Tutorials & E-Library

In this part you will start to implement recording and saving of a segmented simulation, I followed a pattern similar to what worked for a full run.

Create a hoc file called netrecord_segrun.hoc that contains statements that execute a user-specified number of simulation segments and save each segment's results to a separate file.

Copy initnet_fullrun.hoc to initnet_segrun.hoc, and edit this new file to change the load_file("netrecord_fullrun.hoc") statement to load_file("netrecord_segrun.hoc").

This tutorial guides you through the simulation of a model cell in Neuron through toy models with minimal instrumentation. In this second step you will learn how to easily implement recording and saving of a full run.

This tutorial guides you through the simulation of a model cell in Neuron through toy models with minimal instrumentation. In this first step you will learn how to implement and test the model.

Reconstituting the results of a complete simulation from the segmentxx.dat files.

Reconstituting the results of a complete simulation from the segmentxx.dat files.

To implement recording and saving of a segmented simulation, I followed a pattern similar to what worked for a full run.

Create a hoc file called cellrecord_segrun.hoc that contains statements that execute a user-specified number of simulation segments and save each segment's results to a separate file.

Copy initcell_fullrun.hoc to initcell_segrun.hoc, and edit this new file to change the load_file("cellrecord_fullrun.hoc") statement to load_file("cellrecord_segrun.hoc").

It was very easy to implement recording and saving of a complete simulation of the network.

Create a hoc file called netrecord_fullrun.hoc that contains statements to accomplish these tasks:

launch a simulation (netrig.hoc already takes care of recording spike times and cell IDs to a pair of Vectors)
write the results to a file

Add a load_file("netrecord_fullrun.hoc") statement to the end of a copy of initnet_basic.hoc, and save this as initnet_fullrun.hoc

The EBRAINS Live Papers are structured and interactive supplementary documents to complement journal publications, that allow users to readily access, explore, and utilize the various kinds of data underlying scientific studies. Interactivity is a prominent feature with several integrated tools and services that will allow users to download, visualize, or simulate data, models, and results presented in the corresponding publications.

In this video, we provide a quick overview of the purpose of EBRAINS Live Papers.

The EBRAINS Live Papers are structured and interactive supplementary documents to complement journal publications, that allow users to readily access, explore, and utilize the various kinds of data underlying scientific studies. Interactivity is a prominent feature with several integrated tools and services that will allow users to download, visualize, or simulate data, models, and results presented in the corresponding publications.

In this tutorial-cum-demonstration, you will learn how to create a Collab on the EBRAINS Collaboratory and basically everything that there is to learn about creating a new Live Paper.

Siibra Explorer is bridging the gap between human brain mapping and accessible exploration of the Julich Brain Atlas.

In this tutorial, we will cover the very first steps of using NEST Desktop by means of a simple example network. In order to reproduce those steps, you will need both a NEST Desktop and a NEST Server instances running.

If you do not have it installed, you can use NEST Desktop on the EBRAINS platform (https://ebrains.eu/service/nest-desktop, free user account required).

This example builds the same single cell model as A simple single cell model, except using a arbor.recipe and arbor.simulation instead of a arbor.single_cell_model.

Recipes are an important concept in Arbor. They represent the most versatile tool for building a complex network of cells. We will go though this example of a model of a single cell, before using the recipe to represent more complex networks in subsequent examples.