Machado Genomics

Machado Genomics 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 or in the PDF manual.

Features

• There are data loaders for the major bioinformatics formats: fasta, gff, obo, bibtex, blast, interproscan, orthomcl
• The Machado Genomics API delivers data directly to the JBrowse genome browser
• Full-text search powered by PostgreSQL (no external search service needed)
• Fully customizable landing page layout and integrated release notes section (see the customization guide)

Installation

Please refer to the installation guide.

Docker

You can build your Machado Genomics instance using Docker: https://github.com/lmb-embrapa/machado-docker

Demo

https://www.machado.cnptia.embrapa.br

Contributing

Machado Genomics 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 Genomics - A Django implementation of Chado's schema. Copyright (C) 2018 Embrapa

Machado Genomics 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 Genomics: Open source genomics data integration framework.
GigaScience, Volume 9, Issue 9, September 2020, giaa097