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Fix broken links in documentation
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jessica-mitchell authored Mar 5, 2024
2 parents 4136d6d + 1967302 commit 5639572
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5 changes: 2 additions & 3 deletions doc/htmldoc/connect_nest/using_nest_with_music.rst
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Expand Up @@ -7,7 +7,7 @@ Introduction
------------

NEST supports the `MUSIC interface
<http://software.incf.org/software/music>`__, a standard by
<https://github.com/INCF/MUSIC>`__, a standard by
the INCF, which allows the transmission of data between applications at
runtime [1]_. It can be used to couple NEST with other simulators, with
applications for stimulus generation and data analysis and visualization
Expand All @@ -28,7 +28,7 @@ Reference
.. [1] Djurfeldt M, et al. 2010. Run-time interoperability between neuronal
simulators based on the MUSIC framework. Neuroinformatics, 8.
`doi:10.1007/s12021-010-9064-z*
<http://www.springerlink.com/content/r6j425027lmv1251/>`__.
<https://link.springer.com/article/10.1007/s12021-010-9064-z>`_.
Sending and receiving spike events
----------------------------------
Expand Down Expand Up @@ -384,4 +384,3 @@ which yields the following output:
Nov 23 11:33:28 SimulationManager::run [Info]:
Simulation finished.
(array([ 0., 1., 2., 3., 4., 5., 6., 7., 8., 9.]),)

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Expand Up @@ -76,7 +76,7 @@ Our ``clang-format`` configuration is specified in the
``clang-format`` is run automatically with ``pre-commit``.

We supply the
`build_support/format_all_c_c++_files.sh <https://github.com/nest/nest-simulator/blob/master/build_support/format_all_c_c++_files.sht>`_
`build_support/format_all_c_c++_files.sh <https://github.com/nest/nest-simulator/blob/master/build_support/format_all_c_c++_files.sh>`_
shell script to run ``clang-format`` manually:

.. code-block:: bash
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Expand Up @@ -83,7 +83,7 @@ Coding style

In the following the coding style guidelines are explained by example and some
parts are adopted from `Google C++ Style
Guide <https://google-styleguide.googlecode.com/svn/trunk/cppguide.html>`_.
Guide <https://google.github.io/styleguide/cppguide.html>`_.

