Summary

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

Details

Page properties

Content

...	...	@@ -105,15 +105,51 @@
105	105
106	106	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.
107	107
108		-We start here with the installation of Brian2.
	108	+We start here with the installation of Brian2. Brian2 can be installed simply using the pip command.
109	109
110	110	(% class="box infomessage" %)
111	111	(((
112	112	**Screencast** - terminal
113		-
	113	+\\(% style="color:#000000" %)pip install brian2
114	114	)))
115	115
	116	+This will install Brian2, along with all its dependencies such as 'cython', 'numpy', etc. We can now go back into our virtual environment's 'site-packages' directory to see how it is now populated with all these packages.
116	116
	118	+(% class="box infomessage" %)
	119	+(((
	120	+**Screencast** - file explorer
	121	+\\(% style="color:#000000" %)<< show directory contents lib/python3.9/site-packages >>
	122	+)))
	123	+
	124	+To confirm that we have properly installed Brian2 on our computer, we can test as follows:
	125	+
	126	+(% class="box infomessage" %)
	127	+(((
	128	+**Screencast** - terminal
	129	+\\(% style="color:#000000" %)python
	130	+\\import brian2
	131	+\\exit()
	132	+)))
	133	+
	134	+If there are no error messages here, and the import is successful, then we have completed installing Brian2.
	135	+
	136	+
	137	+We shall now move on to install the NEST simulator. Unlike Brian2, NEST is not a Python package and therefore its installation is a bit more involved. We shall install the NEST module along with PyNEST, which is a Python interface for controlling the NEST kernel.
	138	+
	139	+We first install the NEST module. Version 2.20 is currently supported by PyNN, and it is likely that other versions of NEST might have issues when used with the current version of PyNN. The installation is done by first adding the PPA repository for NEST and updating apt, followed by the installation of NEST itself.
	140	+
	141	+(% class="box infomessage" %)
	142	+(((
	143	+**Screencast** - terminal
	144	+\\(% style="color:#000000" %)sudo add-apt-repository ppa:nest-simulator/nest
	145	+sudo apt-get update
	146	+\\sudo apt-get install nest
	147	+)))
	148	+
	149	+At this point, we have installed the NEST module, but it is still not usable via Python. To do so, we next install PyNEST.
	150	+
	151	+
	152	+
117	117	(% class="box successmessage" %)
118	118	(((
119	119	**Slide** recap of learning objectives