Main Page

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 evidenced by a highlight of some of the 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 the ultimate import of FASTA data
• 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

A summary of the available features is here. A list of projects with publicly accessible front ends is available here. A list of labs, publications, talks, and meetings that have utilized or referenced mx is available here.

Highlights of some functionality that makes mx special:

• Multi-user, multi-project support on a single server
• A universal tagging system for workflow management or annotations
• Implementation of a OTU ('O'perational 'T'axonomic 'U'nit) as the core data object- this eliminates messy dependencies on nomenclature hierarchies
• A completely open-source based approach, code updates are not squirreled away until research is published

A roadmap briefly (very) outlines future development plans.

How do I use it?

There are two general paths:

1. Find someone who is hosting a installation of mx and ask them to create a project for you.
2. Install you're own version and create your own projects. See Installation and the FAQ for more on this option.

Credit

mx is coded by Matt Yoder, Krishna Dole (retired), Katja Seltmann and with help from Andy Deans. Johan Lijleblad has provided documentation and much useful feedback. Many others, in particular the Wharton (TAMU), Cognato (MSU), Deans (NCSU), and Heraty (UCR) labs have provided valuable feedback. We are very open to having others join us.

There is no formal means of citing mx, you might use something like this:

 Yoder, M.J., Dole, K., Seltmann, K., and Deans, A. 2006-Present. Mx, a collaborative web based
   content management for biological systematists.

Various previous projects influenced the development of mx, in particular:

• The table structure for specimens and collecting event related data is loosely based on the TAMUIC insect collection's database programmed by Yoder and Oswald. That database was in turn loosely based on a very early draft (pre 1998) of the Specify table structure.
• Some of the tables containing matrix related data are based on Yoder's early MS Access database mtrx, which was greatly simplified from Gregor Hagedorn's software Delta Access (apparently no longer available on-line, but see here).
• We presently have some tables that have not been developed (i.e. we have no working front end) that are very loosely based on the Metacanthomorpha database.
• There are a various Open source plugins/widgets used in mx

Support

The following sources of funding have directly or indirectly supported the development of mx, or have used mx to manage data:

• NSF DEB-0842289 (Deans)
• NSF DBI-0847924 (Deans and Wiegmann)
• NSF DBI-0850223 (Deans and Yoder)
• Nescent DB Hackathon Workshop (Matt Yoder participant)
• NSF PEET grant (Heraty and Woolley)
• NSF TOL grant (Heraty via Sharkey et al.)
• NSF TOL grant (M. Ramirez and Jonathon Coddington)
• NSF PEET grant (Anthony Cognato)
• NSF PEET grant DEB-0328922 (Dr. Bob Wharton)
• A Texas A&M Ecology and Evolutionary Biology Graduate Student Travel Grant to Matt Yoder