The #define guard
~~~~~~~~~~~~~~~~~
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Expand Up @@ -267,7 +267,7 @@ Roles look like this ``:role-name:`content```.
We will only cover a few examples here. You can find more information at the following links:


* `reStructuredText User Documentation <https://docutils.sourceforge.io/rst.html#id24>`_
* `reStructuredText User Documentation <https://docutils.sourceforge.io/rst.html>`_

* `reStructuredText Primer <https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html>`_

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Expand Up @@ -197,7 +197,7 @@ It is extremely important to work on the latest available source code. If you
work on old code, it is possible that in the meantime, someone else has
already made more changes to the same files that you have also edited. This
will result in `merge conflicts
<https://git-scm.com/book/en/v2/Git-Branching-Basic-Branching-and-Merging#Basic-Merge-Conflicts>`_
<https://git-scm.com/book/en/v2/Git-Branching-Basic-Branching-and-Merging>`_
and resolving these is extra work for both the development team and you. It
also muddles up the ``commit history`` of the source code.

Expand Down Expand Up @@ -326,7 +326,8 @@ Creating a pull request

When you feel your work is finished, you can create a pull request (PR). GitHub
has a nice help page that outlines the process for
`submitting pull requests <https://help.github.com/articles/using-pull-requests/#initiating-the-pull-request>`_.
`submitting pull requests
<https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests#initiating-the-pull-request>`_.

Please check out our :ref:`coding style guidelines <code_style_cpp>` and
:ref:`code review guidelines <code_guidelines>` prior to submitting it.
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Expand Up @@ -243,7 +243,7 @@ Read the Docs
NEST documentation is hosted on Read the Docs. If you would like to view the documentation
on Read the Docs, you can set up your own account and link it with your Github account.

See `this guide <https://docs.readthedocs.io/en/stable/intro/import-guide.htmli>`_
See `this guide <https://docs.readthedocs.io/en/stable/intro/import-guide.html>`_
for more information.

.. toctree::
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6 changes: 3 additions & 3 deletions doc/htmldoc/developer_space/workflows/nest_with_ides.rst
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Expand Up @@ -276,7 +276,7 @@ We present two ways to install the rest: MacPorts and Homebrew. For both version
Homebrew
^^^^^^^^

1. Follow the install instructions for Homebrew (`short <http://brew.sh/>`_) or `long <https://github.com/Homebrew/homebrew/blob/master/share/doc/homebrew/Installation.md#installation>`_)
1. Follow the install instructions for Homebrew (`short <http://brew.sh/>`_) or `long <https://github.com/Homebrew/brew/blob/master/docs/Installation.md>`_)
2. Open up the Terminal and execute the following lines:

.. code-block:: sh
Expand Down Expand Up @@ -430,8 +430,8 @@ Setting up the CMake configuration in CLion has the following advantages:
.. note::
`CLion <https://www.jetbrains.com/clion/>`_ is a commercial product. It is *your responsibility* to ensure that you have a valid
license permitting you to use CLion (or any software product) for your work on the
NEST Simulator.
license permitting you to use CLion (or any software product) for your work on the
NEST Simulator.
Setting up the project
~~~~~~~~~~~~~~~~~~~~~~
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2 changes: 1 addition & 1 deletion doc/htmldoc/faqs/faqs.rst
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Expand Up @@ -11,7 +11,7 @@ Installation
known issue in some :hxt_ref:`MPI` implementations. A solution is to add
--with-debug="-DMPICH\_IGNORE\_CXX\_SEEK" to the configure command
line. More details about this problem can be found
`here <http://www-unix.mcs.anl.gov/mpi/mpich/faq.htm#cxxseek>`__
`here <https://www.mpich.org/#cxxseek>`__

2. **Configure warns that Makefile.in seems to ignore the --datarootdir
setting and the installation fails because of permission errors**
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4 changes: 2 additions & 2 deletions doc/htmldoc/faqs/qa-precise-spike-times.rst
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Expand Up @@ -29,7 +29,7 @@ Questions and answers about precise neurons
models relevant to Computational Neuroscience the dynamics of the single
neuron is not. Examples are integrate-and-fire models with linear
:hxt_ref:`subthreshold dynamics` and the AdEx model considered in `Hanuschkin
(2010) <http://dx.doi.org/10.3389/fninf.2010.00113>`__. In these cases
(2010) <https://doi.org/10.3389/fninf.2010.00113>`__. In these cases
it is possible to study the accuracy of a solution of the single neuron
dynamics.

Expand Down Expand Up @@ -61,7 +61,7 @@ Questions and answers about precise neurons
A: Although the networks dynamics is chaotic, in some cases mesoscopic
measures of network activity can be affected by the quality of the
single neuron solver. For example, `Hansel et al.
(1998) <http://dx.doi.org/10.1162/089976698300017845>`__ showed that a
(1998) <https://doi.org/10.1162/089976698300017845>`__ showed that a
measure of network synchrony exhibits a considerable error if the single
neuron dynamics is integrated using a grid-constrained algorithm.
Without confidence in the precision of the single neuron solver we
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2 changes: 1 addition & 1 deletion doc/htmldoc/installation/user.rst
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Expand Up @@ -84,7 +84,7 @@ Options for Windows users |windows|
------------------------------------

Please note that NEST does not officially support Windows. Members of our community have had success
using NEST on Windows with the `Windows Subsystem for Linux <https://ubuntu.com/tutorials/install-ubuntu-on-wsl2-on-windows-11-with-gui-support#1-overview>`_.
using NEST on Windows with the `Windows Subsystem for Linux <https://ubuntu.com/tutorials/install-ubuntu-on-wsl2-on-windows-11-with-gui-support>`_.
You can also try our :ref:`docker container <docker_win>`.

