neuroConstruct can be run using this by executing ./nC.sh, either at the command prompt in the installation directory or
- by double clicking on it in the file explorer. You will need to give execute permissions to the file first: chmod u+x nC.sh.
- NOTE: you will have to open nC.sh for editing first and change the value
- of NC_HOME to the installation directory.
-
-
The NC_MAX_MEMORY=450M used in this file changes the maximum amount of memory available to the Java Virtual Machine.
- Alter this according to your machine's capabilities (use approx 50% of max memory available).
-
-
-
The Java source code of neuroConstruct is included in the src directory. This can be recompiled using: ./nC.sh -make.
- You'll need the Java compiler availabe at command line (try typing javac -version).
- It is also possible to install Apache Ant and compile (type ant) and run (type ant run)
- the code using the settings in build.xml.
-
-
-
-
-
-
-
- Installation on Mac
-
-
You'll need to install the Developer Tools (XCode) in addition to the NEURON *.dmg to allow compilation of mod files.
- More tips on interaction with NEURON here
-
-
Make sure you have the correct version of Java installed (see above). Open a terminal window and type java -version.
- The version should be 1.5 or higher.
-
-
There are 2 options available for installation on a Mac machine: automatic installer or zip file.
-
Automatic installer
-
-
-
-
Download the Mac installer from the neuroConstruct download page.
- Note: this is not currently recommended for 64bit Mac machines. It's better to use the zip file below instead.
-
-
-
- Click on the downloaded neuroConstruct_macos_1.x.x.sh file (where 1.x.x represents the current version number), or open a terminal, go to the install
- directory and type ./neuroConstruct_macos_1.x.x.sh. You may need to give exectue permissions to the file first: chmod u+x neuroConstruct_macos_1.x.x.sh.
-
-
-
Select the install location. NOTE: it's best **not** to use a directory with a space in the name.
- The default location is /Applications/neuroConstruct_1.x.x.
-
-
-
The application can be launched via the desktop shortcut, though this is not guaranteed to work on all Mac versions.
- It may be better to open a terminal, go to the install directory and run ./neuroConstruct_1.x.x.
-
-
-
neuroConstruct can also be run/rebuilt using the nC.sh script. See points 3, 4 and 5 below. Note also the information there
- about running neuroConstruct with extra RAM.
-
-
-
-
-
Zip file install
-
-
-
Download neuroConstruct_1.x.x.zip from the download page.
- This contains a directory tree from neuroConstruct_1.x.x, containing the main jar file and directories with the examples, documentation, etc.
-
-
Unzip this to a convenient location e.g. to /home/username/neuroConstruct_1.x.x.
-
-
-
There is a precompiled jar file, (neuroConstruct_1.x.x.jar) present.
- neuroConstruct can be run using this by executing ./nC.sh, either at the command prompt in the installation directory or
- by double clicking on it in the file explorer. You will need to give execute permissions to the file first: chmod u+x nC.sh.
- NOTE: you will have to open nC.sh for editing first and change the value
- of NC_HOME to the installation directory.
-
-
The NC_MAX_MEMORY=450M used in this file changes the maximum amount of memory available to the Java Virtual Machine.
- Alter this according to your machine's capabilities (use approx 50% of max memory available).
-
-
-
The Java source code of neuroConstruct is included in the src directory. This can be recompiled using: ./nC.sh -make.
- You'll need the Java compiler availabe at command line (try typing javac -version).
- It is also possible to install Apache Ant and compile (type ant) and run (type ant run)
- the code using the settings in build.xml.
-
-
-
-
-
-
-
-
-
-
-
-
- Post installation
-
-
-
Check that the location of the NEURON home dir is properly set. Go to Settings -> General Properties & Project
- Defaults for this. Also check on the command line for running executables in a new terminal window via Java.
- The suggested command lines have been tested on WinXP, Red Hat Linux, SUSE and Mac.
-
-
-
When the application is run for the first time, it will create 2 files in a directory .neuroConstruct in your home directory:
-
-
-
-
-
-
{USER_HOME} /.neuroConstruct/neuroConstruct.props
-
Stores project independent information, e.g. default 3D settings, location of NEURON files, etc.
