From 43817519f36d25da001d73b4c02d38bce48ff9cd Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Tue, 6 Aug 2024 11:01:41 +0200 Subject: [PATCH 1/6] update README --- README.md | 117 +++++++++++++++++------------------------------------- 1 file changed, 37 insertions(+), 80 deletions(-) diff --git a/README.md b/README.md index 33a65ddfa1..315a0626a6 100644 --- a/README.md +++ b/README.md @@ -23,8 +23,11 @@ NEST is a simulator for spiking neural network models that focuses on the dynamics, size and structure of neural systems rather than on the exact morphology of individual neurons. The development of NEST is coordinated by the -NEST Initiative. General information on the NEST Initiative can be found at -its homepage at https://www.nest-initiative.org. +NEST Initiative. + +A NEST simulation tries to follow the logic of an electrophysiological +experiment that takes place inside a computer with the difference, that the +neural system to be investigated must be defined by the experimenter. NEST is ideal for networks of spiking neurons of any size, for example: @@ -37,95 +40,49 @@ NEST is ideal for networks of spiking neurons of any size, for example: For copyright information please refer to the `LICENSE` file and to the information header in the source files. -## How do I use NEST? +General information on the NEST Initiative can be found at +its homepage at https://www.nest-initiative.org. -You can use NEST either via Python (PyNEST) or as a stand-alone application -(nest). PyNEST provides a set of commands to the Python interpreter which give -you access to NEST's simulation kernel. With these commands, you describe and -run your network simulation. You can also complement PyNEST with PyNN, a -simulator-independent set of Python commands to formulate and run neural -simulations. While you define your simulations in Python, the actual simulation -is executed within NEST's highly optimized simulation kernel which is written -in C++. +## Key features of NEST -A NEST simulation tries to follow the logic of an electrophysiological -experiment that takes place inside a computer with the difference, that the -neural system to be investigated must be defined by the experimenter. +* NEST provides a Python interface or stand alone application +* NEST provides a large collection of neurons and synapse models +* NEST provides numerous example network scripts along with tutorials and guides to help you + develop your simulation. +* NEST has a large community of experienced developers and users. NEST was first released in 1994 under the name SYNOD, and has been extended and improved ever since. +* NEST is extensible: you can extend NEST by adding your own modules +* NEST is scalable: Use NEST on your laptop or the largest supercomputers +* NEST is memory efficient: It makes best use of your multi-core computer and compute clusters with minimal user intervention. +* NEST is ian open source project and is licensed under the GNU General Public License v2 or later. +* NEST employs continuous integration workflows in order to maintain high code quality standards for correct and reproducible simulations. -The neural system is defined by a possibly large number of neurons and their -connections. In a NEST network, different neuron and synapse models can -coexist. Any two neurons can have multiple connections with different -properties. Thus, the connectivity can in general not be described by a weight -or connectivity matrix but rather as an adjacency list. - -To manipulate or observe the network dynamics, the experimenter can define -so-called devices which represent the various instruments (for measuring and -stimulation) found in an experiment. These devices write their data either to -memory or to file. - -NEST is extensible and new models for neurons, synapses, and devices can be -added. - -To get started with NEST, please see the [Documentation Page for -Tutorials](https://www.nest-simulator.org/documentation/). - -## Why should I use NEST? - -To learn more about the capabilities of NEST, please read the complete [feature -summary](https://www.nest-simulator.org/features/). - -- NEST provides over 50 neuron models many of which have been published. Choose - from simple integrate-and-fire neurons with current or conductance based - synapses, over the Izhikevich or AdEx models, to Hodgkin-Huxley models. -- NEST provides over 10 synapse models, including short-term plasticity - (Tsodyks & Markram) and different variants of spike-timing dependent - plasticity (STDP). -- NEST provides many examples that help you getting started with your own - simulation project. -- NEST offers convenient and efficient commands to define and connect large - networks, ranging from algorithmically determined connections to data-driven - connectivity. -- NEST lets you inspect and modify the state of each neuron and each connection - at any time during a simulation. -- NEST is fast and memory efficient. It makes best use of your multi-core - computer and compute clusters with minimal user intervention. -- NEST runs on a wide range of UNIX-like systems, from MacBooks to - supercomputers. -- NEST has minimal dependencies. All it really needs is a C++ compiler. - Everything else is optional. -- NEST developers are using agile continuous integration-based workflows in - order to maintain high code quality standards for correct and reproducible - simulations. -- NEST has one of the largest and most experienced developer communities of all - neural simulators. NEST was first released in 1994 under the name SYNOD and - has been extended and improved ever since. -## License +## Documentation -NEST is open source software and is licensed under the [GNU General Public -License v2](https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html) or -later. +Please visit our [online documentation](https://nest-simulator.readthedocs.io/en/stable/) for