CoreMS Portal

CoreMS Portal is a full-stack solution for mass spectrometry data processing of small molecule analysis. Currently, there are two workflows: molecular formulae assignment of ultra-high-resolution analysis of complex mixtures and GC-MS-based metabolomics analysis. LC-MS-based metabolomics workflows are presently under development.

Current Version

3.9.7.beta

Services:

• PostgreSQL (Web and Data storage)
• Redis (Task queues storage)
• Flask and Celery ( Web framework and Task queues Client)
• Celery (Task queues runner)

Data input formats

• ANDI NetCDF for GC-MS (.cdf)
• Mass List (centroid mode) (.txt)
• Mass List (Profile mode) (.txt)
• Thermo raw format (.raw)
• Bruker D format (.d)

Data output formats

• Text Files (.csv, tab separated .txt, etc)
• JSON for workflow metadata

Local Deployment using docker-compose

• To start download or git clone this repository :D

• install docker for desktop

  There are two main way to start a local deployment, building from source, our using the images from docker hub.

• To start from the pre built images, open the terminal and cd into local_app directory

  then: ( this command will build and pull the images, create the containers, volumes and network)

  docker-compose up
  

• After the first deployment, and with the services running, we need to start migration and create all the database tables. Open a new terminal, cd into the local_app directory and then type:

  make init-db
  

  or if you don't have make installed, do this three commands:

  docker-compose exec web flask db init
  docker-compose exec web flask db migrate -m "init commit"
  docker-compose exec web flask db upgrade
  

• Open you browser and go to http://localhost

• To take all the services down and remove all the volumes:

  docker-compose down -v