.. |linux| image:: ../static/img/linux.png
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4 changes: 2 additions & 2 deletions doc/htmldoc/model_details/HillTononiModels.ipynb
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@@ -1,5 +1,5 @@
{
"cells": [
"cells": [
{
"cell_type": "markdown",
"metadata": {},
Expand All @@ -10,7 +10,7 @@
"\n",
"## Background\n",
"\n",
"This notebook describes the neuron and synapse model proposed by Hill and Tononi in *J Neurophysiol* 93:1671-1698, 2005 ([doi:10.1152/jn.00915.2004](http://dx.doi.org/doi:10.1152/jn.00915.2004)) and their implementation in NEST. The notebook also contains some tests.\n",
"This notebook describes the neuron and synapse model proposed by Hill and Tononi in *J Neurophysiol* 93:1671-1698, 2005 ([doi:10.1152/jn.00915.2004](https://doi.org/doi:10.1152/jn.00915.2004)) and their implementation in NEST. The notebook also contains some tests.\n",
"\n",
"This description is based on the original publication and publications cited therein, an analysis of the source code of the original Synthesis implementation kindly provided by Sean Hill, and plausibility arguments.\n",
"\n",
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19 changes: 9 additions & 10 deletions doc/htmldoc/model_details/aeif_models_implementation.ipynb
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@@ -1,5 +1,5 @@
{
"cells": [
"cells": [
{
"cell_type": "markdown",
"metadata": {},
Expand Down Expand Up @@ -48,15 +48,14 @@
"\n",
"The reference solution is implemented using the LSODAR solver which is described and compared in the following references:\n",
"\n",
"* http://www.radford.edu/~thompson/RP/eventlocation.pdf (papers citing this one)\n",
"* http://www.sciencedirect.com/science/article/pii/S0377042712000684\n",
"* http://www.radford.edu/~thompson/RP/rootfinding.pdf\n",
"* https://computation.llnl.gov/casc/nsde/pubs/u88007.pdf\n",
"* http://www.cs.ucsb.edu/~cse/Files/SCE000136.pdf\n",
"* http://www.sciencedirect.com/science/article/pii/0377042789903348\n",
"* http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.455.2976&rep=rep1&type=pdf\n",
"* https://theses.lib.vt.edu/theses/available/etd-12092002-105032/unrestricted/etd.pdf"
]

"* Shampine LF, and Thompson S. (2000). Event location for ordinary differential equations. Computers and Mathematics with Applications, 39(5–6), 43–54. https://doi.org/10.1016/S0898-1221(00)00045-6 \n",
"* Thompson S (1987). A collection of test problems for ordinary differential equation solvers which have provisions for rootfinding (ORNL/TM-9912, 6111421; p. ORNL/TM-9912, 6111421). https://doi.org/10.2172/6111421 \n",
"* Dieci L, and Lopez L (2012). A survey of numerical methods for IVPs of ODEs with discontinuous right-hand side. Journal of Computational and Applied Mathematics, 236(16), 3967–3991. https://doi.org/10.1016/j.cam.2012.02.011 \n",
"* Hindmarsh, AC (1983). ODEPACK, a systematized collection of ODE solvers. In R. S. Stepleman & others (Eds.), Scientific computing (Vol. 1, pp. 55–64). North-Holland. https://computing.llnl.gov/sites/default/files/u88007.pdf \n",
"* Petzold L. (1983). Automatic Selection of Methods for Solving Stiff and Nonstiff Systems of Ordinary Differential Equations. SIAM Journal on Scientific and Statistical Computing, 4(1), 136–148. https://doi.org/10.1137/0904010 \n",
"* Kahaner DK, Lawkins WF, and Thompson S. (1989). On the use of rootfinding ODE software for the solution of a common problem in nonlinear dynamical systems. Journal of Computational and Applied Mathematics, 28, 219–230. https://doi.org/10.1016/0377-0427(89)90334-8 \n"
]
},
{
"cell_type": "markdown",
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2 changes: 1 addition & 1 deletion doc/htmldoc/neurons/exact-integration.rst
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Expand Up @@ -208,7 +208,7 @@ Every matrix entry is calculated twice. For inhibitory postsynaptic inputs (with

