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<div style="float: right; margin: 0em 1em 1em 1em; padding: 0em 1em 1em 1em;">__TOC__</div>
 
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== mx ==
 
  
<p> Welcome to the wiki home of the mx ('m'atri'x') project.</p>
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<p> '''Welcome to the homepage for mx.''' ''this page currently being updated''  </p>
  
<p>mx is a collaborative 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.</p>
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<p> 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.</p>  
  
<p>The long term goals of mx are as follows:
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<p> mx is a relatively flexible codebase as evidenced by a highlight of some of the more utilized functionality: </p>
  
* 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
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* Ontologies - A wide range of functionality for creating and develop ontologies (e.g. anatomical) that are exportable to OBO formats
* 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
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* Phylogenetic matrices - A wide range of support for matrix development, including much utility coding very large matrices (e.g. 1000x1000)
* 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of a taxon-concept based OTU ('O'perational 'T'axonomic 'U'nit) as the core data object, such that published and unpublished (working) concepts can be managed
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* Specimen metadata - Museum level specimen curation ''very simple IPT integration coming Spring 2011''
* the use of freely available software (including the mx sourcecode) in an aggressively open-source framework
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* DNA workbench - Audit trails from specimen to sequence including generation of PCR worksheets and the ultimate import of FASTA data
</p>
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* Taxonomic catalogs - Data managed, updated, then presentable to then exportable to various formats (e.g. ITIS)
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* Taxon pages/treatments - Customize templates then add dynamic (e.g. matrix based descriptions) or text content and figures
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* Biological associations - For example- cataloging host-parasite records
  
== What's it being used for? ==
 
 
<p>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, ontologies and more. The database currently has both private and public front ends, each of which are web based.</p>
 
 
<p> A summary of the available [[Features | features is here]]. A list of projects with publicly accessible front ends [[Public projects|is available here]]. A list of labs, publications, talks, and meetings that have utilized or referenced mx is [[Publications| available here]].</p>
 
<p> A summary of the available [[Features | features is here]]. A list of projects with publicly accessible front ends [[Public projects|is available here]]. A list of labs, publications, talks, and meetings that have utilized or referenced mx is [[Publications| available here]].</p>
  
Coming soon, a [[Roadmap | roadmap]] documenting future plans.
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<p> Highlights of some functionality that makes mx special: </p>
 +
 +
* 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 | roadmap]] briefly (very) outlines future development plans.
 +
 
 +
 
  
== Why use mx? ==
 
We've started a [[Why use mx | list of reasons for and against using mx here]].
 
<br/>
 
  
 
== How do I get it? ==
 
== How do I get it? ==
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Instructions for installation can be found [[Installation | here]].
 
Instructions for installation can be found [[Installation | here]].
 
<br/>
 
<br/>
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mx has been used/in development for over 5 years now, as such there are various "legacy" pages that may or may not have as much relevance as they do now. [[Legacy pages]] for references to these.
  
 
== Credit ==
 
== Credit ==

Revision as of 15:20, 12 December 2010

Welcome to the homepage for mx. this page currently being updated

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 get it?

Source

A cutting edge version of the source is always available on the edge branch of the svn repository on Sourceforge. The edge branch tends to be pretty stable and we run our production servers off of it when it tests clean. The trunk branch is stable, but lags significantly behind in features etc. Bug tracking, feature requests etc. are also available at Sourceforge.

Installation

Instructions for installation can be found here.

mx has been used/in development for over 5 years now, as such there are various "legacy" pages that may or may not have as much relevance as they do now. Legacy pages for references to these.

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
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