Difference between revisions of "Main Page"

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<div style="float: right; margin: 0em 1em 1em 1em; padding: 0em 1em 1em 1em;">__TOC__</div>
 
  
== Welcome to the homepage for mx ==
 
  
<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>  
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<div style="padding:1em;border:1px solid red;margin:1em;">
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<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>
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</div>
  
<p> mx is a relatively flexible codebase as evidenced by a highlight of some of the more utilized functionality: </p>
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 +
 
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<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>
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<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>
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 +
 
 +
== Welcome to the homepage for mx ==
 +
<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> mx is a relatively flexible codebase as highlighted by some of its more utilized functionality: </p>
  
 
* Ontologies - A wide range of functionality for creating and develop ontologies (e.g. anatomical) that are exportable to OBO formats  
 
* 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)
 
* 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''
 
* 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
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* 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)
 
* 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  
 
* 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
 
* Biological associations - For example- cataloging host-parasite records
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* Multiple-entry and bifurcating keys
  
<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>
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<p> Features are additionally highlighted in [[Features | this summary]]. </p>
 
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<p> Highlights of some things that makes mx special: </p>
<p> Highlights of some functionality that makes mx special: </p>
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* Multi-user, multi-project support in one installation
 
* Multi-user, multi-project support in one installation
 
* A universal tagging system for workflow management or annotations
 
* 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
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* 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
 
* A completely open-source based approach, code updates are not squirreled away until research is published
 
  
 
== How do I use it? ==
 
== How do I use it? ==
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There are two general paths:
 
There are two general paths:
 
# Find someone who is hosting a installation of mx and ask them to create a project for you.
 
# Find someone who is hosting a installation of mx and ask them to create a project for you.
# Install you're own version and create your own projects.  See [[Installation]] and the FAQ for more on this option.
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# Install your own instance and create your own projects.  See [[Installation]] and the FAQ for more on this option.
 
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<hr style="width: 80%" />
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<div style="text-align: center;">  [[Roadmap | roadmap]] | [[Credit | credit]] </div>
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== The hack-mx workshop ==
  
== Support ==
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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).
  
The following sources of funding have directly or indirectly supported the development of mx, or have used mx to manage data:
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<div style="font-size: larger; padding: 1em; text-align: center; width: 80%; margin-left: auto;margin-right: auto; border-top: 1px dotted silver;">
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[[Public projects| projects with public data]] | [[Publications| publications etc.]] | [[Roadmap | roadmap]] | [[Credit | credit]] | [[Funding | funding/support]] </div>
  
* NSF DEB-0842289 (Deans)
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__NOTOC__
* NSF DBI-0847924 (Deans and Wiegmann)
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* NSF DBI-0850223 (Deans and Yoder)
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* Nescent DB Hackathon Workshop (Matt Yoder participant)
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* NSF PEET grant (Heraty and Woolley)
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* NSF TOL grant (Heraty via Sharkey et al.)
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* NSF TOL grant (M. Ramirez and Jonathon Coddington)
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* NSF PEET grant (Anthony Cognato)
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* NSF PEET grant DEB-0328922 (Dr. Bob Wharton)
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* A Texas A&M Ecology and Evolutionary Biology Graduate Student Travel Grant to Matt Yoder
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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).


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