The update is performed `here <https://github.com/nest/nest-simulator/blob/b3fc263e073f46f0732c10efb34fcc90f3b6771c/models/iaf_psc_alpha.cpp#L305-L307>`_. The first multiplication evolves the external input. The others are the multiplication of the matrix :math:`e^{Ah}` with :math:`y` (for inhibitory and excitatory inputs).

If synaptic and membrane time constants become very close, :math:`\tau_m\approx \tau_{syn}`, the matrix :math:`e^{Ah}` becomes numerically unstable. NEST handles this gracefully as described in the `IAF Integration Singularity notebook <model_details/IAF_Integration_Singularity.ipynb>`_.
If synaptic and membrane time constants become very close, :math:`\tau_m\approx \tau_{syn}`, the matrix :math:`e^{Ah}` becomes numerically unstable. NEST handles this gracefully as described in the `IAF Integration Singularity notebook <../model_details/IAF_Integration_Singularity.ipynb>`_.


For more information see [1]_.
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15 changes: 6 additions & 9 deletions doc/htmldoc/neurons/simulations_with_precise_spike_times.rst
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Expand Up @@ -15,7 +15,7 @@ neurons can propagate their state variables for an entire *h*-step
without interruption by incoming spikes. This enables faster simulations
of neurons with linear sub-threshold dynamics as a precomputed
propagator matrix for a time step of fixed size *h* can be employed
(`Rotter & Diesmann, 1999 <http://dx.doi.org/10.1007/s004220050570>`__).
(`Rotter & Diesmann, 1999 <https://doi.org/10.1007/s004220050570>`__).

Neurons buffer the incoming spikes until they become due, where spikes
can be lumped together provided that the corresponding synapses have the
Expand Down Expand Up @@ -79,25 +79,24 @@ integrate-and-fire neuron model with alpha-shaped postsynaptic
current that employ precise spike times; The grid-constrained
counterpart is ``iaf_psc_alpha``. The neuron models have been developed
in the context of `Morrison et al.
(2007) <http://dx.doi.org/10.1162/neco.2007.19.1.47>`__. As the model
(2007) <https://doi.org/10.1162/neco.2007.19.1.47>`__. As the model
employ interpolation in order to determine the precise location of an
outgoing spike, the achieved precision depends on the simulation
resolution *h*. The models differ in the way they process incoming
spikes, which also affects the attained precision (see `Morrison et al.
(2007) <http://dx.doi.org/10.1162/neco.2007.19.1.47>`__ for details).
(2007) <https://doi.org/10.1162/neco.2007.19.1.47>`__ for details).

``iaf_psc_exp_ps`` is an integrate-and-fire neuron model with
exponentially shaped postsynaptic currents that employs precise spike
times; its grid-constrained counterpart is ``iaf_psc_exp``. It has been
developed in the context of `Hanuschkin et al.
(2010) <http://dx.doi.org/10.3389/fninf.2010.00113>`__, which is a
(2010) <https://doi.org/10.3389/fninf.2010.00113>`__, which is a
continuation of the work presented in `Morrison et al.
(2007) <http://dx.doi.org/10.1162/neco.2007.19.1.47>`__. As the neuron
(2007) <https://doi.org/10.1162/neco.2007.19.1.47>`__. As the neuron
model employs an iterative search in order to determine the precise
location of an outgoing spike, the achieved precision does not depend on
the simulation resolution h. The model can also be used through the
`PyNN
interface <http://neuralensemble.org/trac/PyNN/wiki/ContinuousTimeSpiking>`__.
:doc:`PyNN interface <pynn:backends/NEST>`.

