Welcome to the homepage for mx
mx (preferred reference all lowercase) is a Ruby-based platform that consists of a Ruby on Rails (RoR) application and various supporting gems/libraries. Initially conceived and developed as a collaborative web-based content management system for biosystematists mx now has a wide range of functionality much of which can broadly categorized under the umbrella of biodiversity informatics.
mx is a relatively flexible codebase as highlighted by some of its more utilized functionality:
- Ontologies - A wide range of functionality for creating and develop ontologies (e.g. anatomical) that are exportable to OBO formats
- Phylogenetic matrices - A wide range of support for matrix development, including much utility coding very large matrices (e.g. 1000x1000)
- Specimen metadata - Museum level specimen curation very simple IPT integration coming Spring 2011
- DNA workbench - Audit trails from specimen to sequence including generation of PCR worksheets and FASTA import
- Taxonomic catalogs - Data managed, updated, then presentable to then exportable to various formats (e.g. ITIS)
- Taxon pages/treatments - Customize templates then add dynamic (e.g. matrix based descriptions) or text content and figures
- Biological associations - For example- cataloging host-parasite records
- Multiple-entry and bifurcating keys
Features are additionally highlighted in this summary.
Highlights of some things that makes mx special:
- Multi-user, multi-project support in one installation
- A universal tagging system for workflow management or annotations
- Implementation of an OTU ('O'perational 'T'axonomic 'U'nit) as a core data object- this cleanly separates content from nomenclature
- A completely open-source based approach, code updates are not squirreled away until research is published
How do I use it?
There are two general paths:
- Find someone who is hosting a installation of mx and ask them to create a project for you.
- Install your own instance and create your own projects. See Installation and the FAQ for more on this option.
The hack-mx workshop
In October, 2011 a hack-mx workshop was held for people with a wide range of programming experience (from none, to expert). Download the tutorials/exercises that were used here (.zip, remote site).