Difference between revisions of "Main Page"

From mx Help Wiki
Jump to: navigation, search
m
 
(75 intermediate revisions by 17 users not shown)
Line 1: Line 1:
−
<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>
+
<div style="padding:1em;border:1px solid red;margin:1em;">
 +
<p> The codebase of Mx will being rolled into a new initiative from the Species File Group, [http://taxonworks.org TaxonWorks]. Contact --[[User:Matt|matt]] ([[User talk:Matt|talk]]) 10:06, 25 March 2013 (CDT) if you have questions, or would like to join this effort. Details and resources to follow in May, 2013. </p>
 +
</div>
  
−
<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of a taxon-concept based OTU ('O'perational 'T'axonomic 'U'nit) as the core data object, such that published and unpublished (working) concepts can be managed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? ==
+
<div style="padding:1em;border:1px solid orange;margin:1em;"> <p> The content here is becoming dated, but is largely accurate for the (very-stable) SVN-archived version of mx on Sourceforge (edge branch) that uses Rails version  2.3.18. </p>
  
−
<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> Ongoing development and updates are now on [http://github.com/mx3 GitHub]. Please also join the new [https://groups.google.com/forum/?fromgroups#!forum/mx-developers developers list]. </p> </div>
−
<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 publications, talks, and meetings that have utilized or referenced mx is [[Publications| available here]].</p>
+
  
−
== 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? ==
+
== Welcome to the homepage for mx ==
−
=== Source ===
+
<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>
−
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.
+
<p> mx is a relatively flexible codebase as highlighted by some of its more utilized functionality: </p>
  
−
=== Installation ===
+
* Ontologies - A wide range of functionality for creating and develop ontologies (e.g. anatomical) that are exportable to OBO formats
−
Instructions for installation can be found [[Installation | here]].
+
* Phylogenetic matrices - A wide range of support for matrix development, including much utility coding very large matrices (e.g. 1000x1000)
−
<br/>
+
* 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
  
−
== Credit ==
+
<p> Features are additionally highlighted in [[Features | this summary]]. </p>
 +
<p> Highlights of some things that makes mx special: </p>
 +
 +
* 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
  
−
mx is coded by Matt Yoder, Krishna Dole (retired), Kajta 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/>
+
== How do I use it? ==
  
−
Various previous projects influenced the development of mx, in particular:
+
There are two general paths:
−
* 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.   
+
# Find someone who is hosting a installation of mx and ask them to create a project for you.
−
* 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]).
+
# Install your own instance and create your own projects.  See [[Installation]] and the FAQ for more on this option.
−
* 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 hack-mx workshop ==
  
−
The following sources of funding have directly or indirectly supported the development of mx, or have used mx to manage data:
+
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 [http://www.phenomix.org/phenomix/hack-mx_tutorials/hack-mx_tutorials.zip here] (.zip, remote site).
  
−
* NSF PEET Grant DEB-0328922 to Dr. Bob Wharton
+
<div style="font-size: larger; padding: 1em; text-align: center; width: 80%; margin-left: auto;margin-right: auto; border-top: 1px dotted silver;">
−
* A Texas A&M Ecology and Evolutionary Biology Graduate Student Travel Grant to Matt Yoder
+
[[Public projects| projects with public data]] | [[Publications| publications etc.]] | [[Roadmap | roadmap]] | [[Credit | credit]] | [[Funding | funding/support]] </div>
 +
 
 +
__NOTOC__

Latest revision as of 11:41, 3 April 2014


The codebase of Mx will being rolled into a new initiative from the Species File Group, TaxonWorks. Contact --matt (talk) 10:06, 25 March 2013 (CDT) if you have questions, or would like to join this effort. Details and resources to follow in May, 2013.


The content here is becoming dated, but is largely accurate for the (very-stable) SVN-archived version of mx on Sourceforge (edge branch) that uses Rails version 2.3.18.

Ongoing development and updates are now on GitHub. Please also join the new developers list.


[edit] 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

[edit] 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 your own instance and create your own projects. See Installation and the FAQ for more on this option.

[edit] 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).


Retrieved from "http://mx.phenomix.org/index.php?title=Main_Page&oldid=4100"
Personal tools