Difference between revisions of "Main Page"
From mx Help Wiki
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| + | <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> | ||
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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 (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> | |
| − | <p> mx is a relatively flexible codebase as | + | |
* 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 | + | * 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 | ||
| + | * Multiple-entry and bifurcating keys | ||
| − | <p> | + | <p> Features are additionally highlighted in [[Features | this summary]]. </p> |
| − | + | <p> Highlights of some things that makes mx special: </p> | |
| − | <p> Highlights of some | + | |
| − | * Multi-user, multi-project support | + | * 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 | + | * 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? == | |
| + | There are two general paths: | ||
| + | # Find someone who is hosting a installation of mx and ask them to create a project for you. | ||
| + | # Install your own instance and create your own projects. See [[Installation]] and the FAQ for more on this option. | ||
| + | == 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 [http://www.phenomix.org/phenomix/hack-mx_tutorials/hack-mx_tutorials.zip here] (.zip, remote site). | ||
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| − | + | [[Public projects| projects with public data]] | [[Publications| publications etc.]] | [[Roadmap | roadmap]] | [[Credit | credit]] | [[Funding | funding/support]] </div> | |
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| − | + | __NOTOC__ | |
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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:
- Find someone who is hosting a installation of mx and ask them to create a project for you.
- 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).