Do not edit these files directly! Use Settings -> General Properties for this.
-
-
-
-
-
-
-
-
-
diff --git a/docs/XML/xmlForHtml/docs/interact.xml b/docs/XML/xmlForHtml/docs/interact.xml
deleted file mode 100755
index 579fb615..00000000
--- a/docs/XML/xmlForHtml/docs/interact.xml
+++ /dev/null
@@ -1,89 +0,0 @@
-
-
-
-
-
- Interacting with native simulators on various platforms
-
-
-
-
Outlined here are some points regarding how neuroConstruct deals with the native simulators on
- various operating systems
-
-
-
- General points
-
-
neuroConstruct is written in Java and so can be used on any platform with a Java Virtual Machine
- together with an implementation of Java3D.
-
In general, NEURON and/or GENESIS should be present on the same machine as neuroConstruct. The scripts for the target platform
- are generated based on the network created by neuroConstruct, and these are set running in separate processes via the
- Java Runtime.exec() command.
-
-
-
-
-
-
- Linux
-
-
NEURON
-
-
NEURON hoc and mod files are generated from the network model in neuroConstruct. First, the mod files are compiled using
- nrnivmodl. This executable is found using the value for the NEURON home directory in Settings ->
- General Properties.
-
-
Once the native machine libraries for the channels are generated, the main hoc file is run with nrngui. Note that
- this is executed in a console window (by prefixing the command with gnome-terminal -x (Gnome desktop) or
- konsole (KDE), also set via Settings -> General Properties)
-
-
GENESIS
-
GENESIS script is generated from the network model and the main file can be run straight away. The genesis command,
- together with the name of the main file are executed via Runtime.exec(), therefore the location of this executable
- should be in the PATH variable. The command is executed in a new console window as above.
-
-
-
-
-
-
- Windows
-
-
NEURON
-
-
NEURON hoc and mod files are generated from the network model in neuroConstruct. First, the mod files are compiled using a command of the form
- C:\nrn60\bin\rxvt.exe -e C:\nrn60\bin\sh C:\nrn60\lib\mknrndll.sh C:\nrn60. The C:\nrn60 is found using the
- value for the NEURON home directory in Settings -> General Properties.
-
-
Once the native machine libraries for the channels are generated, the main hoc file is run with neuron.exe.
-
-
GENESIS
-
GENESIS was for many years not available on Windows. A port has
- recently been created, which while slower than under Linux, can be used to test generated GENESIS code under Windows. The
- following assumes Cygwin has been installed at C:\cygwin and GENESIS installed at /usr/local/genesis i.e.
- C:\cygwin\usr\local\genesis.
-
- GENESIS script is generated from the network model and the main file can be run straight away without further compilation.
- The file {NEUROCONSTRUCT_HOME}/templates/genesisUtils/startxwin2.bat is used to launch the genesis executable.
- This is a slightly modified version
- of the startxwin.bat supplied with Cygwin for running an XTerm. This mechanism is a bit flaky (e.g. it doesn't
- like NEURON running under Cygwin at the same time). Please report any problems/solutions to bugs - at - neuroConstruct.org
-
-
-
-
-
- Mac
-
-
neuroConstruct and its 3D visualisation capability has been successfully tested on the Mac, but the interaction with simulation platforms needs more testing.
- NEURON interaction is fine if the Developer Tools (XCode) are installed. Basic GENESIS interaction has been tried successfully too.
-
If you are interested in helping test the application on this platform, please get in touch
Network Connections in neuroConstruct are made between cells in 2 Cell Groups.
-Before a Network Connection can be made a Synaptic Mechanism (e.g. a Double Exponential Synapse) needs to be
-associated with subsets of dendrites/axons on the Cells in these Groups.
-
-
To add a new Synaptic Mechanism for the project, go to tab Cell Mechanism -> Add ChannelML from Template and
-select the Double Exponential Synapse. Enter the name of the Mechanism and then view and possibly edit the parameters describing it. More info on
-Cell Mechanisms available here
-
-
Go to that tab Visualisation, select the Cell Type which is
-associated with the Cell Group in the drop down box and press View
-
-
-
-
- Specifying Groups
-
-
-
Select Groups in the lower right hand drop down box to view the Section Groups.
