[GMOD-devel] Fwd: Nominate software: machado

[Scott C. <sc...@sc...>]

Hello,

I wanted to forward this to a few mailing lists where I think it might be
of interest.  Adhemar is proposing a new project that is a web front end to
Chado based on Django be a GMOD project.  Please feel free to reply to this
email with comments and questions.

Thanks,
Scott


---------- Forwarded message ---------
From: Adhemar <az...@gm...>
Date: Thu, Mar 14, 2019 at 10:09 AM
Subject: Nominate software: machado
To: <he...@gm...>


Nominate software: machado
https://github.com/lmb-embrapa/machado

machado is a Django2-based application that contains tools to interact with
Chado databases. It provides users with a framework to store, search and
visualize biological data.

   - 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


*Requirements for the nomination process*

The development of machado was triggered by an undergoing research project
at EMBRAPA, the largest public research institute on agriculture in Brazil.
In this project we'll analyze over 50 genomes of plants by integrating
diverse data, such as, RNA-Seq, orthology and functional annotation (blast,
diamond, interproscan). As an initial approach, the project leaders chose
to store data in an well-established ontology-based database (chado) using
Python3 and started to develop machado with some objectives in mind: i) to
have it integrated to JBrowse via API, and ii) to implement generic data
loading tools to store data from some of the main bioinformatics data
formats (fasta, gff, obo, bibtex, blast, interproscan, orthomcl). Future
demands include the implementation of databases for mammalians species and
the development of tools for additional data files such as vcf.

The software is in early stage of development and there are many
functionalities still remaining to be concluded, most of them related to
visualization and interfaces. It is open source under the GPL license.
Comprehensive documentation related to software installation/configuration
and the data loading/visualization is available at
http://machado.readthedocs.io

We put extra efforts to make sure it's an inviting open environment in urge
for new developers. It is hosted by Github and has a few quality control
features, such as, continuous integration, and unit tests. The code
contains type annotations and follow the coding styles specified at PEP8
(Style Guide for Python Code) and PEP20 (The Zen of Python). The Github's
'Issues' is the main communication method to inform bugs, request new
functionalities and discuss code contributions.

We intend to massively use it in further research projects and will be
happy to support users and collaborators for the next few years. EMBRAPA is
hosting a demo of machado containing only 4 genomes at
http://www.machado.cnptia.embrapa.br






-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research