details on instaling and using NEST + + +## Cite NEST -## Installing NEST +If you use NEST as part of your research, please cite the *version* of NEST you used. +The full citation for each release can be found on [Zenodo](https://zenodo.org/search?q=title%3ANEST%20AND%20-description%3Agraphical%20AND%20simulator&l=list&p=1&s=10&sort=publication-desc) -Please see the online [NEST Installation Instructions](http://www.nest-simulator.org/installation) -to find out how to install NEST. +For general citations, please use +Gewaltig M-O & Diesmann M (2007) NEST (Neural Simulation Tool) Scholarpedia 2(4):1430. -## Getting help +## Contact -- You can run the `help` command in the NEST interpreter to find documentation - and learn more about available commands. -- For queries regarding NEST usage, please use the [NEST users mailing - list](https://www.nest-initiative.org/mailinglist/). -- Information on the Python bindings to NEST can be found in - `${prefix}/share/doc/nest/README.md`. -- For those looking to extend NEST, developer documentation on [Contributing to - NEST](https://nest-simulator.readthedocs.io/en/latest/contribute/index.html) is available. -## Citing NEST +If you need help or would like to discuss an idea or issue, +you can find [ways to get in touch here](https://nest-simulator.readthedocs.io/en/stable/community.html) -Please cite NEST if you use it in your work. -- You can find all the information for [citing NEST here](https://nest-simulator.readthedocs.io/en/latest/citing-nest.html) +## Publications +You can find a list of NEST [related publications here](https://www.nest-simulator.org/publications/) +## License + +NEST is open source software and is licensed under the [GNU General Public +License v2](https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html) or +later. From 0c2d7bf0b3fdd073b5167f7896cc4e77fd820d9b Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Tue, 6 Aug 2024 11:14:32 +0200 Subject: [PATCH 2/6] fix line --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 315a0626a6..385c528ab6 100644 --- a/README.md +++ b/README.md @@ -68,7 +68,8 @@ If you use NEST as part of your research, please cite the *version* of NEST you The full citation for each release can be found on [Zenodo](https://zenodo.org/search?q=title%3ANEST%20AND%20-description%3Agraphical%20AND%20simulator&l=list&p=1&s=10&sort=publication-desc) For general citations, please use -Gewaltig M-O & Diesmann M (2007) NEST (Neural Simulation Tool) Scholarpedia 2(4):1430. + +`Gewaltig M-O & Diesmann M (2007) NEST (Neural Simulation Tool) Scholarpedia 2(4):1430.` ## Contact From 3f3a83b4c1b735327068ab33400c305746b69eef Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Tue, 6 Aug 2024 11:34:36 +0200 Subject: [PATCH 3/6] udpate wording --- README.md | 33 +++++++++++++++++++++------------ 1 file changed, 21 insertions(+), 12 deletions(-) diff --git a/README.md b/README.md index 385c528ab6..7432e45549 100644 --- a/README.md +++ b/README.md @@ -26,14 +26,14 @@ morphology of individual neurons. The development of NEST is coordinated by the NEST Initiative. A NEST simulation tries to follow the logic of an electrophysiological -experiment that takes place inside a computer with the difference, that the +experiment that takes place inside a computer with the difference that the neural system to be investigated must be defined by the experimenter. NEST is ideal for networks of spiking neurons of any size, for example: -- Models of information processing e.g. in the visual or auditory cortex of +- Models of information processing, e.g., in the visual or auditory cortex of mammals, -- Models of network activity dynamics, e.g. laminar cortical networks or +- Models of network activity dynamics, e.g., laminar cortical networks or balanced random networks, - Models of learning and plasticity. @@ -45,21 +45,21 @@ its homepage at https://www.nest-initiative.org. ## Key features of NEST -* NEST provides a Python interface or stand alone application +* NEST provides a Python interface or a stand-alone application * NEST provides a large collection of neurons and synapse models * NEST provides numerous example network scripts along with tutorials and guides to help you - develop your simulation. -* NEST has a large community of experienced developers and users. NEST was first released in 1994 under the name SYNOD, and has been extended and improved ever since. + develop your simulation +* NEST has a large community of experienced developers and users; NEST was first released in 1994 under the name SYNOD, and has been extended and improved ever since * NEST is extensible: you can extend NEST by adding your own modules * NEST is scalable: Use NEST on your laptop or the largest supercomputers -* NEST is memory efficient: It makes best use of your multi-core computer and compute clusters with minimal user intervention. -* NEST is ian open source project and is licensed under the GNU General Public License v2 or later. -* NEST employs continuous integration workflows in order to maintain high code quality standards for correct and reproducible simulations. +* NEST is memory efficient: It makes the best use of your multi-core computer and compute clusters with minimal user intervention +* NEST is an open source project and is licensed under the GNU General Public License v2 or later +* NEST employs continuous integration workflows in order to maintain high code quality standards for correct and reproducible simulations ## Documentation -Please visit our [online documentation](https://nest-simulator.readthedocs.io/en/stable/) for details on instaling and using NEST +Please visit our [online documentation](https://nest-simulator.readthedocs.io/en/stable/) for details on installing and using NEST. ## Cite NEST @@ -75,12 +75,21 @@ For general citations, please use If you need help or would like to discuss an idea or issue, -you