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mx

Welcome to the home of the mx ('m'atri'x', yes we're considering other names ) project.

mx is a collaborative on-line (completely web-based) content management system for evolutionary systematists, particularly those working on descriptive taxonomy. The project is in active development, with features being added as needed to those using the system.

The long term goals of mx are as follows:

• the desire to ultimately capture all data pertinent to a modern taxonomic revision (including phylogenetic data) during the revisionary process such that simultaneous publication of all data in print and electronic forms is possible
• the development of a web-based multi-user front end whose components may also be used (or translated relatively seamlessly) for public display of data
• the implementation of a taxon-concept based OTU ('O'perational 'T'axonomic 'U'nit) as the core data object, such that published and unpublished (working) concepts can be managed
• the use of freely available software (including the mx sourcecode) in an aggressively open-source framework

What's it being used for?

mx presently handles a wide range of data. Researchers are presently using it to manage morphological matrices, specimen and sequence data, references, taxonomic descriptions, bifurcating and multi-entry keys, biological associations, images, collecting events, taxonomic hierarchies and more. The database currently has both private and public front ends, each of which are web based. Search forms or other public accessible components can be wrapped is different layouts relatively easily. To share data with the rest of the world we will be using pyWrapper, which we are working on configuring now.

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  Manage OTUs

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  Manage matrices

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  Manage images (or link to MorphBank)

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  Compose descriptions

Projects accessible to public

Note that the data for all of these projects are served by a single instance of mx.

• Catalogous Evaniidorum
• The Diapriidae
• Hymenoptera Glossary and see the wiki for that project and the API discussion link for discussion on how we might make the ontology more interactive.
• The American Entomological Institute
• The jRNA Website (Reference/Citation management)

Screenshots

Researchers use a private set of forms to enter and manage their data, see these screen shots.

Publications

• Yoder, M.J. 2007. Mannomicrus (Hymenoptera: Diapriidae), a new genus of myrmecophilic diapriid, with a digital version of Masner and Garcia's (2002) key to New World Diapriinae and an illustration of digital description and key markup using an ontology. Zootaxa 1439: 47-55 pdf

• Yoder, M.J. 2007. Collaboration in systematic biology. TAMU Dept. of Entomology Seminar Series.

• Deans, A.R. and Yoder, M.J. 2006. Ontologizing morphological terms for Hymenoptera - implementing and benefiting from a controlled vocabulary. Entomological Society of America. Indianapolis, IN.

• Yoder, M.J., Dole, K, Deans, A. 2006. Introducing 'mx', a sharable digital workbench for systematic biologists. Taxonomic Databases Working Group 2006 Annual Meeting

• Yoder, M.J. 2006. 'mx' - A digital workbench for evolutionary systematists. TAMU Dept. of Entomology Annual Graduate Student Forum

Why use mx?

We've started a list of reasons for and against using mx here.

How do I get it?

Source

• A typically slightly dated copy of the source is presently available from Sourceforge. Developers are currently using SVN to manage sourcecode, but the SVN repository is not yet on Sourceforge. If you are interested in developing via SVN contact us.
• Bug tracking, feature requests etc. are also available at Sourceforge.

Installation

Instructions for installation can be found here.

Credit

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

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.

• mx integrates a number of Integrated open source tools

Support

Activities relating to the development and promotion of mx have been funded directly or indirectly by the following sources:

• NSF PEET Grant DEB-0328922 to Dr. Bob Wharton
• A Texas A&M Ecology and Evolutionary Biology Graduate Student Travel Grant to Matt Yoder