-There are four Section Groups always present:
-
-
-
-
-all: Every Section is included in this Group
-
-soma_group: This Group should contain only one Section, representing the soma
-
-dendrite_group: The Group of dendritic Sections
-
-axon_group: The Group of axonal Sections
-
-
-
-
Network Connections will always initiate on a Section in either the soma_group or the
-axon_group. Similarly, the connections will terminate on a Section in either the soma_group
-or the dendrite_group.
Not every Section of the Cell would be a suitable location of a particular synapse,
-so other subgroups can be defined which specify where the connections should be made. By pressing Edit Groups,
-new Section Groups can be made (e.g. basal/apical dendrites, parallel fibers), grouping Sections into biophysically
-interesting regions of the cell.
-
-
Select Synaptic Connection Location in the drop down box. Click Edit Synaptic Locations.
-The added Synaptic Mechanism should be in the drop down list. Select this and then select the Section Groups where the
-synapse can be found.
-
-
It is important to point out again that the PRE synaptic location will be the intersection of the Sections in the (soma_group or the
-axon_group) and the Group(s) selected here. Similarly for the POST synaptic location. Therefore if the
-Group all is selected as a Synaptic Connection Location, synapses can be made on the axons (PRE),
-dendrites (POST) and soma (PRE and POST). However if only the Group dendrite_group is selected as a
-Synaptic Connection Location (or another Group only containing dendrites), then this particular Cell Type will only have
-POST synaptic connections. Axons on another Cell Type will need to be specified as Synaptic Connection Locations for
-this Synaptic Mechanism to make a Network Connection.
-
-
-
-
-
- Creating Network Connections
-
-
Now that it is specified on which parts of the Cells synapses can be made, Network Connections can be created.
-
Go to tab Network Settings and click on Add Network Connection... under Network Connections.
-
-
Select the source Cell Group and the Target Cell Group, ensuring PRE Synaptic Connection Locations are
- allowed on Cell Types of the former and POST Synaptic Connection Locations on Cell Types of the latter.
-
-
-
Select the Synaptic Properties, including which Synaptic Mechanism is involved in the Network Connection, the voltage threshold
- which will cause the synapse to fire, the delay after passing the threshold, and the weight of the synapse. These past two
- values can be given fixed or variable values, in which case a new value will be generated for each instance of the synapse.
-
-
-
Other options include the method for searching for the connection point, the max and min lengths of the allowed
- connections, and a number of other Connection Conditions. These are explained in more detail in the Tool Tips which
- pop up when the cursor hovers over the relevant panel/label. Ensure viewing Tool Tips is enabled in
- Settings -> General Properties & Project Defaults
-
-
-
-
Once a Network Connection is made, generate the network, and view the latest positions in tab Visualisation.
- You will see the generated Network Connections as lines going from green (PRE synaptic location) to red
- (POST synaptic location) between the Sections which are connected by the synapse. If the option is selected in
- 3D Settings a sphere will be placed at each of the Synaptic Endpoints.
-
-
-
-
-
-
-
-
-
-
diff --git a/docs/XML/xmlForHtml/docs/neuroml.xml b/docs/XML/xmlForHtml/docs/neuroml.xml
deleted file mode 100644
index b54a099e..00000000
--- a/docs/XML/xmlForHtml/docs/neuroml.xml
+++ /dev/null
@@ -1,118 +0,0 @@
-
-
-
-
-
- Support for NeuroML in neuroConstruct
-
-
-
-
Listed here are all the possible ways neuroConstruct can import/export data in NeuroML format
-
-
-
-
- Cell morphologies (Levels 1-3)
-
-
neuroConstruct uses an internal data model for cells which is closely linked to MorphML. See
- here for more details.
-
-
-
Level 1: only the anatomy of the cell (MorphML description)
-
IMPORT: go to Cell Types press Add new Cell Type to project... and select NeuroMLConverter in the scroll down menu.
-
EXPORT: go to Export -> NeuroML tab and press Export all Cell Types with the Level 1 button selected,
- a file for each cell type will be saved in the generatedNeuroML folder of the current project.
