osparc-simcore platform

The SIM-CORE, named o²S²PARC – Open Online Simulations for Stimulating Peripheral Activity to Relieve Conditions – is one of the three integrative cores of the SPARC program’s Data Resource Center (DRC). The aim of o²S²PARC is to establish a comprehensive, freely accessible, intuitive, and interactive online platform for simulating peripheral nerve system neuromodulation/ stimulation and its impact on organ physiology in a precise and predictive manner. To achieve this, the platform will comprise both state-of-the art and highly detailed animal and human anatomical models with realistic tissue property distributions that make it possible to perform simulations ranging from the molecular scale up to the complexity of the human body.

Getting Started

This is the common workflow to build and deploy locally:

  # clone repo
  git clone https://github.com/ITISFoundation/osparc-simcore.git
  cd osparc-simcore

  # show setup info and build core services
  make info build

  # starts swarm and deploys services
  make up-prod

  # display swarm configuration
  make info-swarm

  # open front-end in the browser
  #  127.0.0.1.nip.io:9081 - simcore front-end site
  #
  xdg-open http://127.0.0.1.nip.io:9081/

  # stops
  make down

Some routes can only be reached via DNS such as UUID.services.DNS. Since UUID.services.127.0.0.1 is not a valid DNS, the solution is to use nip.io. A service that maps <anything>[.-]<IP Address>.nip.io in "dot", "dash" or "hexadecimal" notation to the corresponding <IP Address>.

Services are deployed in two stacks:simcore-stack comprises all core-services in the framework and ops-stack is a subset of services from ITISFoundation/osparc-ops used for operations during development. This is a representation of simcore-stack:

Requirements

To verify current base OS, Docker and Python build versions have a look at:

• Travis CI config
• GitHub Actions config

To build and run:

• docker
• make >=4.2
• awk, jq (optional tools within makefiles)

To develop, in addition:

• python 3.6 (this dependency will be deprecated soon)
• nodejs for client part (this dependency will be deprecated soon)
• swagger-cli (make sure to have a recent version of nodejs)
• vscode (highly recommended)

This project works and is developed under linux (Ubuntu recommended).

Setting up Other Operating Systems

When developing on these platforms you are on your own.

In windows, it works under WSL (windows subsystem for linux). Some details on the setup:

• Install chocolatey package manager
  • choco install docker-for-windows
  • choco install wsl or using instructions
• Follow all details on how to setup flawlessly docker for windows and WSL

In MacOS, replacing the MacOS utilities with GNU utils might be required.

Upgrading services requirements

Updates are upgraded using a docker container and pip-sync. Build and start the container:

cd requirements/tools
make build
make shell

Once inside the container navigate to the service's requirements directory.

To upgrade all requirements run:

make reqs

To upgrade a single requirement named fastapirun:

make reqs upgrade=fastapi

Releases

WARNING This application is still under development.

• Git release workflow
• Public releases
• Production in https://osparc.io
• Staging instructions
• User Manual

Contributing

Would you like to make a change or add something new? Please read the contributing guidelines.

License

This project is licensed under the terms of the MIT license.

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