{"id":22354268,"url":"https://github.com/netzkolchose/brainage-designer","last_synced_at":"2025-06-15T11:37:03.558Z","repository":{"id":206233089,"uuid":"716139934","full_name":"netzkolchose/brainage-designer","owner":"netzkolchose","description":"BrainAGE (Brain Age Gap Estimation) framework with browser interface","archived":false,"fork":false,"pushed_at":"2023-11-17T12:52:54.000Z","size":6106,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-01-31T13:43:45.789Z","etag":null,"topics":["age-estimation","brainage","machine-learning","mri-images","web-ui"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/netzkolchose.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null}},"created_at":"2023-11-08T14:21:15.000Z","updated_at":"2023-11-22T11:53:57.000Z","dependencies_parsed_at":"2024-04-18T23:22:42.073Z","dependency_job_id":"7cd8f140-5de0-4ac1-a28b-cc2eec319e5c","html_url":"https://github.com/netzkolchose/brainage-designer","commit_stats":null,"previous_names":["defgsus/brainager-designer","defgsus/brainage-designer","netzkolchose/brainage-designer"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/netzkolchose%2Fbrainage-designer","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/netzkolchose%2Fbrainage-designer/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/netzkolchose%2Fbrainage-designer/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/netzkolchose%2Fbrainage-designer/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/netzkolchose","download_url":"https://codeload.github.com/netzkolchose/brainage-designer/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245658958,"owners_count":20651517,"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","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":["age-estimation","brainage","machine-learning","mri-images","web-ui"],"created_at":"2024-12-04T13:12:08.960Z","updated_at":"2025-03-26T12:40:29.448Z","avatar_url":"https://github.com/netzkolchose.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# BrainAGE Designer\n\n[![test](https://github.com/defgsus/brainage-designer/actions/workflows/tests.yml/badge.svg?branch=main)](https://github.com/defgsus/brainage-designer/actions/workflows/tests.yml)\n[![test](https://github.com/defgsus/brainage-designer/actions/workflows/build-frontend-main.yml/badge.svg?branch=main)](https://github.com/defgsus/brainage-designer/actions/workflows/build-frontend-main.yml)\n\n**Brain** **A**ge **G**ap **E**stimation framework with browser-based user interface.\n\n![screenshot](docs/img/screenshot-analysis.png)\n\nSome of the features:\n\n- all experiments are controlled from the web-UI\n- supports arbitrary preprocessing pipelines\n- fine control over analysis / model creation\n- all experiments are stored to database for revisiting them later\n\n\n## Installation\n\n### Requirements\n\n- [Python](https://www.python.org/) 3.8 or later\n- [MongoDB](https://www.mongodb.com/) 3.6 or later \n- [Matlab Runtime](https://www.mathworks.com/products/compiler/matlab-runtime.html) v93 (optional)\n\n### Download\n\nUsing the git command-line tool:\n\n```shell\ncd /my/projects  # or where you want to place it\ngit clone https://github.com/defgsus/brainage-designer.git\ncd brainage-designer\ngit checkout development-frontend\n```\n\nor you can download [a zip file](https://github.com/defgsus/brainage-designer/archive/refs/heads/development-frontend.zip)\nand extract it.\n\n### Running on localhost\n\n```shell\n# create new python environment\npython -m venv env\n# activate     \nsource env/bin/activate\n# install python packages\npip install -r requirements.txt\npip install https://github.com/JamesRitchie/scikit-rvm/archive/master.zip\n```\n\n[Install MongoDB](https://www.mongodb.com/docs/manual/installation/)\n\nStart server and worker:\n\n```shell\n./start-server.sh\n```\n\nvisit [http://localhost:9009](http://localhost:9009)\n\n#### Configuration\n\nThe local setup can be configure by creating a `.env` file\nin the root directory. It can have the following entries:\n\n```shell\n# enable debugging mode (mainly for web-server, more text output)\nBAD_DEBUG=true\n\n# -- directories --\n\n# the root path below which everything can be accessed\nBAD_DATA_PATH=/home/me\n# temporary directory to use\nTEMP_PATH=/tmp/brainage-designer\n\n# -- matlab --\n\n# path to the matlab runtime \nMATLAB_PATH=/home/me/MATLAB_Runtime/v93\n# path to the matlab-based CAT12 toolbox\nCAT12_PATH=/home/me/CAT12.8.1_r2042_R2017b_MCR_Linux\n\n# -- API server --\n\n# change the address of the API (and frontend) server\nSERVER_HOST=localhost\nSERVER_PORT=9009\n\n# -- mongodb --\n\n# rename the database\nDATABASE_NAME=brainage-designer\n# location of the mongodb server\nDATABASE_HOST=localhost\nDATABASE_PORT=27017\n# to handle authentication with mongodb\nDATABASE_USER=brainage-user\nDATABASE_PASSWORD=brainage-password\n```\n\n\n\n## Installation via 'Docker' \n\nInstall a recent version of [Docker Engine](https://docs.docker.com/engine/install/) \nor the **Docker Desktop** if you can't help it.\n\n#### Ubuntu 18.04\n```shell\nmkdir tmp\ncd tmp\nwget https://download.docker.com/linux/ubuntu/dists/bionic/pool/stable/amd64/containerd.io_1.6.9-1_amd64.deb\nwget https://download.docker.com/linux/ubuntu/dists/bionic/pool/stable/amd64/docker-ce-cli_20.10.9~3-0~ubuntu-bionic_amd64.deb\nwget https://download.docker.com/linux/ubuntu/dists/bionic/pool/stable/amd64/docker-ce_20.10.9~3-0~ubuntu-bionic_amd64.deb\nwget https://download.docker.com/linux/ubuntu/dists/bionic/pool/stable/amd64/docker-compose-plugin_2.6.0~ubuntu-bionic_amd64.deb\n\nsudo dpkg -i *.deb\n\ncd ..\nrm -r tmp/\n```\n\n### run with docker compose\n\nCopy the file [docker-compose-EXAMPLE.yml](docker-compose-EXAMPLE.yml) to `docker-compose.yml` and\nreplace the `\u003cPATH-TO-...\u003e` entries:\n\n    \u003cPATH-TO-DATA\u003e:   the top-most directory where all data read and written to\n    \u003cPATH-TO-MATLAB\u003e: the directory of the matlab (v93 / R2017) runtime\n    \u003cPATH-TO-CAT12\u003e:  the directory of the CAT12 standalone version\n\n```shell\ndocker compose build\ndocker compose up\n```\nand visit [http://localhost](http://localhost).\n\n\n### run single docker images\n\n```shell\n# ./build-frontend.sh\n\ndocker build --tag brainage-designer .\ndocker run -ti -p 80:9009 brainage-designer\n```\n\n\n# Development\n\n### prepare environments\n\n```shell\n# for python the typical..\npython -m venv env\nsource env/bin/activate\npip install -r requirements.txt\n\n# for frontend\ncd frontend\nyarn\n```\n\n\n### run server on localhost\n\nIn project root: \n```shell\n# transpile with yarn \u0026 parcel\n./build-frontend.sh\n# start the python server\n./start-server.sh\n```\nand visit [http://localhost:9009](http://localhost:9009).\n\n### run server on localhost with hot-reloading\n\nIn project root:\n```shell\n# start the python server\n./start-server.sh\n```\n\nIn another shell in `frontend` directory:\n```shell\nyarn start\n```\nand visit [http://localhost:1234](http://localhost:1234).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnetzkolchose%2Fbrainage-designer","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnetzkolchose%2Fbrainage-designer","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnetzkolchose%2Fbrainage-designer/lists"}