Summary

• Page properties (1 modified, 0 added, 0 removed)

Details

Page properties

Content

...	...	@@ -123,8 +123,15 @@
123	123	\\You might be required to run the above command every time you open a new terminal window. Do verify that the terminal command prompt indicates the name of your virtual environment to confirm that you have indeed activated it.
124	124	)))
125	125
126		-Now that we have our project's virtual environment setup, we are now ready to install PyNN and other simulators. In general, it is advisable to install the various simulators (especially NEURON and NEST) prior to installing PyNN, because PyNN will then auto compile NEURON's NMODL fles and NEST's extensions during installation. Alternatively, this would need to be done manually as described on the PyNN website. In this tutorial, we will adopt the easier approach and begin by installing the simulators. For the purposes of this tutorial, we shall demonstrate the installation of Brian2, NEURON and NEST simulators.
	126	+Now that we have our project's virtual environment setup, we are now ready to install PyNN and other simulators. In general, it is advisable to install the various simulators (especially NEURON and NEST) prior to installing PyNN, because PyNN will then auto compile NEURON's NMODL fles and NEST's extensions during installation. In this tutorial, we will adopt this approach and begin by installing the simulators. For the purposes of this tutorial, we shall demonstrate the installation of Brian2, NEURON and NEST simulators.
127	127
	128	+(% class="box errormessage" %)
	129	+(((
	130	+**Note:**
	131	+\\If you have previously already installed NEURON or NEST on your system and are installing PyNN now, then you would require to compile NEURON's NMODL fles and NEST's extensions manually. For more instructions on this, take a look at:
	132	+[[(% style="color:#000000" %)http:~~/~~/neuralensemble.org/docs/PyNN/installation.html>>http://neuralensemble.org/docs/PyNN/installation.html]]
	133	+)))
	134	+
128	128	We start here with the installation of Brian 2. Brian 2 can be installed simply using the pip command.
129	129
130	130	(% class="box infomessage" %)
...	...	@@ -195,7 +195,7 @@
195	195	\\I find that I receive a "no module named nest" error, when trying this right after installing NEST. But it succeeds after a restart. So if you do observe an error, close all programs and restart your computer, and try again. This time it should execute as expected.
196	196	)))
197	197
198		-If there are no error messages here, and the import is successful, then we have completed installing NEST simulator, and are able to load it on Python.
	205	+If there are no error messages here, and the import is successful, then we have completed installing NEST simulator, and are able to load it via Python.
199	199
200	200	We next move on to the third simulator, NEURON. The installation for NEURON used to be more involved previously, but can now be easily completed using the 'pip' command:
201	201
...	...	@@ -223,17 +223,61 @@
223	223	\\exit()
224	224	)))
225	225
	233	+If there are no error messages here, and the import is successful, then we have completed installing NEURON simulator, and are able to load it via Python.
226	226
	235	+Now that we have installed all the simulators we intend to use, we move on to installing PyNN itself. As PyNN is a Python package, we can install it easily using the 'pip' command:
227	227
	237	+(% class="box infomessage" %)
	238	+(((
	239	+**Screencast** - terminal
	240	+\\(% style="color:#000000" %)pip install pyNN
	241	+)))
	242	+
	243	+To verify that PyNN has been successfully installed on our system, and that it is indeed able to communicate with the other simulators that we installed earlier, we can try running:
	244	+
	245	+(% class="box infomessage" %)
	246	+(((
	247	+**Screencast** - terminal
	248	+
	249	+(% style="color:#000000" %)python
	250	+\\import pyNN.brian2 as sim
	251	+
	252	+(% style="color:#000000" %)sim.setup()
	253	+
	254	+(% style="color:#000000" %)sim.end()
	255	+)))
	256	+
	257	+This confirms that PyNN has been properly setup, and also that is able to employ Brian 2. To verify similary test that PyNN is also able to communicate with NEURON and NEST simulators:
	258	+
	259	+(% class="box infomessage" %)
	260	+(((
	261	+**Screencast** - terminal
	262	+
	263	+(% style="color:#000000" %)python
	264	+\\import pyNN.nest as sim
	265	+
	266	+(% style="color:#000000" %)sim.setup()
	267	+
	268	+(% style="color:#000000" %)sim.end()
	269	+
	270	+
	271	+
	272	+(% style="color:#000000" %)import pyNN.neuron as sim
	273	+
	274	+(% style="color:#000000" %)sim.setup()
	275	+
	276	+(% style="color:#000000" %)sim.end()
	277	+)))
	278	+
	279	+A
	280	+
228	228	(% class="box successmessage" %)
229	229	(((
230	230	**Slide** recap of learning objectives
231	231	)))
232	232
233		-That is the end of this tutorial, in which I've demonstrated how to install PyNN, and other required simulators, in a Linux system. You are now ready to start modeling! To learn about model development in PyNN, do take a look at our next tutorial.
	286	+That is the end of this tutorial, in which I've demonstrated how to install PyNN, and other required simulators, in a Linux system. You are now ready to start modeling! To learn about model development in PyNN, do take a look at our next tutorial. Also, we will be releasing a series of tutorials, throughout the rest of 2021 and 2022, to introduce these more advanced features of PyNN, so keep an eye on the EBRAINS website.
234	234
235		-Als,  we will be releasing a series of tutorials, throughout the rest of 2021 and 2022, to introduce these more advanced features of PyNN, so keep an eye on the EBRAINS website.
236		-
237	237	(% class="box successmessage" %)
238	238	(((
239	239	**Slide** useful links
...	...	@@ -243,6 +243,7 @@
243	243	[[(% style="color:#000000" %)https:~~/~~/neuron.yale.edu/neuron/>>https://neuron.yale.edu/neuron/]]
244	244	)))
245	245
	297	+We have listed here some links that might be of interest to users who wish to find more details about the various softwares employed in this tutorial.
246	246
247	247	(% class="box successmessage" %)
248	248	(((