-
-
-
Level 2: Level 1 plus cell biophysics (passivel electrical properties and channel placement)
-
IMPORT: go to Cell Types tab press Add new Cell Type to project... and select NeuroMLConverter in the scroll down menu.
-Note that there should be channel mechanisms present in the project with names corresponding to those in the <biophysics> element of the file.
-
EXPORT: go to Export -> NeuroML tab and press Export all Cell Types with the Level 2 button selected,
- a file for each cell type will be saved in the generatedNeuroML folder of the current project.
-
-
-
Level 3: Level 2 plus network aspects (allowed locations of synapse types)
-
IMPORT: go to Cell Types press Add new Cell Type to project... and select NeuroMLConverter in the scroll down menu.
-Note that there should be channel and synaptic mechanisms present in the project with names corresponding to those in the <biophysics> and <connectivity> elements of the file.
-
EXPORT: go to Export -> NeuroML tab and press Export all Cell Types with the Level 3 button selected,
- a file for each cell type will be saved in the generatedNeuroML folder of the current project.
-
-
-
-
-
-
-
-
-
- ChannelML
-
-
ChannelML files can be used for Cell Mechanisms in neuroConstruct. They can be used for channels
- (e.g. Na+, K+ distributed ion channels), synapses (fixed and plastic chemical synaptic mechanisms), gap junctions, ion concentrations (e.g. pool of internal
- Ca2+) and point processes (e.g. simple integrate and fire mechanisms). The ChannelML file, a number of XSL mappings to simulators and a properties.xml file are stored for
- each cell mechanism in the cellMechanism folder of a neuroConstruct project. Details of the process to convert an existing channel script, e.g. a mod file, to ChannelML
- is outlined here
-
-
-
-
IMPORT: to use a ChannelML based cell mechanism in neuroConstruct, ensure the file only contains a single
-<channel_type> element, go to the Cell Mechanisms tab, press Create ChannelML Mechanism, name the new mechanism
- and select the file containing the ChannelML description. XSL mappings for
-NEURON and GENESIS can be found under templates/xmlTemplates/Schemata/vx.x.x/Level2 in the local folder of neuroConstruct. Alternatively, a small number of example ChannelML
-mechanisms can be imported (and altered afterwards) by pressing Add ChannelML from Template.
-
-
-
EXPORT: go to Export -> NeuroML tab and press Generate all NeuroML scripts,
- a file for each ChannelML based cell mechanism is saved in the generatedNeuroML folder of the current project.
-
-
-
-
-
-
- NetworkML
-
NetworkML files can be saved and reloaded in neuroConstruct in either XML or HDF5 formats.
-
The NetworkML files read by neuroConstruct can come from any application which generates valid NetworkML, but nothe that the cell group
- and cell type names used in the <populations> element, and the network connection names used in the <projections>
- element must match the names of these already present in the project.
-
Included with neuroConstruct are a number of Python
- scripts, and these allow reading/writing of NetworkML (in the pythonNeuroML/Examples folder in the install directory) and interaction with
- neuroConstruct through Jython to generate a network which can then be saved as NetworkML (e.g. Ex4_SaveNetworkML.py
- in the pythonnC folder in the install directory). More details can be found here.
-
-
-
-
-
IMPORT: go to the Generate tab, press Load NetworkML and select the XML or HDF5 file containing the NetworkML description.
-
-
-
-
EXPORT: go to the Generate tab, press Save NetworkML,
-a NetworkML description of the generated network will be saved in the savedNetworks folder of the current project.
-
-
-
-
- Level 3 NeuroML
-
-
neuroConstruct is able to generate and import and export single files containing all the model elements covered from Levels 1-3.
-This file is fully NeuroML compliant and allow easy exchange of self-sufficient models between neuroConstruct users.
-
-
IMPORT: select File -> Import NeuroML Levels 1, 2, 3... from the main menu and
-select the Level 3 file to be imported. If the file contains elements (e.g. cell types) with the same names as are used
-in the project, warnings will be shown. It is possible to import a Level 3 file into a new, empty project (or select Import NeuroML Levels 1, 2, 3...
-when no project is open) and neuroConstruct specific entities (e.g. 3D Regions) will be created to accomodate the elements in the file.