can find [ways to get in touch here](https://nest-simulator.readthedocs.io/en/stable/community.html) +you can find [ways to get in touch here](https://nest-simulator.readthedocs.io/en/stable/community.html). + + +## Contribute + +NEST is built on an active community and we welcome contributions to our code and documentation. + +You can create a [GitHub issue](https://github.com/nest/nest-simulator/issues/new/choose), for bug reports, feature requests, documentation improvements, or other issues. + +For working with NEST code and documentation, [see our documentation](https://nest-simulator.readthedocs.io/en/stable/developer_space/index.html#contribute-to-nest) ## Publications -You can find a list of NEST [related publications here](https://www.nest-simulator.org/publications/) +You can find a list of NEST [related publications here](https://www.nest-simulator.org/publications/). ## License From 6129998f6898950c081eedf6c443ec6d72800b39 Mon Sep 17 00:00:00 2001 From: jessica-mitchell Date: Tue, 27 Aug 2024 09:24:13 +0200 Subject: [PATCH 4/6] Apply suggestions from code review Co-authored-by: Dennis Terhorst --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 7432e45549..27ace907b3 100644 --- a/README.md +++ b/README.md @@ -59,7 +59,7 @@ its homepage at https://www.nest-initiative.org. ## Documentation -Please visit our [online documentation](https://nest-simulator.readthedocs.io/en/stable/) for details on installing and using NEST. +Please visit our [online documentation](https://nest-simulator.org/documentation) for details on installing and using NEST. ## Cite NEST From 117669dd781f3a34049acedcde534e46485f24f3 Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Tue, 27 Aug 2024 12:00:27 +0200 Subject: [PATCH 5/6] update readme based on code comments --- README.md | 29 +++++++++++++++++------------ 1 file changed, 17 insertions(+), 12 deletions(-) diff --git a/README.md b/README.md index 27ace907b3..8805809f00 100644 --- a/README.md +++ b/README.md @@ -37,18 +37,12 @@ NEST is ideal for networks of spiking neurons of any size, for example: balanced random networks, - Models of learning and plasticity. -For copyright information please refer to the `LICENSE` file and to the -information header in the source files. - -General information on the NEST Initiative can be found at -its homepage at https://www.nest-initiative.org. - ## Key features of NEST * NEST provides a Python interface or a stand-alone application -* NEST provides a large collection of neurons and synapse models -* NEST provides numerous example network scripts along with tutorials and guides to help you - develop your simulation +* NEST provides a large collection of [neurons and synapse models](https://nest-simulator.org/documentation/models/index.html) +* NEST provides numerous [example network scripts](https://nest-simulator.org/documentation/examples/index.html) along with + [tutorials and guides](https://nest-simulator.org/documentation/get-started_index.html) to help you develop your simulation * NEST has a large community of experienced developers and users; NEST was first released in 1994 under the name SYNOD, and has been extended and improved ever since * NEST is extensible: you can extend NEST by adding your own modules * NEST is scalable: Use NEST on your laptop or the largest supercomputers @@ -75,16 +69,23 @@ For general citations, please use If you need help or would like to discuss an idea or issue, -you can find [ways to get in touch here](https://nest-simulator.readthedocs.io/en/stable/community.html). +join our [maling list](https://nest-simulator.org/documenation/developer_space/guidelines/mailing_list_guidelines.html), +where we encourage active participation from our developers and users to share their knowledge and experience with NEST. + + +You can find other [ways to get in touch here](https://nest-simulator.readthedocs.io/en/stable/community.html). ## Contribute NEST is built on an active community and we welcome contributions to our code and documentation. -You can create a [GitHub issue](https://github.com/nest/nest-simulator/issues/new/choose), for bug reports, feature requests, documentation improvements, or other issues. -For working with NEST code and documentation, [see our documentation](https://nest-simulator.readthedocs.io/en/stable/developer_space/index.html#contribute-to-nest) +For bug reports, feature requests, documentation improvements, or other issues, +you can create a [GitHub issue](https://github.com/nest/nest-simulator/issues/new/choose), + +For working with NEST code and documentation, you can find guidelines for contributions +[in our documentation](https://nest-simulator.readthedocs.io/en/stable/developer_space/index.html#contribute-to-nest) ## Publications @@ -93,6 +94,10 @@ You can find a list of NEST [related publications here](https://www.nest-simulat ## License + NEST is open source software and is licensed under the [GNU General Public License v2](https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html) or later. + +General information on the NEST Initiative can be found at +its homepage at https://www.nest-initiative.org. From f77c2aa7aacfaac9c0157c0cc8b7b74940b922f1 Mon Sep 17 00:00:00 2001 From: Jessica Mitchell Date: Wed, 4 Sep 2024 13:04:41 +0200 Subject: [PATCH 6/6] rm line --- README.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/README.md b/README.md index 8805809f00..0a545b45fa 100644 --- a/README.md +++ b/README.md @@ -22,8 +22,7 @@ NEST is a simulator for spiking neural network models that focuses on the dynamics, size and structure of neural systems rather than on the exact -morphology of individual neurons. The development of NEST is coordinated by the -NEST Initiative. +morphology of individual neurons. A NEST simulation tries to follow the logic of an electrophysiological experiment that takes place inside a computer with the difference that the