Questions and answers about precise neurons
-------------------------------------------
Expand All @@ -106,5 +105,3 @@ During the review process of the above mentioned papers, we came up with
a list of questions and answers pertaining to the implementation and
usage of precise spiking neurons. This list can be found
:ref:`here <faqs_precise_neurons>`.


3 changes: 1 addition & 2 deletions models/aeif_psc_delta_clopath.h
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Expand Up @@ -188,8 +188,7 @@ References
in STDP – a unified model. Frontiers in Synaptic Neuroscience. 2:25
DOI: https://doi.org/10.3389/fnsyn.2010.00025
.. [3] Voltage-based STDP synapse (Clopath et al. 2010) on ModelDB
https://senselab.med.yale.edu/ModelDB/showmodel.cshtml?model=144566&file=%2f
modeldb_package%2fVoTriCode%2faEIF.m
https://modeldb.science/144566?tab=1
See also
++++++++
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2 changes: 1 addition & 1 deletion models/clopath_synapse.h
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Expand Up @@ -98,7 +98,7 @@ References
in STDP – a unified model. Frontiers in Synaptic Neuroscience 2:25.
DOI: https://doi.org/10.3389/fnsyn.2010.00025
.. [3] Voltage-based STDP synapse (Clopath et al. 2010) on ModelDB
https://senselab.med.yale.edu/ModelDB/showmodel.cshtml?model=144566
https://modeldb.science/144566?tab=1
See also
++++++++
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2 changes: 1 addition & 1 deletion models/glif_psc_double_alpha.h
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Expand Up @@ -124,7 +124,7 @@ condition of
``tau_syn_in``, respectively, to avoid numerical instabilities.
For implementation details see the
`IAF_neurons_singularity <../model_details/IAF_neurons_singularity.ipynb>`_ notebook.
`IAF Integration Singularity <../model_details/IAF_Integration_Singularity.ipynb>`_ notebook.
Parameters
++++++++++
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20 changes: 13 additions & 7 deletions models/hh_cond_beta_gap_traub.h
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Expand Up @@ -78,24 +78,24 @@ based on a model of hippocampal pyramidal cells by Traub and Miles [1]_.
The key differences between the current model and the model in [1]_ are:
- This model is a point neuron, not a compartmental model.
- This model includes only ``I_Na`` and ``I_K``, with simpler ``I_K`` dynamics than
- Following [2]_, this model includes only ``I_Na`` and ``I_K``, with simpler ``I_K`` dynamics than
in [1]_, so it has only three instead of eight gating variables;
in particular, all Ca dynamics have been removed.
- Incoming spikes induce an instantaneous conductance change followed by
exponential decay instead of activation over time.
- The model incorporates gap junctions [3]_.
For details on asynchronicity in spike and firing events with Hodgkin Huxley models
see :ref:`here <hh_details>`.
See also [2]_.
Postsynaptic currents
---------------------
Incoming spike events induce a postsynaptic change of conductance modelled by a
beta function as outlined in [3]_ [4]_. The beta function is normalized such that an
beta function as outlined in [4]_ [5]_. The beta function is normalized such that an
event of weight 1.0 results in a peak current of 1 nS at :math:`t = \tau_{rise,xx}`
where xx is ex or in.
where xx is `ex` or `in`.
Spike Detection
---------------
Expand Down Expand Up @@ -151,11 +151,17 @@ References
.. [1] Traub RD and Miles R (1991). Neuronal Networks of the Hippocampus.
Cambridge University Press, Cambridge UK.
.. [2] http://modeldb.yale.edu/83319
.. [3] Rotter S and Diesmann M (1999). Exact digital simulation of
.. [2] Brette R, et al (2007). Simulation of networks of spiking neurons:
A review of tools and strategies. J Comput Neurosci, 23, 349–398
DOI: https://doi.org/10.1007/s10827-007-0038-6
.. [3] Hahne J, Helias M, Kunkel S, Igarashi J, Bolten M, Frommer A,
and Diesmann M. (2015). A unified framework for spiking and gap-junction
interactions in distributed neuronal network simulations.
Frontiers in Neuroinformatics, 9. DOI: https://doi.org/10.3389/fninf.2015.00022
.. [4] Rotter S and Diesmann M (1999). Exact digital simulation of
time-invariant linear systems with applications to neuronal modeling.
Biological Cybernetics 81:381 DOI: https://doi.org/10.1007/s004220050570
.. [4] Roth A and van Rossum M (2010). Chapter 6: Modeling synapses.
.. [5] Roth A and van Rossum M (2010). Chapter 6: Modeling synapses.
in De Schutter, Computational Modeling Methods for Neuroscientists,
MIT Press.
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4 changes: 1 addition & 3 deletions models/hh_psc_alpha_clopath.h
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Expand Up @@ -163,9 +163,7 @@ References
DOI: https://doi.org/10.3389/fnsyn.2010.00025
.. [6] Voltage-based STDP synapse (Clopath et al. 2010) connected to a
Hodgkin-Huxley neuron on ModelDB:
https://senselab.med.yale.edu/ModelDB/showmodel.cshtml?model=144566&file
=%2fmodeldb_package%2fstdp_cc.mod
https://modeldb.science/144566?tab=1
Sends
+++++
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2 changes: 1 addition & 1 deletion models/sigmoid_rate_gg_1998.h
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Expand Up @@ -103,7 +103,7 @@ References
.. [3] Hahne J, Helias M, Kunkel S, Igarashi J, Bolten M, Frommer A, Diesmann M
(2015). A unified framework for spiking and gap-junction interactions
in distributed neuronal network simulations. Frontiers in
Neuroinformatics, 9:22. DOI: https://doi/org/10.3389/fninf.2015.00022
Neuroinformatics, 9:22. DOI: https://doi.org/10.3389/fninf.2015.00022
Sends
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2 changes: 1 addition & 1 deletion pynest/examples/Potjans_2014/README.rst
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Expand Up @@ -56,7 +56,7 @@ To run the simulation, simply use:
The output will be saved in the ``data`` directory.

