GitPlanet

Cheap and reliable Node.js hosting starts at $3/month, and $1/month static HTML hosting

Created with love in Canada, visit hostnodejs.com today

Feel like to post an Ad? Learn Details
All Projects → metaspace2020 → metaspace

metaspace2020 / metaspace

Licence: Apache-2.0 license
Cloud engine and platform for metabolite annotation for imaging mass spectrometry

Programming Languages

typescript
32286 projects
python
139335 projects - #7 most used programming language
Vue
7211 projects
javascript
184084 projects - #8 most used programming language
SCSS
7915 projects
shell
77523 projects

Labels

cloudbioinformaticsmetabolomics

Projects that are alternatives of or similar to metaspace

MS-CleanR
No description or website provided.
Stars: ✭ 21 (-41.67%)
Mutual labels:  metabolomics
ElMaven
LC-MS data processing tool for large-scale metabolomics experiments.
Stars: ✭ 84 (+133.33%)
Mutual labels:  metabolomics
nPYc-Toolbox
The nPYc-Toolbox defines objects for representing, and implements functions to manipulate and display, metabolic profiling datasets.
Stars: ✭ 14 (-61.11%)
Mutual labels:  metabolomics
CoreMS
CoreMS is a comprehensive mass spectrometry software framework
Stars: ✭ 20 (-44.44%)
Mutual labels:  metabolomics
isicle
In silico chemical library engine for high-accuracy chemical property prediction
Stars: ✭ 31 (-13.89%)
Mutual labels:  metabolomics
DAtest
Compare different differential abundance and expression methods
Stars: ✭ 34 (-5.56%)
Mutual labels:  metabolomics
tools-metabolomics
Galaxy tools for metabolomics maintained by Workflow4Metabolomics
Stars: ✭ 13 (-63.89%)
Mutual labels:  metabolomics
sirius
SIRIUS is a software for discovering a landscape of de-novo identification of metabolites using tandem mass spectrometry. This repository contains the code of the SIRIUS Software (GUI and CLI)
Stars: ✭ 32 (-11.11%)
Mutual labels:  metabolomics
melonnpan
Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles
Stars: ✭ 20 (-44.44%)
Mutual labels:  metabolomics
QFeatures
Quantitative features for mass spectrometry data
Stars: ✭ 12 (-66.67%)
Mutual labels:  metabolomics
GNPS Workflows
Public Workflows at GNPS
Stars: ✭ 31 (-13.89%)
Mutual labels:  metabolomics
pyqms
pyQms, generalized, fast and accurate mass spectrometry data quantification
Stars: ✭ 22 (-38.89%)
Mutual labels:  metabolomics
xcms
This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis
Stars: ✭ 124 (+244.44%)
Mutual labels:  metabolomics
RHermes
RHermes is a semi-targeted metabolomics package to deeply characterize biological and environmental samples.
Stars: ✭ 22 (-38.89%)
Mutual labels:  metabolomics
q2-qemistree
Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".
Stars: ✭ 23 (-36.11%)
Mutual labels:  metabolomics
GNPSDocumentation
Documentation for GNPS and related tools as written in mkdocs
Stars: ✭ 26 (-27.78%)
Mutual labels:  metabolomics

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.

Note that the project description data, including the texts, logos, images, and/or trademarks, for each open source project belongs to its rightful owner. If you wish to add or remove any projects, please contact us at [email protected].