Machado
Machado is a Django application that contains tools to interact with a Chado database. It provides users with a framework to store, search and visualize biological data. Detailed documentation can be found in the docs directory (Read the docs).
Features
- There are data loaders for the major bioinformatics formats: fasta, gff, obo, bibtex, blast, interproscan, orthomcl
- The Machado API delivers data directly to the JBrowse genome browser
- The Haystack framework provides a very fast query interface using the Elasticsearch engine
Installation
Please refer to the complete documentation at Read the docs.
Docker
You can build your Machado instance using Docker: https://github.com/lmb-embrapa/machado-docker
Demo
https://www.machado.cnptia.embrapa.br
Contributing
Machado is run by volunteers and we are always looking for people interested in helping with code development, documentation writing, and bug report.
If you wish to contribute, please create an issue.
License
Machado - A Django implementation of Chado's schema. Copyright (C) 2018 Embrapa
Machado is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.
Additional permission under GNU GPL version 3 section 7
If you modify this Program, or any covered work, by linking or combining it with Chado (or a modified version of that library), containing parts covered by the terms of Artistic License 2.0, the licensors of this Program grant you additional permission to convey the resulting work. {Corresponding Source for a non-source form of such a combination shall include the source code for the parts of Chado used as well as that of the covered work.}
See LICENSE.txt for complete gpl-3.0 license.
Please cite
Machado: Open source genomics data integration framework.
GigaScience, Volume 9, Issue 9, September 2020, giaa097
