{"id":32649010,"url":"https://github.com/hbpvis/viola","last_synced_at":"2025-10-31T06:50:33.258Z","repository":{"id":75348032,"uuid":"49558782","full_name":"HBPVIS/VIOLA","owner":"HBPVIS","description":"Web-based visualization tool for spiking neuronal network simulation data","archived":false,"fork":false,"pushed_at":"2018-11-27T11:05:11.000Z","size":16256,"stargazers_count":6,"open_issues_count":14,"forks_count":6,"subscribers_count":9,"default_branch":"master","last_synced_at":"2023-10-25T18:41:03.324Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"JavaScript","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/HBPVIS.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2016-01-13T07:56:54.000Z","updated_at":"2023-08-26T06:24:57.000Z","dependencies_parsed_at":null,"dependency_job_id":"f8119e4b-07b0-4e37-beba-3828ce369460","html_url":"https://github.com/HBPVIS/VIOLA","commit_stats":null,"previous_names":[],"tags_count":0,"template":null,"template_full_name":null,"purl":"pkg:github/HBPVIS/VIOLA","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HBPVIS%2FVIOLA","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HBPVIS%2FVIOLA/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HBPVIS%2FVIOLA/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HBPVIS%2FVIOLA/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/HBPVIS","download_url":"https://codeload.github.com/HBPVIS/VIOLA/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/HBPVIS%2FVIOLA/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":281946317,"owners_count":26587973,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-10-31T02:00:07.401Z","response_time":57,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2025-10-31T06:50:27.694Z","updated_at":"2025-10-31T06:50:33.242Z","avatar_url":"https://github.com/HBPVIS.png","language":"JavaScript","funding_links":[],"categories":[],"sub_categories":[],"readme":"# VIOLA\n\nVIOLA (VIsualization Of Layer Activity) is an interactive, web-based tool\nto visualize activity data in multiple 2D layers such as\nthe simulation output of neuronal networks with 2D geometry.\n\nA usage example demonstrates the visualization of spike data resulting from a\n[NEST](http://nest-simulator.org) simulation of a spatially structured\npoint-neuron network with excitatory and inhibitory neuron populations and an\nexternal stimulus.\n\n## Getting started\n\nTwo steps are necessary to run the visualization:\nfirst, you need to [get test data](#1-getting-test-data), and, second, you need\nto [start the tool](#2-starting-viola) and load the data.\n\n### 1. Getting test data\n\nSpatially resolved time series data to be visualized with VIOLA can have two\ndifferent formats:\n* **raw:** spike times associated with spatial locations of spiking neurons\n* **preprocessed:** spatially and temporally binned spike data including LFP\nsignals\n\nWe have prepared one data set of each format that can be downloaded here:\n* [RawData.zip](https://hbpvis.github.io/VIOLA/downloads/RawData.zip)\n* [PreprocessedData.zip](https://hbpvis.github.io/VIOLA/downloads/PreprocessedData.zip)\n(recommended to start with for testing out VIOLA)\n\nExtract the archived files, e.g., using `unzip PreprocessedData.zip`.  \nEach data set contains text files with the data to be visualized and a\ncorresponding configuration file for VIOLA:\n\n#### Configuration files\n\nraw                    | preprocessed\n---------------------- | -----------------\nconfig_raw.json        | config_proc.json\n\n#### Data files\n\nraw                    | preprocessed\n---------------------- | -----------------\nspikes-0.gdf           | binned_sprates_rs_EX.dat\nspikes-1.gdf           | binned_sprates_rs_IN.dat\nspikes-2.gdf           | binned_sprates_rs_STIM.dat\nneuron_positions-0.dat | LFPdata.lfp\nneuron_positions-1.dat |\nneuron_positions-2.dat |\n\nAlternatively, you can generate test data yourself as described in\n[Generating test data](#generating-test-data-optional).\n\n### 2. Starting VIOLA\n\nVIOLA runs in a web browser and the preferred browser is\n[Google Chrome](https://www.google.de/chrome).\n\nStart VIOLA from its [GitHub Page](http://hbpvis.github.io/VIOLA).  \nNote that this version of the tool may differ from the current master branch of\nthis repository.  \nTo get the latest version, you can clone the repository (e.g.,\n`git clone https://github.com/HBPVIS/VIOLA.git`),\nnavigate to the directory **VIOLA**, and open the contained file index.html in\nthe browser.\n\nUpon startup, VIOLA opens the **Setup Page** to configure the visualization for\na specific data set.  \nJust upload the configuration file (config_proc.json for preprocessed data), and\nthen click the button **Setup visualization** to get to the **Main Page**.\n\nUsing the **Upload Panel** to the left, you can upload all data files (see the\n[Tables](#configuration-files) above) to be visualized:  \neither by dragging and dropping the files to the blue box or by opening a file\nexplorer with the corresponding button.  \nIf the background color of the field for a data file changes from red to green,\nthe upload has been successful.  \nAs soon as all files are uploaded, close the upload panel by clicking the **x**\nat its top right corner.\n\nPress **Play** in the control bar that is located at the bottom to start the\nvisualization.\n\nFor further documentation, please refer to the\n[VIOLA Wiki](https://github.com/HBPVIS/VIOLA/wiki) containing the\n[User Manual](https://github.com/HBPVIS/VIOLA/wiki/VIOLA-User-Manual)\nand the\n[Developer Manual](https://github.com/HBPVIS/VIOLA/wiki/VIOLA-Developer-Manual).\n\n## Generating test data (optional)\n\nThe scripts to simulate a spatially structured network of spiking point-neurons\nare in the directory **test_data** in this repository.\nYou can clone the repository, e.g., with\n`git clone https://github.com/HBPVIS/VIOLA.git`.  \nSimulations rely on the simulator [NEST](http://nest-simulator.org) and are\nimplemented using the [Python](http://www.python.org) interface.  \nSoftware dependencies for the simulation scripts are summarized together with\nthe tested version numbers [below](#software-dependencies).\n\nFor generating **raw data**, run\n\n    python topo_brunel_alpha_nest.py out_raw\n\nThe created directory **out_raw** contains configuration and data files for raw\ndata and the [Tables](#configuration-files) above indicate which files need to\nbe uploaded to VIOLA for visualization.\n\nHaving generated raw data, you can generate **preprocessed data** by running\n\n    python nest_preprocessing.py out_raw out_proc\n\nTo speed up the preprocessing step, you can also use OpenMPI und run instead\n\n    mpirun -np 2 python nest_preprocessing.py out_raw out_proc\n\nAfterwards, generate LFP data. You need to compile the\n[NEURON](https://neuron.yale.edu) model once on your system by\nexecuting\n\n    nrnivmodl alphaisyn.mod\n\nand then you can run\n\n    python fake_LFP_signal.py out_raw out_proc\n\nThe created directory **out_proc** contains configuration and data files for\npreprocessed data and the [Tables](#configuration-files) above indicate which\nfiles need to be uploaded to VIOLA for visualization.\n\n### Software dependencies\n* [NEST](http://nest-simulator.org) v2.10.0\n* [NEURON](https://neuron.yale.edu) v7.4\n* [Python](http://www.python.org) v2.7.11\n  * numpy v1.10.4\n  * matplotlib v2.0.2\n  * scipy v0.17.0\n  * h5py v2.5.0\n  * mpi4py v2.0.0\n  * LFPy v2.0.0\n  * quantities v0.12\n\n## Authors\n\n* Corto Carde, Johanna Senk, Espen Hagen, Benjamin Weyers\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhbpvis%2Fviola","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhbpvis%2Fviola","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhbpvis%2Fviola/lists"}