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metaspace2020 / metaspace

Cloud engine and platform for metabolite annotation for imaging mass spectrometry
https://metaspace2020.eu/
Apache License 2.0
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bioinformatics cloud metabolomics

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METASPACE

Build Status Documentation Status codecov

The METASPACE platform hosts an engine for metabolite annotation of imaging mass spectrometry data as well as a spatial metabolite knowledgebase of the metabolites from thousands of public datasets provided by the community.

The METASPACE platform is developed by software engineers, data scientists and mass spectrometrists from the Alexandrov team at EMBL. This work is a part of the European project METASPACE.

Projects

Project Description
engine Contains a daemon that runs the metabolite annotation engine, and a REST API for sending jobs to the daemon
graphql A GraphQL API for accessing the annotations database and metabolite annotation engine
webapp A web application for submitting datasets and browsing results
python-client A Python library and set of example Jupyter notebooks for performing data analysis on the annotations database
ansible Ansible playbooks for deploying to AWS
docker Docker Compose configuration for making development and testing environments

Development documentation for each of these projects is available in the wiki

Installation

Please check the ansible documentation for production installations on AWS, and the docker documentation for development installations with Docker.

Uploading Dataset and Browsing Results

Please visit the help page of our web application running on AWS:

https://metaspace2020.eu/help

Acknowledgements

BrowserStack

METASPACE is tested with BrowserStack to ensure cross-browser compatibility. This service is provided for free under BrowserStack's Open Source plan.

Amazon Web Services and the “Powered by AWS” logo are trademarks of Amazon.com, Inc. or its affiliates in the United States and/or other countries.

METASPACE is hosted on Amazon Web Services with the support of AWS Cloud Credits for Research.

Funding

We acknowledge funding from the following sources:

Funder / project(s)
EU European Union Horizon 2020 Programme
under grant agreements 634402 / 773089 / 825184
EU National Institutes of Health NIDDK
Kidney Precision Medicine Project (kpmp.org)
EU National Institutes of Health NHLBI
LungMAP Phase 2 (lungmap.net)

and internal funds from the European Molecular Biology Laboratory.

License

Unless specified otherwise in file headers or LICENSE files present in subdirectories, all files are licensed under the Apache 2.0 license.