https://github.com/bluebrain/bluenaas-subcellular
A web environment for the simulation of brain molecular networks.
Science Score: 33.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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○DOI references
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✓Academic publication links
Links to: zenodo.org -
✓Committers with academic emails
4 of 4 committers (100.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.7%) to scientific vocabulary
Keywords
Repository
A web environment for the simulation of brain molecular networks.
Basic Info
- Host: GitHub
- Owner: BlueBrain
- License: apache-2.0
- Language: Vue
- Default Branch: main
- Homepage: https://github.com/bluebrain/bluenaas-subcellular#readme
- Size: 5.44 MB
Statistics
- Stars: 4
- Watchers: 8
- Forks: 2
- Open Issues: 0
- Releases: 2
Topics
Metadata Files
README.md
BlueNaaS-Subcellular
BlueNaaS-Subcllular was developed as a software environment for simulation of brain molecular networks. It was designed to reach several objectives related to major restrictions of currently available software tools, such as the lack of integration with existing biological data relevant for modeling and low compatibility of different types of models.
System design
Dev env run
There are targets in makefile to start development environment for all parts of the app.
Backend dev setup needs docker image to be present in the system when starting, which can
be build with make docker_build_latest from ./backend directory.
Backend dev environment requires docker engine to be installed and consists of:
- mongoDB instance
- backend server
- sim worker replica with minimum one instance
Check the ./backend/docker-compose.yml for more information.
To start:
bash
make run_dev_backend
Dev frontend env is powered by Webpack and can be started with:
bash
make run_dev_frontend
To start both dev envs in a single session use:
bash
make run_dev
Usage
See Guidebook
Deployment
Makefile has a create_oo_deployment target that will deploy current version of the app to an
OpenShift instance. This target will create OpenShift deployment configs, services and external
routes needed by the app to function.
See makefile for configuration and options; requires OpenShift CLI.
Citation
When you use this software, we kindly ask you to cite the following DOI (under "Cite as"):
Funding & Acknowledgment
The development of this software was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government's ETH Board of the Swiss Federal Institutes of Technology.
This project/research received funding from the European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Framework Partnership Agreement No. 650003 (HBP FPA).
Copyright (c) 2022-2024 Blue Brain Project/EPFL
Owner
- Name: The Blue Brain Project
- Login: BlueBrain
- Kind: organization
- Email: bbp.opensource@epfl.ch
- Location: Geneva, Switzerland
- Website: https://portal.bluebrain.epfl.ch/
- Repositories: 226
- Profile: https://github.com/BlueBrain
Open Source Software produced and used by the Blue Brain Project
GitHub Events
Total
- Fork event: 1
Last Year
- Fork event: 1
Committers
Last synced: 8 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Pavlo Getta | p****a@e****h | 223 |
| Gil Arturo Barrios Del Villar | g****r@e****h | 144 |
| Mike Gevaert | m****t@e****h | 1 |
| Dries Verachtert | d****t@e****h | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 8 months ago
All Time
- Total issues: 0
- Total pull requests: 35
- Average time to close issues: N/A
- Average time to close pull requests: about 2 hours
- Total issue authors: 0
- Total pull request authors: 3
- Average comments per issue: 0
- Average comments per pull request: 0.09
- Merged pull requests: 34
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
Pull Request Authors
- g-bar (21)
- stefanoantonel (1)
- bbpgithubaudit (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- @types/lodash ^4.14.165 development
- @typescript-eslint/eslint-plugin ^2.33.0 development
- @typescript-eslint/parser ^2.33.0 development
- @vue/cli ^4.5.8 development
- @vue/cli-plugin-babel ^4.1.2 development
- @vue/cli-plugin-eslint ^4.1.2 development
- @vue/cli-plugin-typescript ~4.5.0 development
- @vue/cli-service ^4.1.2 development
- @vue/eslint-config-airbnb ^5.0.2 development
- @vue/eslint-config-typescript ^5.0.2 development
- babel-eslint ^10.0.3 development
- eslint ^8.2.0 development
- eslint-config-airbnb-base 15.0.0 development
- eslint-import-resolver-alias ^1.1.2 development
- eslint-plugin-import ^2.25.2 development
- prettier ^2.1.2 development
- sass-loader ^8.0.2 development
- typescript ~3.9.3 development
- vue-template-compiler ^2.6.11 development
- @msgpack/msgpack ^1.11.0
- @sentry/browser ^5.12.1
- @sentry/integrations ^5.12.0
- @types/plotly.js ^1.54.2
- @types/uuid ^8.3.0
- ajv ^6.11.0
- axios ^0.23.0
- chroma-js ^2.1.0
- codemirror ^5.51.0
- core-js ^3.6.4
- cytoscape ^3.19.0
- cytoscape-cose-bilkent ^4.1.0
- distinct-colors ^2.1.0
- file-saver ^2.0.2
- localforage ^1.7.3
- lodash ^4.17.15
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- plotly.js-basic-dist ^1.52.2
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- three ^0.113.2
- toggle-fullscreen ^0.4.2
- uuid ^3.4.0
- uuidv4 ^6.2.6
- view-design ^4.1.2
- vue ^2.6.11
- vue-class-component ^7.2.3
- vue-codemirror ^4.0.6
- vue-property-decorator ^8.4.2
- vue-router ~3.1.5
- vuex ^3.1.2
- 1556 dependencies
- Cython ==0.29.13
- motor ==2.3.0
- msgpack ==0.6.2
- networkx ==2.5
- numpy ==1.17.2
- pandas ==0.25.3
- pydantic ==1.6.1
- pygraphviz ==1.7
- pymongo ==3.11.2
- pysb ==1.9.1
- python-libsbml ==5.19.0
- requests >=2.28.1
- sentry-sdk ==0.19.5
- sympy ==1.5.1
- tornado ==6.0.3
- types-requests >=2.28.9
- typing-extensions >=3.7.4.3
- wrapt ==1.12.1
- wsaccel ==0.6.2
- xlrd ==1.2.0
- actions/checkout v3 composite
- ubuntu 20.04 build
- mongo latest
- sc-svc latest
- nginx alpine build
- wei/git-sync v3 composite