The code can be `parallelized <https://nest-simulator.readthedocs.io/en/latest/guides/parallel_computing.html>`_ using OpenMP and MPI, if NEST has been built with these features.
The code can be :ref:`parallelized <parallel_computing>` using OpenMP and MPI, if NEST has been built with these features.
The number of threads (per MPI process) can be chosen by adjusting ``local_num_threads`` in ``sim_params.py``.


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2 changes: 1 addition & 1 deletion pynest/examples/iaf_tum_2000_short_term_depression.py
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Expand Up @@ -62,7 +62,7 @@
20,RC50:1-5. URL: https://infoscience.epfl.ch/record/183402
.. [2] Tsodyks M, Pawelzik K, Markram H (1998). Neural networks with dynamic synapses. Neural
computation, http://dx.doi.org/10.1162/089976698300017502
computation, https://doi.org/10.1162/089976698300017502
See Also
~~~~~~~~
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2 changes: 1 addition & 1 deletion pynest/examples/intrinsic_currents_spiking.py
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Expand Up @@ -39,7 +39,7 @@
.. [1] Hill and Tononi (2005) Modeling sleep and wakefulness in the
thalamocortical system. J Neurophysiol 93:1671
http://dx.doi.org/10.1152/jn.00915.2004.
https://doi.org/10.1152/jn.00915.2004
See Also
~~~~~~~~
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