{"id":13676304,"url":"https://github.com/dissagaliyeva/sim2bids","last_synced_at":"2026-01-16T14:21:11.483Z","repository":{"id":36956428,"uuid":"481992446","full_name":"dissagaliyeva/sim2bids","owner":"dissagaliyeva","description":"App to load, transform \u0026 download BIDS compliant data","archived":false,"fork":false,"pushed_at":"2023-07-03T02:30:49.000Z","size":249749,"stargazers_count":3,"open_issues_count":0,"forks_count":2,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-08-29T22:57:12.165Z","etag":null,"topics":["bids","computational-neuroscience","conversion","neuroscience"],"latest_commit_sha":null,"homepage":"https://sim2bids.readthedocs.io/en/latest/","language":"HTML","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/dissagaliyeva.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":"2022-04-15T14:55:46.000Z","updated_at":"2023-08-01T08:11:55.000Z","dependencies_parsed_at":"2023-09-23T18:51:59.741Z","dependency_job_id":null,"html_url":"https://github.com/dissagaliyeva/sim2bids","commit_stats":{"total_commits":468,"total_committers":2,"mean_commits":234.0,"dds":0.002136752136752129,"last_synced_commit":"bde211c05d6d1a9d8ffaa6305619956a51fc89c1"},"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/dissagaliyeva/sim2bids","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dissagaliyeva%2Fsim2bids","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dissagaliyeva%2Fsim2bids/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dissagaliyeva%2Fsim2bids/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dissagaliyeva%2Fsim2bids/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dissagaliyeva","download_url":"https://codeload.github.com/dissagaliyeva/sim2bids/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dissagaliyeva%2Fsim2bids/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28479393,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-16T11:59:17.896Z","status":"ssl_error","status_checked_at":"2026-01-16T11:55:55.838Z","response_time":107,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["bids","computational-neuroscience","conversion","neuroscience"],"created_at":"2024-08-02T13:00:22.336Z","updated_at":"2026-01-16T14:21:11.478Z","avatar_url":"https://github.com/dissagaliyeva.png","language":"HTML","funding_links":[],"categories":["Converters"],"sub_categories":["others"],"readme":"# SIM2BIDS: convert computational data to BIDS standard\n\n---\n\n[![Documentation Status](https://readthedocs.org/projects/sim2bids/badge/?version=latest)](https://sim2bids.readthedocs.io/en/latest/?badge=latest)\n\n\nThis app is created to convert computational data to BIDS standard as proposed by [Michael Schirner and Petra Ritter](https://docs.google.com/document/d/1NT1ERdL41oz3NibIFRyVQ2iR8xH-dKY-lRCB4eyVeRo/edit?usp=sharing).\nThe specification proposes a data structure schema for neural network computer models that aims to be generically applicable to all kinds of neural network simulation software, mathematical models, computational models, and data models, but with a focus on dynamic circuit models of brain activity. Importantly, they not only propose suggestions for a BIDS schema for computer models, but they also propose extensions to the entire BIDS standard that solve several other problems.\n\n### Installation\n\nSimply run the following command to get the app up and running:\n\n```\npip install sim2bids\n```\n\nAlternatively, either fork or obtain the latest sim2bids version by running the following:\n\n```\ngit clone https://github.com/dissagaliyeva/sim2bids\n\ncd sim2bids\n\npython setup.py install\n```\n\nThen, open up your notebook and import the following packages:\n\n```\nimport sim2bids\nfrom sim2bids.sim2bids import MainArea\n\nimport warnings\nimport panel as pn\n\nwarnings.filterwarnings('ignore')\npn.extension('tabulator', 'ace', 'jsoneditor', 'ipywidgets', sizing_mode='stretch_width', notifications=True)\n```\n\nThere are two options to proceed:\n\n1. Run the app locally (yields the best user experience) by calling `pn.serve(MainArea().view())`. This will take you to \na localhost page where you'll see the app. \n\n2. Run the app inline (might have small differences in layout) by calling `MainArea().view().servable()`. \n\n### Important ❗\n\n- **Provide SoftwareVersion, SoftwareRepository, and SoftwareName** \n\nThe final conversion includes JSON sidecars for each file that is created. Some folders (*param, eq, code, ts*) require \nadditional information on the software you're using to produce simulations. \n\nIn case you're using [TVB (The Virtual Brain)](https://github.com/the-virtual-brain) workspaces, you can copy this snippet\nand paste before calling `pn.serve(MainArea().view())` or `MainArea().view().servable()`:\n\n```\n# set required fields\nsim2bids.app.app.SoftwareVersion = 2.6\nsim2bids.app.app.SoftwareRepository = 'https://github.com/the-virtual-brain/tvb-root/releases/tag/2.6'\nsim2bids.app.app.SoftwareName = 'TVB'\n\n# start the app\npn.serve(MainArea().view())\n```\n\nAlternatively, customize the above cells. \n\n\n- **Give your project a meaningful short description**\n\nAll simulations are unique, that is why it will be much easier for everyone if you give a meaningful name to your work. \nThere is an input field on the left-hand side in the `Settings` where you can supplement that information. \n\n**NOTE**: make sure to give the description **before** picking the folder you need to convert.  \n\nExample:\n\n![Change description](https://raw.githubusercontent.com/dissagaliyeva/sim2bids/main/static/readme/change_desc.png)\n\n\n- **Provide additional information**\n\nSince there is a huge number of descriptions, parameters, and other variables, the app gives you the right to provide additional description.\n**After the conversion**, you can click on `View Results` and then `JSON files` tab to supplement user-specific input. \n\n**NOTE**: Make sure to click on `Update JSON` button to update default values. \n\nExample:\n\n![Add input in View Results tab](https://raw.githubusercontent.com/dissagaliyeva/sim2bids/main/static/readme/add_input.png)\n\n\n### Resources\n\nWe want to ensure you have the best user experience. Therefore, on top of documentation page, we have included a presentation\nthat covers the main functionality; it also includes a step-by-step image/video walk-through with different datasets. [The link is right here](https://docs.google.com/presentation/d/12sUkOP7iv3CEn1pecu3ABiBBhPIFromMwfJXmnjbebQ/edit?usp=sharing).\n\n\n### Getting help\n\nThe app is still under active development, if you don't see the information you're looking for, please open a new issue or [email me directly](mailto:dinarissaa@gmail.com). I'll be happy to answer your questions! :)\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdissagaliyeva%2Fsim2bids","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdissagaliyeva%2Fsim2bids","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdissagaliyeva%2Fsim2bids/lists"}