Changes for page 02. Installing PyNN - Linux
Last modified by adavison on 2022/10/04 13:53
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... ... @@ -49,66 +49,34 @@ 49 49 **Slide** listing learning objectives 50 50 ))) 51 51 52 -In this tutorial, Iwill guide you through setting up PyNN, together with the NEST, NEURON and Brian2 simulators, inaLinuxenvironment. Note that we have a dedicated version of this tutorial for other environments, such as Mac OS,Windowsand EBRAINS Jupyter Lab.52 +In this tutorial, we will guide you through setting up PyNN, together with the NEST, NEURON and Brian2 simulators, in the EBRAINS Jupyter Lab environment. Note that we have a dedicated version of this tutorial for other environments, such as Linux, Mac OS and Windows. 53 53 54 -(% class="box successmessage" %) 55 -((( 56 -**Slide** listing prerequisites 57 -))) 54 +. 58 58 59 - Ishall be demonstratingtheinstallation on a computer with Ubuntu 18.04 OS installed. The steps are likely to remainverysimilarforother versionsof UbuntuOS, and also notexpected tovary significantly for other Linux distributions. In the latter case, you willfind on the Internet about how to carry out the equivalent of the tasks demonstrated here usingUbuntu OS. Also,the tutorialwillfocus only on Python 3, as Python 2 has now been deprecated. On my system56 +=== State the learning objectives (In this tutorial, you will learn to do X…) === 60 60 61 -(% class="box infomessage" %) 62 -((( 63 -**Screencast** - blank document in editor 64 -))) 58 +. 65 65 66 - Weshall make use of virtual environments in this tutorial. This allows multiplePythonprojects to coexist on the same computer,even when they might have different, and even conflicting, requirements. It helpsisolateprojectsand thereby preventing unrequested changes in others, when any one of them is updated.60 +=== State prerequisites === 67 67 68 -(% class="box infomessage" %) 69 -((( 70 -**Screencast** - current state of editor 71 -\\(% style="color:#000000" %)"""install and setup new virtualenv project"""(%%) 72 -\\(% style="color:#000000" %)sudo pip install virtualenv 73 -\\"""if already installed, ensure we have latest package by upgrading""" 74 -\\pip install ~-~-upgrade virtualenv 75 -\\"""create a directory for project""" 76 -\\cd ~~ 77 -mkdir pynn_project 78 -cd pynn_project 79 -\\"""create a virtual environment for this project""" 80 -python -m venv pynn_env 81 -\\ls 82 -<< show created directory >> 83 -))) 62 +. 84 84 85 - Nowthat wehave our project'svirtual environment setup, we are now readytoinstall PyNN andother simulators. Ingeneral,it is advisableto install the various simulators (especially NEURONand NEST) prior to installing PyNN, because PyNN willthen auto compile NEURON's NMODL fles and NEST's extensions during installation. Alternatively,this would need to be done manually asdescribedon the PyNN website. In this tutorial, we will adopt the easierpproach and begin by installing thesimulators. For the purposes of this tutorial, we shall demonstrate the installation of Brian2, NEURON and NEST simulators.64 +=== Description, explanation, and practice === 86 86 87 - We start here with the installation of Brian2.66 +. 88 88 89 -(% class="box infomessage" %) 90 -((( 91 -**Screencast** - current state of editor 92 -\\ 93 -))) 68 +=== Summary (In this tutorial, you have learned to do X…) === 94 94 70 +. 95 95 96 -(% class="box successmessage" %) 97 -((( 98 -**Slide** recap of learning objectives 99 -))) 72 +=== Acknowledgements if appropriate === 100 100 101 - 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.74 +. 102 102 103 - Als,wewill beleasing a seriesoftutorials,throughout therest of 2021 and 2022, tointroducethesemoreadvancedfeaturesof PyNN, sokeepan eye ontheEBRAINS website.76 +=== References to websites (For more information, visit us at…) === 104 104 105 -(% class="box successmessage" %) 106 -((( 107 -**Slide** acknowledgements, contact information 108 -))) 78 +. 109 109 110 -(% class="wikigeneratedid" %) 111 -PyNN has been developed by many different people, with financial support from several different organisations. I'd like to mention in particular the CNRS and the European Commission, through the FACETS, BrainScaleS and Human Brain Project grants. 80 +=== Contact information (For questions, contact us at…) === 112 112 113 -(% class="wikigeneratedid" %) 114 -For more information visit neuralensemble.org/PyNN. If you have questions you can contact us through the PyNN Github project, the NeuralEnsemble forum, EBRAINS support, or the EBRAINS Community. 82 +.