-
-
EXPORT: go to Export -> NeuroML tab and press Generate all NeuroML scripts with the Generate single NeuroML Level 3 file box ticked,
-a single file containing all the generated elements will be saved in the savedNetworks folder of
-the current project. Tick the Add neuroConstruct annotations box if you wish to include the neuroConstruct
-specific settings like regions, simulation configurations etc. This will still produce a valid NeuroML Level 3 file (other
-applications can ignore these annotations), but this will facilitate importing the model in the file into a new neuroConstruct project.
A volume in 3D space which can be filled with cells. Regions defined at the tab Regions can be also used for specifying bounding regions for selecting cells, for example:
-
-
-
To selectively apply stimulations to a subset of cells, either inside or outside a given region, via tab Input/Output
-
To select a subset of cells in a 3D network visualisation. Select Select many... in the drop down box for Cell Number.
-
To select a subset of cells to analyse (e.g. to generate a rasterplot for) when a previous simulation is reloaded.
-
-
-
-
Regions can also be used for:
-
-
Defining extent in 3D of axonal arbours for use in Volume Based Connections. These can be added in the single cell 3D view when a segment is being edited (select function in drop down box)
-
-
-
-
In the current version of neuroConstruct, these can be
-
-
-
Rectangular boxes (i.e. cuboids): where the width, height and depth are specified, along with the location of one of the lower corners
-
Spheres: the centre point and the radius are specified
-
Cylinders: the centre points of the base and top are specified, as is the radius
-
Cones: the centre points of the base and apex are specified, as is the base radius
-
-
-
-
neuroConstruct can be extended (at the source code level) to include more complex 3D Regions,
-e.g. folium like constructs, etc. by extending the Java class Region.
Most neuroConstruct Projects will illustrate not just a single aspect of a cell
- or network, but will seek to show how the cells react under different inputs, or how a network behaves
- with different Cell Groups/cell populations present, etc. A particular Simulation
- Configuration has a number of Cell Groups, Network Connections, Electrical Inputs, and Plots
- associated with it, along with a simulation duration.
-
-
One of these configurations must be specified
- when the network is generated, indicating which of the aspects of the model is to be simulated. A Default
- Simulation Configuration is always present, and if there is only this one, all new Cell Groups, etc. will be
- automatically associated with it; otherwise new Cell Groups, Network Connections, etc. have to be manually added to
- whichever particular Simulation Configuration they are required for.
-
-
-
Ideally there will be one Simulation Configuration associated with the project for each aspect being illustrated by the model as
- a whole. If the model is accompanied by a paper, this could translate to one Simulation Configuration for each figure. If a published
- model is being reproduced in neuroConstruct, it would be a useful goal to include Simulation Configurations reproducing the figures
- of the paper as closely as possible. New Simulation Configurations can also be added to test new features of the network. Having a number
- of 'working' Simulation Configurations is useful when a model is being developed, as following changes in the cells/cell mechanisms, the
- older Simulation Configurations can be tested to ensure they are still producing the desired results.
These tutorials will give an introduction to the main functionality contained in neuroConstruct
-
Note: These are not intended as introductory tutorials for computational neuroscience.
-
-
-
They assume a
- basic knowledge of the concepts behind simulation of neuronal processes. Introductory tutorials on
- GENESIS or
- NEURON will provide this.
-
-
Very quick
-
-
-
For those with little time on their hands, a very quick tutorial
-gives an insight to the main concepts of neuroConstruct
Enter the project name and the directory in which to place the main project folder. Click OK
-
-
Accept the offer to create a few sample objects in the new project.
-
-
-
Select the tab Generate. Press the Generate Cell Positions and Connections button.
-
-
-
Go to Visualisation. In the drop down box, select Latest Generated Positions.
-Press View. You should see an abstract neuron placed in a 3D box. There will also be a pipette like structure
-signifying an electrical input.
-
-
-
If NEURON or GENESIS are installed (assuming NEURON) go to tab
-Export and select the NEURON tab.
-Select the Show 3D potential plot checkbox, and click Create hoc simulation. This will create the hoc code
-for the main file, and a template for the cell, as well as NMODL code for the channels. The NMODL files
-will be compiled and a confirmation shown. If there is a problem, go to Settings -> General Properties and check location there for the NEURON home directory.
