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mtblisa: MetaboLights-ISA slicer

Version: 1.0.0

Short Description

A container image definition for the mtbls module of the ISA API

Description

The ISA API is a Python 3 library that can create, manipulate, and convert ISA formatted content. The mtbls.py module provides the functionality to access MetaboLights ISA-Tab data, wrapped up as the mtblisa container.

Key features

• Retrieve metadata from MetaboLights studies in the ISA-Tab and JSON formats
• Query MetaboLights studies for factors used.
• Query MetaboLights studies for factor values used for a given factor.
• Query MetaboLights studies to retrieve data file names filtered on factor and factor value.

Functionality

• Other Tools

Approaches

Instrument Data Types

Tool Authors

• ISA Team

Container Contributors

• David Johnson (University of Oxford)

Website

• [***]

Git Repository

• [***]

Installation

For local individual installation:

bash
docker pull docker-registry.phenomenal-h2020.eu/phnmnl/mtblisa

Usage Instructions

For direct docker usage:

bash
docker run docker-registry.phenomenal-h2020.eu/phnmnl/mtblisa ...

Publications

• Haug, K., Salek, R. M., Conesa, P., Hastings, J., de Matos, P., Rijnbeek, M., ... & Maguire, E. (2012). MetaboLights—an open-access general-purpose repository for metabolomics studies and associated meta-data. Nucleic acids research, gks1004.

• Sansone, Susanna-Assunta, Rocca-Serra, Philippe, Gonzalez-Beltran, Alejandra, Johnson, David, & ISA Community. (2016, October 28). ISA Model and Serialization Specifications 1.0. Zenodo. [***]