Difference between revisions of "Main Page"
From mx Help Wiki
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| − | <div style=" | + | <div style="float: right; margin: 0em 1em 1em 1em; padding: 0em 1em 1em 1em;">__TOC__</div> |
| + | == mx == | ||
| − | < | + | <p> Welcome to the wiki home of the mx ('m'atri'x') project.</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> | ||
| + | <p>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of a taxon-concept based OTU ('O'perational 'T'axonomic 'U'nit) as the core data object, such that published and unpublished (working) concepts can be managed | ||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 | ||
| + | </p> | ||
| − | + | == 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> | ||
| + | Coming soon, a [[Roadmap | roadmap]] documenting future 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? == | ||
| + | === Source === | ||
| + | A typically slightly dated copy of the source is presently available [http://sourceforge.net/projects/mx-database 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 [[Installation | here]]. | |
| − | + | <br/> | |
| − | + | ||
| − | + | == 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), and Heraty (UCR) labs have provided feedback. We are very open to having others join us. <br/> | |
| − | + | ||
| − | + | 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 [http://www.specifysoftware.org 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 [http://freedelta.sourceforge.net/ 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 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15545259&dopt=Abstract 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: | |
| − | + | ||
| − | + | * 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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Revision as of 15:53, 28 October 2009
Contents |
mx
Welcome to the wiki home of the mx ('m'atri'x') project.
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.
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, ontologies and more. The database currently has both private and public front ends, each of which are web based.
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.
Coming soon, a roadmap documenting future plans.
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, 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), and Heraty (UCR) labs have provided 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:
- 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