-The contents of the *.mod and *.hoc files can be viewed by selecting the filename and pressing View.
-
-
-
Click on Run Simulation. This should start NEURON and run the simulation you have just created.
-
-
-
Back in neuroConstruct, once the simulation has finished, go to tab Visualisation, and click on Previous Simulations
-You will see a list of all recorded simulations. Click on the simulation just completed and click Load Simulation.
-The generated cell appears again. Press Replay to view the recorded simulation.
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Have a look here to see the various options which can be set when viewing cells in 3D.
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- Tutorial of basic neuroConstruct functionality
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- Set up project and add cell
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Enter the project name and the directory in which to place
- the main project folder. Click OK
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Ignore the offer to create a few sample objects in the new project. That would be too easy.
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Add a Cell Type. Select the tab Cell Types and
-press Add New Cell Type to Project.
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-Add a SimpleCell to the project (select in drop down menu), naming it Simple. More on Cell Types
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Now press the View/edit morphology button below the panel giving details on the cell. This will change to the Visualisation tab and display the cell in 3D. For
- various tips on what's possible when the cell is displayed in 3D see here.
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- Add channel mechanism
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There is a morphologically reasonable cell in the project now, but there is something missing. Click on the Validate button below the main menu.
- This signals the fact that there are no cell density mechanisms present. A cell needs these for simulation of realistic electrophysiological behaviour. Other project or cell specific errors
- will appear here as they occur.
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First a cell mechanism will be added to the project. Go to tab Cell Mechanisms. Click Add ChannelML from Template. This presents a list
- of Channel Mechanisms and Synaptic Mechanisms whose parameters are
- specified in ChannelML that serve as templates for your own channels/synapses. Select Leak Conductance, which represents
-a passive conductance on the membrane of the cell, i.e. current will leak out/in to the cell if its membrane potential is different from the reversal potential of this channel. Press OK
-and accept the name of the cell mechanism. You are presented with a summary of the parameters of the mechanism. Select the second tab ChannelML file to see what's actually in the XML file.
-Note: it is also possible to use a cell mechanism based on a NMODL file or GENESIS channel script. See here for an outline of the process
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Close this and return to Visualisation. Select the cell name in the drop down box and press View. Select Cell density mechanisms in the lower right drop
-down box and press Edit density mechanisms. Under Cell Mechanisms select the mechanism you've just added. Select all and press the right arrow to indicate this mechanism is
-present on all sections. Accept the default value for maximum conductance density. Press OK. Now click Validate again and you'll see that the cell meets the minimum requirements for
-use in a simulation.
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- Packing in 3D
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Now we need to specify a Region in which to place the cells. Go to the tab
- Regions, select Add New Region. Accept the defaults and press OK.
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Go to the tab Cell Groups and click New Cell Group. This results in a dialog to
-specify the name, Cell Type (here the only choice is Simple),
-which Region the cells will be placed in, the colour, and the packing pattern.
-Press the Choose... button next to Packing Pattern. In the field for Cell Number, enter the number
-of cells you want randomly placed in the Region.
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A dialog box will ask if you wish to record the membrane potential of the cell during simulations. Press Yes. It would be good to also view the membrane potential while the simulation is running.
- Go to tab Input/Output. Click on the entry for saving the voltage in the lower table and click Edit selected plot. This dialog specified what variable to save and/or plot during a simulation,
- which cells of the Cell Group to record, etc. In the bottom drop down box select Plot and save. Press OK.
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A stimulation must be applied to the cell or it will be an uninteresting simulation. Still at tab Input/Output,
- select Add electrophysiological input. Keep the default values (a single current pulse on the soma of all cells in the Cell Group) and press Ok.
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Select the tab Generate. Press the Generate Cell Positions and Connections button.
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Go to Visualisation. In the drop down box, select Latest Generated Positions.
- Press View.
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- Running/replaying simulation
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If NEURON or GENESIS are installed (assuming NEURON) go to tab
-Export and select the NEURON tab.
-Select the Show 3D potential plot checkbox, and click Create hoc simulation. This will create the hoc code
-for the main file, and a template for the cell, as well as NMODL code for the channels. The NMODL files
-will be compiled and a confirmation shown.
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Click on Run Simulation. This should start NEURON and run the simulation you have just created.
- If there is a problem starting, and it is installed correctly go to Settings -> General Properties and check the entries there.
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Back in neuroConstruct, once the simulation has finished, go to tab Visualisation, and click on Previous Simulations
-You will see a list of all recorded simulations. Click on the simulation just completed and click Load Simulation.
-The generated cell appears again. Press Replay to view the recorded simulation.
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Select the Cell Group and Cell Number in the drop down boxes followed by Plot selected. This shows the recorded
-voltage trace. Individual cells can also be selected by clicking on them in the 3D view. Note however, if the cell is inside a transparent
-3D Region or if there are other cells close by it may be difficult to select the correct object. Click 3D Settings and deselect displaying of Regions
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- Further things to try...
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Change the layout of the cells generated. In tab Cell Groups, click the table entry under
- Cell Packing Adapter. This will open up the packing pattern dialog. If the random packing adapter is selected,
- the number of cells to pack into the Region can be changed. There are also options to change settings on whether the cell bodies
- can overlap, and whether the whole cell body should stay inside the region, or just the centres. The packing pattern itself can be changed too,
- from randomly placed to a single cell placed at a precise 3D point, a hexagonal pattern, cubic close packed, etc.
- More on the various types of packing patterns available.
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Change the size/shape of the Region. Go to tab Region, select the line with the Region details,
- click on Edit Selected Region, and either change the position and size of the Rectangular region
- or change it to a Spherical Region placed in 3D.
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Edit the morphology of the cell. Go to tab Visualisation, select 3D Settings and make sure display is on All solid
- and the 3D axes are not shown. Save these settings and view the cell you've added. Click on any of the segments. Make sure Pick Segments/Sections is selected
- in the lower right drop down box. It will turn red (if there are any other segments in the same section they will turn yellow). Click on Edit... and you can alter the end points, etc.
- At the drop down box in the Segment selector, there are a number of functions for adding new segments, specifying axonal arbours for Volume Based Connections, etc.
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Add some other Cell Mechanisms to the project (e.g. NaConductance, KConductance) and apply these to the cell membrane in the same way as the leak conductance.
Network Connections in neuroConstruct are made between cells in 2 Cell Groups.
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Run neuroConstruct. Click on File -> New Project.
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-Enter the project name and the directory in which to place the main project folder. Click OK
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-Reject the offer to create a few sample objects in the new project.
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Add 2 cell types to the project. Go to Cell Types -> Add New Cell Type to Project and specify GranuleCell in the drop down box (naming the cell Granule). Add a PurkinjeCell calledPurkinje also.
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Before a Network Connection can be made a Synaptic Mechanism (e.g. a Double Exponential Synapse) needs to be
-associated with subsets of dendrites/axons on the Cells in these Groups.
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To add a new Synaptic Mechanism for the project, go to tab Cell Mechanism -> Add ChannelML from Template and
-select the Double Exponential Synapse. Enter the name of the Mechanism (e.g. PF_Purk_Syn) and the new mechanism will be opened for editing. You can view the HTML representation of the ChannelML file (1st tab) or the original ChannelML file (2nd tab).
-Pressing Validate file will validate the XML against the latest XML Schema file describing the content of ChannelML files. Pressing Generate relevant plots
-creates a plot of the conductance waveform in the file (note the implementation of plot generation is hardcoded in Java for a subset of ChannelML files). The 3rd tab can be used to edit the XML in an external text editor.
-The 4th and 5th tabs show the XSD files which transform the XML into NEURON and GENESIS format.
-More info on Cell Mechanisms available here.
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Go to the tab Visualisation, select View with the granule cell selected in the drop down box.
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- Specifying Groups
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Select Groups in the lower right hand drop down box to view the Section Groups.
-There are four pre defined Section Groups:
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-all: Every Section is included in this Group
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-soma_group: This Group should contain only one Section, representing the soma
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-dendrite_group: The Group of dendritic Sections
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-axon_group: The Group of axonal Sections
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Network Connections will generally initiate on a Section in either the soma_group or the
-axon_group, and the connections will generally terminate on a Section in either the soma_group
-or the dendrite_group. These can be changed at the bottom of the Morphology based connection dialog to allow, e.g. axo-axonic or dendrodendritic
-connections, which can be quite useful for electrical synapses.
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Not every Section of the Cell would be a suitable location of a particular synapse,
- so other subgroups can be defined which specify where the connections should be made. By pressing Edit Groups,
- new Section Groups can be made (e.g. basal/apical dendrites, parallel fibers), grouping Sections into biophysically
-interesting regions of the cell. A Section will always belong to at most one of soma_group, dendrite_group or axon_group.
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For the granule cell, click on Edit Groups, add a new group called parallel_fibers, and add the sections parallelFiberPos and parallelFiberNeg to the group.
Select Synaptic Connection Location in the drop down box. Click Edit Synaptic Locations.
- The added Synaptic Mechanism (PF_Purk_Syn) should be in the drop down list. Select this and then select the Section Group, parallel_fibers, where the
-synapse can be found.
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It is important to point out again that the PRE synaptic location will be the intersection of the Sections specified in the GUI for presynaptic connections (nromally soma_group or the
-axon_group, but see above) and the Group(s) selected here. Similarly for the POST synaptic location. Therefore if the
-Group all is selected as a Synaptic Connection Location, synapses can be made on the axons (PRE),
-dendrites (POST) and soma (PRE and POST). However if only the Group dendrite_group is selected as a
-Synaptic Connection Location (or another Group only containing dendrites), then this particular Cell Type will only have
-POST synaptic connections. Axons on another Cell Type will need to be specified as Synaptic Connection Locations for
-this Synaptic Mechanism to make a Network Connection.
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View the PurkinjeCell now. There should be a group main_dends already defined. Associate this group with the Synaptic Mechanism (PF_Purk_Syn) also.
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- Specifying packing of Cell Groups
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Add 2 regions as in Tutorial 2. Make both rectangular boxes, the first with lower point (0,0,0) measuring 120x50x120 (default values).
- The second region will automatically be placed on top of this starting at (0,50,0) with the same dimensions.
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Add 2 Cell Groups. The first named GranuleCells, associate with the lower region, fill with 12 granule cells (click on Choose... beside Packing Pattern in the New Cell Group dialog
- and enter 12 beside CellNumber). The Second, PurkinjeCell, place in the upper region, and fill with a single Purkinje cell.
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- Creating Network Connections
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Now that it is specified on which parts of the Cells synapses can be made, Network Connections can be created.
Select the source Cell Group (GranuleCells) and the Target Cell Group (PurkinjeCell).
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Select the Synaptic Properties, including which Synaptic Mechanism is involved in the Network Connection, the voltage threshold
- which will cause the synapse to fire, the delay after passing the threshold, and the weight of the synapse. These past two
- values can be given fixed or variable values, in which case a new value will be generated for each instance of the synapse.
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Other options include the method for searching for the connection point, the max and min lengths of the allowed
- connections, and a number of other Connection Conditions. These are explained in more detail in the Tool Tips which
- pop up when the cursor hovers over the relevant panel/label. Ensure viewing Tool Tips is enabled in
- Settings -> General Properties & Project Defaults.
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Once a Network Connection is specified, generate the network, and view the latest positions in tab Visualisation.
- You will see the generated Network Connections as lines going from green (PRE synaptic location) to red
- (POST synaptic location) between the Sections which are connected by the synapse. If the option is selected in
- 3D Settings a sphere will be placed at each of the Synaptic Endpoints.
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- Further things to try...
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Try adjusting the parameters in the Network Connection. Set max and min values for the lengths of the connections. Distances from pre to post synaptic location can be checked by clicking
- Analyse connection lengths after generation of the network.
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Add more Purkinje cells and see how many connections go to each. Select Analyse number of connections at tab Generate.
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Try adding cell mechanisms to the cell as in Tutorial 2, adding input to the Granule cells and running the network. Note these cells are greatly simplified versions of the
- cells in the cerebellum and are unlikely to show very many of the properties of their biological counterparts. Look at the included examples, e.g. GranuleCellLayer.ncx for more realistic cells.